See discussions, stats, and author profiles for this publication at: https://www.researchgate.

net/publication/376306056

Applications of DNA Barcoding in Fisheries: A Review

Article in UTTAR PRADESH JOURNAL OF ZOOLOGY · December 2023

DOI: 10.56557/upjoz/2023/v44i233796

CITATIONS READS

3 758

2 authors:

Ashwit Shetty Hitesh Shingadia

Mithibai College Mithibai College
4 PUBLICATIONS 2 CITATIONS 36 PUBLICATIONS 64 CITATIONS

SEE PROFILE SEE PROFILE

All content following this page was uploaded by Ashwit Shetty on 07 December 2023.

The user has requested enhancement of the downloaded file.

 Uttar Pradesh Journal of Zoology

Volume 44, Issue 23, Page 351-371, 2023; Article no.UPJOZ.3014

ISSN: 0256-971X (P)

Applications of DNA Barcoding in

Fisheries: A Review
Ashwit S. Shetty a* and Hitesh U. Shingadia a
a Department
of Zoology, SVKM's Mithibai College of Arts, Chauhan Institute of Science and
Amrutben Jivanlal College of Commerce and Economics (Autonomous) Bhaktivedanta Swami Marg,
Mumbai 400056, Maharashtra, India.

Authors’ contributions

This work was carried out in collaboration between both authors. Both authors read and approved the
final manuscript.

Article Information
DOI: 10.56557/UPJOZ/2023/v44i233796

Editor(s):
(1) Dr. Takashi Ikeno, National Cancer Center Hospital East, Japan.
Reviewers:
(1) Bhukya Bhaskar, MPEDA-RGCA, India.
(2) Anselmo Enrique Ferrer Hernandez, Havana University-Cuba, Cuba.

Received: 25/09/2023
Review Article Accepted: 02/12/2023
Published: 07/12/2023

ABSTRACT
The review article focuses on the widespread application of DNA barcoding in the fishery
background. With the advancement in science and technology, there is a dire necessity for
upgradation in approaches for taxonomy, wildlife conservation, and health management in the
fishery industry. To reduce invasiveness, illegal fishing, and health complications in fish in both
marine as well aquaculture ecosystems different required mitigative measures need to be enforced.
DNA barcoding is one important tool in biological science. It involves the sequencing of a small
DNA segment called a ‘barcode’ of 648 base pairs. In animals and protists, the specific barcode is
the mitochondrial gene cytochrome oxidase Ⅰ (COⅠ or COX 1) and it has proven to be extremely
effective in identifying metazoans such as birds, butterflies, fish, flies, and many other animal
groups. The use of DNA Barcoding has been proven to be effective in taxonomical classification of
every group of organisms. In fishery, the application of barcoding created an avenue in marine
conservation and aquaculture caretaking.

Keywords: COI; metabarcoding; fish; taxonomy; aquaculture.

_____________________________________________________________________________________________________

*Corresponding author: Email: [email protected];

Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

1. INTRODUCTION analyses in scientific research often brings

controversies and concerns. Hence, initially,
“With the advancement of science and DNA barcoding also faces the same fate in the
technology, the species-level identification of field of taxonomy. However, DNA barcoding can
organisms has been more precise. Thanks to help remedy field misidentification, helps to make
DNA Barcoding which comprises short DNA species identification more accurate, creates
sequences that are drawn from a standardized open-access databases, and expands technical
part of the genome and can be used as a unique expertise by allowing taxonomists to accurately
identification marker to recover and characterize sort samples and by highlighting divergent taxa
species” [1]. “DNA barcodes are a novel that may represent new species” [1]. “DNA
molecular diagnostic tool that has been utilized barcoding has many advantages with criticisms
as a recognition marker to address questions raised against the ability to discover new species
pertaining to species or genus level identification and its reliability” [1].
(taxonomy), community ecology, conservation
biology, and evolution of certain functional traits The primary goal of this review is to highlight the
in organisms” [1]. “The main goal of DNA use of DNA barcoding for a wide range of tasks
Barcoding is to create a genomic library for each in the life sciences, as well as to demonstrate its
species of different life forms i.e., Flora, Fauna, value in each discipline and to discuss the
Fungi, bacteria, and viruses. With the help of reliability and future prospects of DNA barcoding.
DNA barcoding such as eDNA (Environmental
DNA) metabarcoding, the conservation of marine 3. METHODOLOGY
life that are on the verge of extinction such as
high elasmobranchs due to illegal marketing for Species identification by DNA Barcode is carried
fin soup or dried form eDNA would be really out by amplifying highly variable regions, here it
efficient for the specificity of species in taxonomic is the DNA barcode region of nuclear,
level. Applications for DNA barcodes can be chloroplast, or mitochondrial genomes which are
found in a wide range of disciplines, including amplified with the help of PCR (Polymerase
ecology, biomedicine, epidemiology, evolutionary Chain Reaction). DNA-based species
biology, biogeography, conservation biology, and identification systems are based on standard
the bio-industry. It is simpler to enable automated molecular biology techniques. The steps included
species identification because of the process's in the DNA Barcoding are as follows (Fig 1): -
low cost and speed” [2].
1) Sample collection;
2. DEFINITION & SCOPE 2) DNA Extraction from the sample
3) Amplification of DNA Barcode region with
“DNA Barcoding is a part of Molecular the help of Polymerase Chain Reaction;
characterization utilized for species identification 4) Sequencing and referencing through
and phylogenetics. In layman's terms, DNA software or databases like BOLD
Barcoding is like Barcode used for identifying SYSTEMS or NCBI [1, 5].
shopping grocery products instead it is for
species identification or phylogenetics” [3]. “DNA 4. STEPS INVOLVED IN DNA
barcodes comprise a standardized short BARCODING PROCEDURE
sequence of DNA (400-800 bp) that in principle
should be easily generated and characterized for 1) Extraction and Purification of DNA from
all species on the planet” [4]. “DNA Barcoding is the samples: Isolation of high-quality DNA
advantageous over the morphological from various biological sources under
identification key since it is a molecular-level sterilized conditions is a critical step in
study to create a systematic identification key. achieving successful DNA barcoding. Before
Ideally, DNA barcodes have low intraspecific and DNA Extraction the given biological sample
high interspecific distinction” [1]. “The intra- and that contains less amount of DNA must be
interspecific differences taken from DNA homogenized properly [6]. “There are quite a
barcoding help us enormously in deciding number of DNA Extraction methods such as
evolutionary history and relationships among Sodium Dodecyl Sulfate (SDS) extraction,
species. Historically, DNA barcoding has been guanidinium thiocyanate-phenol-chloroform
claimed to be a revolutionary and innovative extraction, silica matrix purification, and
approach to the identification of living organisms. magnetic bead-based purification” [7]. For
However, the introduction of novel methods for DNA purification from delicate and

352
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

contaminated samples, there are sensitive primers to use across a wide range
commercially available DNA isolation kits. of taxons. This is only practically feasible
2) Barcode genetic markers: when the DNA barcodes have a low
“Barcodes/markers in the DNA Barcoding intraspecific and high interspecific variability,
are nucleotide signatures that are used to so the use of one barcode is not enough for
identify a particular species. DNA Barcodes all taxons. Hence, different barcodes are
have conserved flanking sites that are utilized for different groups of organisms” [8]
essential for the development of PCR- (Table 1).

Fig. 1. Diagrammatic representation of DNA Barcoding

Table 1. Various barcodes of different groups of organism [8]

Organisms Type Locus/Loci used for barcoding

Animals COI (Cytochrome oxidase subunit 1), Cytb (Cytochrome b), 12S, 16S
Plants matK (maturase K), rbcL (ribulose 1,5-biphosphate carboxylase), psbA-trnH
(intergenic non-transcribed spacer), ITS (internal transcribed spacer)
Bacteria COI (Cytochrome oxidase subunit 1), rpoB (DNA-directed RNA polymerase
subunit beta), 16S, cpn60 (Chaperonin-60), tuf, RIF, gnd
Fungi ITS (internal transcribed spacer), TEF1α (Translation elongation factor 1
alpha), RPB1 (LSU-Large Subunit), RPB2 (LSU-Large Subunit), 18S (SSU-
Small Subunit)
Protists ITS (internal transcribed spacer), COI (Cytochrome oxidase subunit 1), rbcL
(ribulose 1,5-biphosphate carboxylase), 18S, 28S

353
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

The mitochondrial DNA is most favoured over mini-barcoding is performed where this
nuclear DNA for barcode development due to the universal primer is not beneficial instead
lack of introns and less recombination followed primers such as 16S rDNA are developed.
by a haploid of inheritance [9]. Mitochondrial Apart from primers, the efficiency of PCR is
Cytochrome oxidase subunit 1 which is amplified also regulated by 3 following conditions viz.
to 648 bp is universally utilized as a standard Heat-stable DNA polymerases, the annealing
barcode for animals followed by Cytb, 12S, or temperature, and dNTP mixtures along with
16S [8]. Cytochrome oxidase subunit 1 is a specific PCR conditions. Therefore, it is
maternally inherited mitochondrial enzyme necessary to select more precise primers
complex that plays an important role in oxidative and PCR conditions for better amplification
phosphorylation and is greatly conserved across of barcoding locus and use of DNA signature
living organisms [8]. to develop species-specific barcode [8].
Thus, Cytochrome oxidase subunit 1 based 4) Nucleotide/ molecular signature:
primers are mostly utilized for identification and Nucleotide signatures are nucleotide
discrimination of insects with a 100% success sequences which are obtained from the
rate. These COI primers consist of 20-30 sequencing of PCR products. It is used to
nucleotides and are designed by aligning several detect the presence of an organism and
COI genes derived from closely related taxa compare it with other species for the
[10]. development of a phylogenetic tree. For
sequencing of PCR products method such
Mitochondrial DNAs make them unproductive in as Sanger dideoxy sequencing is employed
the barcoding of plant species due to their high which sequences short sequences (400-800
rate of mutation. Plants barcodes are developed bp) of PCR amplified DNA. Globally, it is a
from the Chloroplast. 2 gene loci are identified widely used method to sequence several
from the chloroplast viz. rbcL and matK which PCR products and has the potential to
can be amplified to 600 and 800 bp fragments, generate a sequence read of up to 1000 bp
respectively for effective barcode development [15]. Though this method is highly effective in
for plants [11]. For the identification of fungi, sequencing the DNA barcode obtained from
barcodes are developed successfully from ITS a single species at a small scale, it is less
rDNA and also proved to be promising even in rewarding when it comes to bulk samples
plants [12, 13]. In Protists, the barcoding is a [16, 17]. But with the help of NGS (Next
unique two-step process. In the 1st step, the V4 Generation Sequencing) Technology
region of the 18S rDNA is analyzed as a sequencing of bulk samples can be done in a
prebarcode followed by various barcode sets single reaction [17]. Next Generation
specifically developed for different clades of Sequencing has been a successful method
Protista [14]. in sequencing multiple barcoding regions
from the mixed DNA samples acquired from
3) Barcode and Polymerase Chain Reaction:
environmental specimens, food products,
Polymerase Chain Reaction (PCR) helps in
and medicinal preparations. Advanced
amplifying the barcoding locus from the
bench-top sequencing systems such as
purified DNA with a specific set of primers,
Roche 454 GS Junior System, IonProton
which anneals to target DNA at a particular
System, Illumina MiSeq and MiniSeq are in
annealing temperature. It is necessary to
use for barcode sequencing at different
choose the most appropriate set of primers
laboratories [8].
for the development of barcodes due to the
sensitivity of PCR and Amplification 5) Reference libraries and databases:
efficiency of the barcoding region [6]. Design Reference libraries online repositories that
and evaluation of primers for DNA Barcoding are accessible to the public where
are done by using software and websites sequenced barcodes are submitted in the
such as Primer Premier, Oligo, and databases and the species-specific analysis
Whitehead. Selection of primers is based on is performed with phylogenetic study. Data
two criteria: - Versatility across a wide range available in such libraries plays an important
of species and Affinity toward DNA with a role in the identification of the organisms with
balanced melting temperature. Due to this utmost accuracy and comparative analysis of
criterion, Cytochrome oxidase subunit 1 Novel sequences/ barcodes with those that
(COI) is considered as a universal primer for are already deposited in the library with the
most animals and insects [8]. In some taxon, help of bioinformatics [6]. Currently, there are

354
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

many online repositories such as GenBank, management of humans as well as animals,

Barcode of Life Data System (BOLD), wildlife conservation, phylogenetics and many
Medicinal DNA Barcode Database more. Storage or preservation of such biological
(MMDBD), International Nucleotide components is a challenging task. DNA being a
Sequence Database Collaboration (INSDC), biological material it easily degrades due to
and Barcode Index Number System (BIN) factors such as temperature, pH or
that authorize the submission of the novel morphological fixatives such as formalin. DNA
sequence by the researches [6]. samples are usually preserved with the aid of
cryopreservation or freeze-drying. When cell
6) Barcoding sequence analysis: It is the membranes disintegrate during an organism's
most important step in identifying an death, DNA degradation begins. This permits the
organism precisely, which is accomplished entry of bacteria and other pathogens as well as
through the use of various online and offline the release of DNAses, which are enzymes that
Bioinformatic tools. The primary goal of gradually cut single nucleotides from DNA until
sequence analysis is to compare novel the molecule is too short to be referred to as
barcode sequences to an array of sequences DNA [19].
deposited in a database for taxonomic
identification accuracy. Several methods are DNA should ideally be extracted as soon as
involved in sequence analysis such as tissue is sampled, or it should be frozen and
Comparative analysis which includes extracted soon after (for example, within 24
similarity-, distance- and tree-based hours). Nonetheless, funding constraints and
approaches which allow researchers to field conditions frequently limit the resources
recognize variations present in the available for sample preservation. This makes it
sequences. In similarity search, BLAST necessary for researchers to operate within strict
(Basic Local Alignment Search Tool) is one guidelines in order to minimise DNA deterioration
of the algorithms that are used to match the [20]. DNA samples are usually preserved with
query sequence with those sequences that the aid of cryopreservation or freeze-drying.
are already present in the databases. In this, Depending upon the nature of the specimen, the
a similarity score is generated based on the preservation technique varies. There are some
part of the query sequence aligned to the techniques and solutions which have proven to
reference sequences [8]. For distance-based be effective in DNA preservation.
analysis, the K2P (Kimura 2 parameter)
model is one best methods. K2P calculates Biological samples have long been stabilised
the intraspecific and interspecific genetic over time through the use of freeze-drying, also
distances among sequences, which is known as lyophilization [21, 22]. DNA
important for the evaluation of the barcoding preservation can be achieved easily and
gap for species delimitation [8]. In the tree- conveniently by freezing tissue samples at
based sequencing method, the phylogenetic −20°C. It only requires a household freezer; in
relationship of the query sequence with the the most basic scenario, electricity is the only
reference sequences is analysed [8]. additional supply needed. Furthermore, simple
freezing can be effectively combined with other
By clustering the query and reference sequences methods to achieve optimal storage conditions.
according to sequence similarities, a barcode- Using additional techniques (most notably
based phylogenetic tree can be built [6]. MEGA, ethanol or buffers) provides a safeguard in the
PHYLIP, and PAUP are among the bioinformatic event of a power outage [23]. However, there is
tools that make it easier to construct and still enzymatic activity and degradation at this
visualise phylogenetic trees based on temperature, so freezing alone is not suitable for
hierarchical clustering algorithms like Maximum long-term storage. Furthermore, freezing at 20°C
Likelihood (ML), Maximum Parsimony (MP), is not ideal for preserving living cells; in yeasts,
Neighbor-Joining (NJ), and Bayesian Inference freezing-thawing events have been shown to be
(BI) [9, 18]. mutagenic [24].

5. DNA PRESERVATION Another freezing method is ultra-low temperature

which comprises two temperatures -80 ˚C and -
DNA is one of the important biological 150˚C. The use of ultra-low temperature freezing
components which aids in identifying a particular at 80°C results in good and consistent
species of an unknown specimen, health preservation quality. There are two methods for

355
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

achieving this temperature. (1) Dry ice (frozen The FTA card technique for preserving DNA
CO2) can be used in the field or for sample entails applying the sample to a filter card that
transport; all that is required is a well-isolating has been chemically treated. This lyses the cells
(e.g., styrofoam- or vacuum-insulated) box. It is and protects the DNA within the thick
only a good choice, though, for comparatively macroporous cellulose matrix filter matrix [26,
small sample sizes. The packed goods quickly 27]. This card can be folded after freeze-drying
become heavy because of the volume that is and can be stored for years. After cleaning, a tiny
taken up by the insulating material, packing, and portion of the card is used straight into the PCR.
dry ice. Additionally, there are specific rules that Particularly advised for fluid samples, it typically
must be followed when carrying dry ice on an produces satisfactory results when applied to
aircraft. (2) Ultra-low temperature freezers are blood samples, blood clots, small tissue samples
available for archival storage; however, their cost (maximum 3-5 mm in diameter; fish fin clips have
and power consumption are high. When also been successfully tested), saliva, sperm, or
combined with automated alarm systems, CO2 or even cheek wipes [23]. DNA from human buccal
N2 backup, and/or backup power, they offer a cells [28], fish mucus [29], coral tissue and
reasonably safe choice, even in the event of a zooxanthellae [30], and pure bacterial cultures
brief power outage. The technique works well [31, 32] have all been preserved using this
when paired with some preservation media to technique. After being spotted on 1 cm2
create ideal storage circumstances. For (very) Whatman 3 mm paper, 50 µl of 2% SDS, 10 mM
long-term storage, ultra-low temperature freezing EDTA, and 60 mM Tris are impregnated into the
with ethanol or 30% glycerol is ideal. However, paper and allowed to dry [23]. FTA cards can be
due to low enzymatic activity, DNA degradation stored at room temperature for years. Even
continues towards the upper end of the ultra-low though the technique is efficient it is quite
temperature range. There has been significant expensive.
advancement in ultra low-temperature freezing,
with freezers operating at approximately −150 Similar to the FTA card, there is a device called
°C. This temperature provides an ideal storage FTA elute that keeps the DNA in the filter matrix
environment for any tissue sample because it is but is designed to release it into the eluent rather
below the water's recrystallization point, which is than the card punch remaining in the PCR tube.
approximately −130°C. For extended or This technology has been used in the
"permanent" storage, this is the suggested— preservation of human cells as well as the
albeit pricy—method. These freezers use a lot of detection of viruses [33].
power, but the equipment and sample RNAlater is an extremely effective fluid for
maintenance are much simpler, and as a result, preserving DNA and RNA that is slightly to non-
the costs are lower than when liquid nitrogen is toxic and non-flammable in nature. RNAlater®, a
preserved [23]. solution-based formula rich in salts, preserves
tissues for up to one week at room temperature,
Flash-freezing in liquid nitrogen is one of the one month at 4 °C, and an infinite amount of time
successful methods for DNA preservation in at about 20 °C. This material is particularly useful
many environments. It has been used to for RNA preservation, DNA/RNA microarray
preserve coral samples [25]. Samples being analysis, gene expression studies, and complex
stored in liquid nitrogen (around -200 ˚C) have genetic research involving high-molecular-weight
proven to be effective in the storage of all types RNA or DNA [34, 35]. Fresh samples are
of macromolecules, Keeping biological samples submerged in the solution, allowed to saturate
in liquid nitrogen (around -200°C) results in very the tissue overnight in the refrigerator, and then
good storage quality for all types of frozen for long-term storage. It has been
macromolecules, as no chemical or biological demonstrated that RNAlater® provides greater
processes work at such extremely low DNA yield than FTA cards, along with the
temperatures. Additionally, keeping samples advantage of reduced PCR inhibition [36].
below 130°C prevents recrystallization. The
method is suitable for long-term storage of DNA, DNAgard, like RNAlater, is intended to permeate
RNA, and protein samples, as well as living cells cells and preserve DNA in a solution. In contrast
(for example, reproductive cells). Even though to RNAlater, this technology preserves the DNA's
this preservation is effective, the transportation of stability during long-term storage without the
liquid nitrogen through shipping is quite difficult, need for freezing or refrigeration. Samples can
especially in the tropics [26]. be kept in liquid form for one month at room

356
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

temperature, or the solution can be dried for is defined here as fragments larger than 10 kb.
longer storage [37]. The %R and nY of HMW DNA from extracts of
fresh tissues and those kept in 95% EtOH were
Other than these techniques mentioned above also measured for comparison over the same
there are chemical solutions that have shown a time periods. It was discovered that in situations
potential to store DNA. One of them is where DESS functioned optimally (producing ≥
cryoprotectants. A number of chemical agents, 20%R of HMW DNA), all EDTA-containing
that are related to freezing techniques, can be solutions were equally or more efficient than
used to shield macromolecules and/or tissue DESS. On the other hand, none of the six DESS-
integrity from the freezing damage brought on by variant storage solutions offered superior
ice formation and other crystallization events. protection of HMW DNA than DESS in situations
Numerous forms of glycol (ethylene, propylene, where DESS performed less well. Furthermore,
and glycerol), DMSO (Dimethyl sulfoxide), tissues stored in solutions containing DMSO
sugars (particularly trehalose, glucose, and alone, NaCl alone, or DMSO and NaCl in
sucrose), amino acids, methanol, polymers or combination produced %R and nY of HMW DNA
colloids, and other particular mixtures are the significantly lower than those of fresh tissues for
most often utilized cryoprotectants [23]. all taxa and storage intervals longer than one
day. These findings show that only EDTA directly
The inexpensive, easily obtainable, and non- aided in the preservation of high molecular
refrigerated nature of room-temperature ethanol weight DNA for the taxa, solutions, and time
makes it a convenient substitute. Because traces periods studied [38].
of benzene in 100% ethanol can affect DNA
preservation, and 70% will cause DNA Depending upon the type of specimen, the body
degradation, the ideal ethanol concentration is parts, and the body fluids of the samples the
between 95% and 99%. Because tissues are preservation solution and method vary. Also, the
composed primarily of water, the ratio of tissue collection of the sample on the field and its
volume to ethanol should be at least 1:5 in order storage method can also impact the integrity of
to maintain the proper ethanol concentration the DNA. One of the major concerns while
(>70%) [19, 23]. Although preservation in collecting and storing samples from the field is
ethanol, RNAlater, and DESS at room the sterilization of the equipment and the
temperature may be suitable substitutes if chemicals that are being utilized in storage.
refrigeration is not possible, ethanol at -20 ˚C is
the ideal method for preservation. It is not 6. TYPES OF DNA BARCODING
advised to store unpreserved material at -20 ˚C
since the easily broken cold chain will In DNA Barcoding, genomic DNA is directly
compromise DNA integrity [19]. extracted from an organism’s body parts such as
legs, antennae, tissues, or a mixture of
A formulation called DESS is frequently used to organisms preferably referred to as a bulk
protect DNA in samples of biological tissue. Its sample. Usually, the bulk samples consist of
three ingredients are sodium chloride (NaCl), taxonomically different groups of organisms
ethylenediaminetetraacetic acid (EDTA), and obtained from any environment that comprises
dimethyl sulfoxide (DMSO), but it is commonly high-quality DNA. Organisms that are under
called a DMSO-based preservative. In a study on study usually live in a habitat where they leave
understanding the role of EDTA in the protection their DNA such as water, soil, faeces, blood, etc.
of high molecular weight DNA in tissue Such an environment is where there is a rich
preservation. In this investigation, the tissues of source of cellular debris mixed with extracellular
three aquatic species—the blue mussel Mytilus DNA, which is referred to as environmental DNA
edulis, the virile crayfish Faxonius virilis, and the (eDNA) [8]. There are 2 types of barcoding
clam worm Alitta virens—were preserved in depending upon their function viz. Meta-
DESS, as well as solutions comprising all barcoding and Mini-barcoding.
possible pairings of the two DESS components.
The researcher extracted DNA from each tissue 1) Meta- barcoding: Barcoding eDNA
after storing it at room temperature for periods (Environmental DNA) is called Meta-
ranging from one day to six months. The barcoding. It is significantly used for species-
percentage of high molecular weight (HMW) specific identification through the sequence
DNA recovered (%R) and the normalised HMW from a mixture of DNA, which is amplified
DNA yield (nY) were then calculated. HMW DNA with the help of a universal barcode. Due to

357
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

the mixture of DNA obtained from an mass spectrometry, and high-performance liquid
environment (eDNA), there is the possibility chromatography [45, 46]. However, this method
of coamplification more in conventional is not very effective due to the chemical variation
sequencing. This creates false sequencing in different batches of Natural Herbal Products
data due to multiple or overlapping sequence depending on geographical locations, storage
peak [16]. To avoid false sequencing, meta- conditions, and processing methods that create
barcoding is a useful method to identify difficulty for proper chemical analyses. But with
multiple species in a mixture of DNA by the help of DNA mini-barcoding, smaller
using NGS (Next Generation Sequencing) amplicons from NHP can be amplified in PCR
technology and mitochondrial 16S rRNA [8]. and can be applied to identify species rapidly
NGS is very efficient in multitaxon [41].
identification from the sequenced mixture of
DNA or degraded DNA samples [39]. 7. GENERAL APPLICATIONS OF DNA
Applications for meta-barcoding go beyond BARCODING
species-specific identification to include
ecological management, community DNA barcoding being a modern-day technology
analysis, water quality, air quality, diet have a widespread application in different fields
analysis, biodiversity monitoring, and many of biological science. The main characteristics of
more [40]. DNA barcoding include the ability to easily
associate all life cycle stages and genders,
2) Mini-barcoding: Mini-barcoding as the especially when morphology, living behaviour,
name suggests is a type of barcoding, where and habitat are consistently different, to identify
small segments of DNA (less than 200 bp) any organism from parts or pieces, and to
are used for PCR amplification and has been discriminate single species co-existing within
developed extensively over past decades [8, complex matrices containing a mixture of species
41]. Compared to traditional DNA barcodes, [47]. In general, DNA barcoding helps species-
mini-barcodes are more diversified and are specific identification from samples collected
able to distinguish between limited spaces from anatomical parts of organisms or
[41]. A decade of research studies on mini- environmental entities such as water, soil,
barcoding has put light on its application faeces, and air. Below are some applications of
using short-length segments of DNA where DNA Barcoding: -
traditional barcoding is not feasible. In
chloroplast, a short region of tRNA-Leu (trnL) 1) Taxonomic characterisation (New species
called P6 loop which is 10-143 base pairs Identification): The main objective of DNA
can be amplified from processed food and barcoding is to identify species from
permafrost samples [42]. In 2008, Meusnier unknown groups of organisms from samples
et al. proposed that mini-barcodes can solve taken from the organism’s body parts or from
problems associated with amplifying the environment. The sequencing is species-
degraded DNA. By analysing 100-250 bp in specific and reveals a phylogenetic relation
the COI region of DNA it achieved a success among different taxa [41]. This is useful in
of 90-95% in identification rate [43]. In this those organisms or life stages of organisms
study, a universal primer pair for mini- such as a larval form with limited diagnostic
barcodes of 120-150 bp was developed and characteristics.
accomplished a higher success rate in terms
of small-length barcoding versus full-length There are a number of examples of species
barcoding [43]. identification with the help of DNA Barcoding.
Neolissochilus kaladanensis sp. nov., a new
One study found shorter amplicons have a higher cyprinid species, is described from the Kaladan
PCR success rate [44]. Many studies on Mini- River drainage of Mizoram [48]. N. kaladanensis
barcoding are done on Natural Herbal Products sp. nov., differs from other Neolissochlus species
(NHP). NHP utilizes herbs and it includes herbal in having a higher number of gill rankers on the
medicines, dietary supplements, and herbal arm of the 1st gill arch (13–14 vs. 12 or below in
extracts [41]. Due to their increased demand all the species) [48]. The mtDNA sequence of
worldwide in recent years, there has been a lot of cytochrome c oxidase subunit 1 (CO1) separated
adulteration and counterfeiting of these products. N. kaladanensis sp. nov. from all other
For adulteration check, NHP chemical detection Neolissochilus and Tor species with an average
methods such as thin-layer chromatography, genetic distance of 6.0% [48].

358
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

With the help of DNA Barcoding, issues related this invasive species is a challenge due to
to wildlife crimes that include illegal trading of their intricate life cycles, parthenogenetic
animal body parts or whole organisms that are reproduction mode, sex, and colour morphs
endangered in conservation status can be [50]. Study conducted by Rebijith et al., on
resolved [8]. In the case of Invasive Alien aphids during 2008-2012 [50]. They
Species (IAS) which cause destruction in the generated CO-I barcoding sequences for
ecological balance of native species. IAS have 142 individual specimens that represented
limited morphological variations making it quite 32 aphid species from India [50]. Sequence
difficult to analyse [8]. DNA Barcoding is an analysis showed that intraspecific and
efficient method for identifying alien species and interspecific distances ranged from zero to
maintaining the ecological balance [8]. 3.8% and 2.31% to 18.9% respectively [50].
Also, with the help of DNA Barcoding study
2) Livestock management: DNA Barcoding also revealed 3 cryptic species viz. y
application is not limited to wild animal and Brevicoryne brassicae (Linnaeus),
plant identification. It is also applicable to Hyperomyzus carduellinus (Theobald) and
domestic animals including livestock. With Brachycaudus helichrysi (Kaltenbach) from
advancements in DNA Barcoding, there has India. This study shows a great potential for
been a notable improvement in the livestock pest management strategies that involve
maintenance and livestock food industries biocontrol [50].
[8]. Species-specific barcode development
acts as a unique nucleotide signature to 4) Barcode-based diet analysis in animals:
identify the exact taxon in the mixed samples Diet study of any organism or predator within
[8]. Due to this, it is widely utilized for genetic a particular ecosystem is necessary to
traceability via the identification and understand feeding habits and also identify
authentication of livestock-based food the animals they prey on. Basically, it gives
products such as meat and milk-based access to the food web within a particular
products [8]. At the commercial level, ecosystem. One of the types of DNA
livestock and its by-products are solely Barcoding called Metabarcoding (eDNA) is
dependent on the type of food. Nevertheless, highly efficient for the diet analysis of
the diet of the grazing domestic animals can organisms by identifying the specific prey
significantly vary depending on the type of taxon from the various samples derived from
habitat they live in. Therefore, it is very the ecosystem such as faeces, saliva, or
necessary to run down the feeding habits of sometimes from the whole body of an
the animals for their better maintenance [8]. organism [8].

3) Cryptic species demarcation: Two or more 8. APPLICATIONS IN FISHERIES:

species that are nearly identical in their
appearance, yet reproductively isolated, are Fisheries is the biggest sector in India which
referred to as sibling or cryptic species [49]. includes Fish production and Aquaculture. India
Cryptic species are usually misleading is the 3rd largest in fish production and 2nd largest
biodiversity in any ecological context [8]. in aquaculture in the world after China [51].
DNA Barcoding is a useful tool in However, issues such as problems such as
distinguishing cryptic species with less overfishing, bycatch, and illegal fishing cause a
morphological differences [8]. One of the decline in fish population affecting marine
importance of Cryptic demarcation is the ecosystems. Sustainable fisheries are necessary
surveillance over Invasive Alien Species for the conservation of fishes and aquatic lives
which disturb the ecological balance of which are endangered. Molecular
native species living within that particular characterization of fishes and aquatic organisms
ecosystem. It also not only affects the is necessary for having of Barcoding database
ecosystem but also affects the food security. library. This helps in having accuracy in the
Here, DNA Barcoding role is to detect the identification of species for precise assessment
cryptic species and the ways to prevent their of the stock size and recruitment. Molecular
harmful effects on crops. For e.g., Invasive markers are useful tools when it comes
Alien Species such as Aphid are pest to differentiation of species with accuracy [52].
many varieties of crop plants. Aphids
outnumber all other insects in terms of both Mitochondrial DNA (mtDNA) maker is mostly
number and diversity [50]. Identification of favoured over nuclear DNA marker due to lack of

359
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

introns, less recombination and haploid mode of Egyptian aqua-feed samples was analysed
inheritance [8]. For e.g., Mitochondrial with the help of DNA metabarcoding based
cytochrome c oxidase subunit 1 (COI) has been on 454 Next Generation Sequencing. Four
utilized as a standardized barcode gene for orders of fish viz. Clupeiformes, Perciformes,
animals that also includes fishes for developing Aulopiformes, and Siluriformes with up to 13
an accurate taxonomic database. DNA species each were identified exclusively. The
Barcoding has been utilized in fisheries to following species were identified as major
document fish diversity, ichthyoplankton constituents: Saurida undosquamis,
identification, prey list of particular organisms Sardinella jussieu, Pangasianodon
under study, invasive species, and parasites, and hypophthalmus, and Chelidonichthys kumu.
to test processed fish products [52]. DNA metabarcoding revealed minor
differences in aquafeed compositions for
DNA Barcoding applications in fisheries are herbivorous and omnivorous fish. More
divided into 2 parts: - Capture fisheries and importantly, approximately 46% of all
Aquaculture. detected fish species are either
overexploited or in severe decline [56]. DNA
1) Applications in capture fisheries: - Since barcoding has been shown to be effective in
India's fishery industry is 3rd worldwide. identifying several cryptic cichlid species
Their issues such as overfishing, bycatch, from Ghanaian and Namibian waters in West
and illegal fishing are causing a Africa [57, 58, 59].
decline in the number of species that are
endangered or usually have non-commercial b) Ecosystem Management: Marine
value. ecosystems such as coral reefs, mangroves,
and wetlands even though secluded in
a) Species Identification: Fishes are one of patches have a high percentage of fishery
the biggest vertebrate groups with more than biodiversity. But due to threats such as
32,000 species. Fishes show a range of anthropogenic pressure, Invasive Alien
morphological characters and there are most Species, and Climate Change there has
fishes which exhibit phenotypic plasticity been a disturbance in ecological balance
[53,54]. Accurate identification of fishes with [60]. Factors such as habitat destruction,
the help of DNA Barcoding would be a way loss of biodiversity and subsequently a
forward for sustainable fishery management reduction in adaptability of the ecosystem.
[52]. Barcoding of fishes is mainly based on Monitoring biodiversity on a regular basis is
species intra-and interspecific genetic necessary to study changes in the pattern of
differences [52]. With the help of DNA biodiversity and the impact of the
Barcoding phylogenetic relationships can environment on biodiversity [52]. To attain
also be studied to resolve taxonomic this, basic information on native biodiversity
ambiguity [52]. The National University of is really important [52]. Species of a
Singapore researchers analysed 144 particular habitat can be a commercially
samples from 45 cat foods produced by 16 targeted fish species. With the assistance of
different brands in Thailand and sold in DNA barcoding, the management of
Singapore [55]. About 31% of the samples sustainable fisheries can be regulated. DNA
contained shark meat. The most common barcoding investigation was carried out on
shark found in cat food was the blue shark coral reef fishes from Weh Island, Sumatra,
(Prionace glauca) which isn’t protected under Indonesia. This island is surrounded by three
CITES, the International Convention on the marine biodiverse areas viz. Indian Ocean,
Wildlife Trade, but the research suggested it Andaman and the Straits of Malacca,
is overexploited [55]. Other species of sharks Sumatra. The waters provide a feeding
discovered in the products were silky sharks ground for the industry of the greater island
(Carcharhinus falciformis) and Whitetip of Aceh, in addition to providing support for
sharks (Triaenodon obesus), both of the artisanal fishing operations. 230 specimens
species are “vulnerable” by the IUCN from 72 species, representing 32 genera, 17
(Alberts, 2022) [55]. Silky sharks are also families, and a significant portion of the
protected under CITES Appendix II captured reef fish taxa were barcoded for
(regulation of trade through a set of this study. This accounted for 25% of the
conditions) [55]. Another research study diversity of fish species that had previously
based on fish species identification within been documented. This study makes a

360
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

substantial contribution to the region's ecosystem that is species-rich,

fisheries statistics, which will help with the difficult to assess, and poorly catalogued
assessment of species catch composition [52].
and, consequently, the planning of
management strategies [61]. e) Mislabelled Seafood Products: Each fish
species has a different nutrient profile. The
c) Identification of Ichthyoplankton: Larval nutrient profile is the face value for the
ecology study includes spatial distribution, pricing of the product [69,70]. It has been
population dynamics and migration reported that processed fish products are
strategies [62, 63]. Ichthyoplankton usually mislabelled, adulterated, and
identification is really important since it would replaced by low-value fish [71,72]. It is
help in tracking breeding habitats and difficult to study the morphological
populations of fishes and also cryptic species characteristics of processed food. Another
distribution [64, 65, 66, 67]. The identification drawback is that the level of DNA
of larval fish species is critical for fisheries degradation is very high and amplification is
resource management because it allows the not feasible. In this case, Mini-barcoding is
amount of parent stock and future an essential tool for the identification of
recruitment to be calculated. Fish eggs/ species. Since a sequence size of 250 -300
larvae can be identified by comparing the bp is feasible for Mini-barcoding. In situations
COI sequences of eggs/ larvae with where there are mixed samples, DNA
reference sequence libraries such as BOLD Metabarcoding complement with Next
(Barcode of Life Database). These Generation Sequencing (NGS) can be
sequences will be assigned for taxon based applied for species identification and
on their similarity/genetic distance values composition of the product [52]. Mini barcode
with sequences in the database [52]. DNA primer pairs were tested against 44 different
barcoding or a partial sequence of the fish products in a study on the authentication
cytochrome c oxidase I (COI) gene was used of processed fish products from North
to identify larval fish species collected at 12 America. 41 (93.2%) of 44 fish products
stations along the upper and middle Ing could be identified at the species or genus
River in northern Thailand between April level. The highest mini-barcoding success
2017 and March 2018. Seventy-six samples rate found with an individual primer pair was
were successfully identified at the species 88.6%, compared to 20.5% for full-length
level in the GenBank and BOLD databases; DNA barcode primers. The mini-barcoding
these samples were classified into 30 system presented in this study can be used
species, 25 genera, 14 families, and 7 orders to identify a variety of fish species in
with 98-100% similarity. Only two samples, commercial products. It can also be applied
Rasbora sp., and Monopterus sp., could be to high-throughput DNA sequencing for the
identified at the genus level because their authentication of heavily processed fish
COI sequences were not found in either products [73].
database. Within each species, the genetic
distance ranged from 0.000 to 0.005. f) Bio-security and Invasive Alien Species:
Furthermore, almost all species were used Biodiversity measures are not only used for
for one or more purposes, such as fisheries, disease-causing agents but also for invasive
aquaculture, and aquariums. Dermogenys species due to which there is a huge loss in
siamensis was found at all stations, with the ecosystem and economy [74]. Invasive
station 8 (Amphoe Dok Khamtai, Phayao species being non-native causes disturbance
Province) having the most larval fish species. in ecosystem balance by increasing in
The findings of this study could be used to population and causing a decline in native
aid conservation efforts and identify the species population. In the last 60 years, India
spawning grounds of larval fish in the Ing has lost $127.3 billion (Rs. 8.3 trillion) to
River [68]. invasive alien species, making the South
Asian nation 2nd most invasive-cost bearing
d) Conservation: DNA Barcoding is a very country [75]. Another surprising fact, the cost
cost-effective technique and species incurred to the Indian economy across
identification is rapid and accurate. DNA multiple sectors is caused by only 3% of
barcoding is an essential tool for the known invasive species and is
characterization of the biodiversity of the underrepresented for the rest 97% of

361
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

invasive species in India [75]. Study shows between H. jerdoni and H. pulchellus. Both
that 35% of all costs are caused by animals, species are morphologically similar,
15% by plants, and 1% by fungi and especially in the juvenile stage. One of the
bacteria, and the rest are accredited to meristic characters is the number of lateral
diverse or unspecified species [75]. Measure line scales (Lls) which was used as a reliable
for such loss can be resolved with the help of character for identifying these two sister
DNA barcoding. eDNA (Environmental DNA) species. The samples were collected from
Metabarcoding has been successfully used the Netravathi River. In terms of phenotypical
to detect invasive species from different features i.e., the number of lateral line
water bodies [75]. scales, both species are different but in
terms of genetically both specimens are
g) Prey-predator relationship: Prey-predator different. This resolves the issue that the
relationship helps in fisheries management. lateral line scale count is questionable when
One of the main limiting factors for stock it comes to the identification of these two
recruitment is predation during early life sister species [80].
stages [76]. Prey-predator interaction
provides information on the use of habitat b) Fingerling Survival: In Aquaculture, the
and critical foraging habitats. Unfortunately, survival of larvae or fingerling in some fishes
non-native (invasive) predator tends to feed is low. The reason is a lack of proper
on a large number of native species causing nutrition or feed. The best way for them to
the decline in the native population [52]. survive is by providing the natural feed that
Most of the time, invasive species are they feed in the wild. Study in cultured
generalist and flexible with the prey items species' diet during their ontogenic stages is
[77]. An investigation on prey items of lacking. DNA Metabarcoding can be a useful
invasive Indo-Pacific lionfish (Pterois tool for analysing the gut content of the
volitans) from Bahamian coral reefs through fingerling/ adult/ brooder to get information
the DNA barcoding approach and reported about their prey items). Then identified prey
37 species [78]. In a study on the gut content item were cultured and provided as live feed
of ocean sunfish Mola mola which is a for fish [52].
generalist predator about 41 prey items were
identified [79]. Gut biota form a complex c) Improved Management/ Production
dynamic ecosystem that influences fish Management: Biofloc technology is a
health. Depending on the diet preference of revolutionary invention in the aquaculture
fish, seasonality, and availability of the food, industry [81]. Mainly due to their waste
the gut content varies. Identification of gut retention and its conversion to Biofloc which
samples can be under microscopic can be used as feed for fish/shrimps. Biofloc
examination but it is easy to characterize a is an association of multiple microorganisms
specific species from the food item. With the such as heterotrophic bacteria, algae such
assistance of DNA barcoding, a species- as dinoflagellates and diatoms, fungi,
specific analysis is achievable. Gut biota ciliates, flagellates, rotifers, nematodes, and
form a complex dynamic ecosystem that metazoans. Biofloc functions collectively in
influences fish health. maintaining water quality and converting
nitrogenous waste into proteins. The
2) Applications in Aquaculture: composition of species in biofloc varies with
the carbon source and their characterization
a) Seed Identification: With the help of will be useful in the management of culture
Metabarcoding accurate seed identification ponds [52]. Metabarcoding would be useful
can be done from samples collected from in revealing the composition of biofloc along
hatchery water [52]. In some cases, one with carbon source information which would
particular morphological character can lead be effective in implementing biofloc
to misidentification of between two sister technology [52]. Barcode markers such as
species. In a study conducted on DNA Internal Transcribed Spacer (ITS), COI, 16S
Barcoding of Hyselobarbus jerdoni (Day, rRNA, and LSU D1/D2 have been
1870) fingerlings which is an important standardized for developing barcodes for
medium-sized barb, indigenous to the central fungi, protozoans/metazoans, and bacteria,
Western Ghats. DNA Barcoding was done to respectively [82, 13].
resolve the taxonomical characterization

362
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

d) Health Management and Disease diagnosis: are serious issues that are getting worse on a
Fishes/shrimps are mostly susceptible to global scale. In this study on Argulus, screening
infections when there is any alteration in biotic of 278 rohu (Labeo rohita) for Argulus infestation
and abiotic factors of the Pond ecosystem. showed 167 fish (60.07%) tested positive for the
Metabarcoding of soil and water during regular bacterium. Light microscopy (LM) and scanning
intervals gives information about changes in electron microscopy (SEM) were used to
bacteria/ microbe composition over time in examine the morphological characteristics of the
response to uneaten, leftover feed and other parasites. The results revealed a dorsoventrally
activities. This information would be a useful flattened body with a head, thorax, abdomen, two
reference for better management of ponds by large compound eyes, suctorial organs with
maintaining optimum water and soil quality sclerotized support structures, and two
parameters [52]. Parasite (monogeneas, spermatheca openings at the posterior end. The
digeneans, and crustaceans) infection causes cephalo-thoracic carapace does not extend past
huge economic losses due to secondary the beginning of the abdomen, nor does the
infection in fish and later mortality. These posterior incision of the abdomen reach the
parasites can be eliminated if detected in early midline. Molecular methods were used for
stages [52]. Larvae and eggs of parasites are additional validation in order to accurately identify
very small in size and not visible to the naked the parasites. Using the Kimura-2 parameter, the
eye [52]. Metabarcoding of pond water samples pair-wise genetic distance value revealed a
can be useful in identifying early stages of fish species-level variation of 0.001 (1%) with A.
parasites [52]. DNA metabarcoding has the foliaceus, but 0.083 and 0.052 (i.e., more than
potential to be a powerful tool in the field of fish 2%) with A. indicus and A. japonicus, in that
pathogen diagnosis because it allows for the order. Pairwise distance values were also
discovery, identification, and characterization of consistent with the phylogenetic tree created by
a diverse range of pathogenic microbes in a the Neighbour-Joining (NJ) and Maximum-
single experiment without pre-cultivation and in Likelihood (ML) methods, which used the
a short period of time [83]. The identification of Kimura-2 parameter. With the current
pathogen fingerprint gene sequences obtained investigated samples, the mitochondrial
directly from infected fish tissues forms the cytochrome c oxidase subunit 1 (COI) sequences
foundation of this approach [84]. DNA of A. foliaceus formed a single cluster, while the
barcoding and metabarcoding can reveal how sequences of A. formed a sister group. By
parasites influence host fish species evolution. combining fast DNA barcoding technology with
For example, genetic markers have revealed morphological analysis, the species was
host-parasite radiations in African cichlid fishes identified as A. foliaceus [88]. Another study on
and Cichlidogyrus (Platyhelminthes) gill DNA barcoding of Neobenedenia sp. was carried
parasites as a macroevolutionary model of out in Antofagasta coast, Chile. Neobenedenia
species-specific interaction. According to spp. are destructive ectoparasites that affect
genetic markers, the cichlid-cichlidogyrus aquaculture systems. Neobenedenia spp. are
network includes 138 parasite species and 416 observed in many teleost species. However,
interactions [85]. delineating the species is of utmost importance
for parasite diagnosis. Neobenedenia sp. has
A false understanding of the true taxonomy of been found in Japan, Australia, Mexico, and
parasitic species may skew research findings Ecuador in captive Seriola species [89, 90, 91,
that try to measure host-use patterns (host 92, 93]. In wild and farmed Seriola species, it has
specificity), disease dynamics, and local parasite been never observed. DNA barcoding was
adaptation. It may also have an impact on animal carried out on Neobenedian specimens from
parasite diagnosis, management, and eradication both host littoral wild species as well as cultured
efforts [86]. Identification of parasites on the S. lalandi. This investigation was done to
species level is a necessary aspect when it whether this ectoparasite is transmitted from
comes to aquaculture maintenance. A study on natural water bodies to aquacultural systems.
species identification of freshwater ectoparasite The result showed the least genetic distance
species, Argulus foliaceus was carried out on the between Neobenedenia spp. from S. lalandi and
basis of classic morphology and DNA Barcoding. Cheilodactylus variegatus (0.2%-1.2%) and
This ectoparasite is found in Labeo rohita. The between S. lalandi and Aplodactylus punctatus
most extensively studied macro ectoparasite in (0.4%-1.4%) was recorded. The specimens of
pisciculture is Argulus spp. or fish lice. [87] Its Neobenedenia from Paralabrax humeralis were
infestation and the ensuing financial loss of fish the most genetically distant from the other

363
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

specimens used for comparison. Neobenedenia includes environmental samples such as faeces,
species from cultured S. lalandi and littoral fish mucus and other organic matter which are
species from the SEP are genetically distinct collected from water bodies. It indicates the
from N. melleni and N. girellae, according to presence of organisms such as fish even though
molecular analysis. Furthermore, their findings the fish is not present at that particular location
indicate the presence of at least two [99]. One of the technical challenges is that
Neobenedenia species in wild fish from the environmental eDNA degradation frequently
Chilean coast. Furthermore, the morphometry of results in the remnants of only small genetic
Neobenedenia specimens varied between host segments, especially in warm, tropical climates.
species. Lastly, this study suggests that these This limits the potential applications of eDNA
wild host fishes were important in transmitting research [100]. When an eDNA particle enters
Neobenedenia sp. to cultured S. lalandi in a the environment, it begins to degrade. The are
hatchery, given the higher genetic similarity many factors involved in the degradation of an
between those parasites from S. lalandi and eDNA. The eDNA particle's ability to persist over
those from the most abundant littoral fish species time depends on its molecular state that is,
(C. variegatus and A. punctatus) [94]. whether it is free or encapsulated in a cell or
mitochondria—as well as on biotic and abiotic
9. CHALLENGES environmental factors that are external [101].
Temperature, solar radiation, and pH are all
DNA Barcoding even though an effective tool in abiotic environmental factors that influence the
the taxonomic world has its own drawbacks. It persistence of eDNA particles [102]. The biotic-
does not have a universal gene for all domains of mediated decay of microbial communities in
organisms. It cannot be used for amplification marine ecosystems contributes significantly to
and sequencing of degraded DNA. The ability to DNA turnover, a process known as natural
distinguish intra-specific genetic variation from transformation [103,104]. The formation of DNA-
inter-specific genetic variation is required for degrading enzymes by bacteria, the bacterial
DNA-based species identification. These types of populations involved, and the rates at which
variation have unknown ranges and may differ eDNA is broken down enzymatically all influence
between taxa. It appears difficult to distinguish the relationship between biotic effects and eDNA
recently diverged species or new species formed degradation [105]. Apart from high temperatures,
through hybridization [95]. conditions such as neutral pH, nutrients, and
moderate UV-B rays can also stimulate microbial
The conventional full-length DNA barcode for growth and activity, leading to an environment
identifying animal species in food products is a with faster rates of degradation [106, 102, 107].
650-base pair (bp) region in the mitochondrial
gene for cytochrome c subunit I (COI). However, 10. CONCLUSION
the quality of DNA in some moderately or highly
processed foods may be severely compromised, DNA Barcoding is a useful tool for Taxonomic
making PCR amplification of full-length barcodes Accuracy and conservation purposes of flora and
from these samples difficult [96]. The single- fauna. DNA Barcoding is the modern era tool for
locus identification system is the main limitation the conservation of fish for tracking down
of the barcoding approach. Even if several endangered species that are threatened by
regions of these organelle DNAs are sequenced, illegal practices and overfishing. In order to
this is still a single-locus approach because prevent overfishing and aid in the recovery of
mitochondrial and chloroplast DNA genes are overfished stocks, a wide range of intricate tasks
linked. It is well understood that identical are involved in the management of fisheries
mitochondrial or chloroplast DNA sequences can [108]. Most research papers have suggested that
exist in different related species due to DNA Barcoding with Next Generation
introgression or incomplete lineage sorting since Sequencing (NGS) is the best way to have an
speciation [97]. accurate taxonomic identification [8, 52]. DNA
Barcoding has become a pioneer in the
DNA can be extracted from an environmental identification of fishes and phylogenetics.
sample without harming the target organism.
This process is known as environmental DNA DNA Barcoding can aid in disease management
extraction (eDNA), and it is a complex mixture of in fisheries in marine and aquaculture. In terms
genetic material shed by those who inhabit a of the identification of disease which is viral,
given environment [98]. eDNA technology fungal, or bacterial it is not easy to characterize

364
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

them morphologically. DNA Barcoding can fill the Convention on Biological Diversity,
gap with such issues. DNA Barcoding as well as Montreal. 2021;66.
eDNA technology are pioneers in the 6. Yang F, Ding F, Chen H, He M, Zhu S, Ma
identification of noninvasive or nonindigenous, X et al. DNA barcoding for the identification
and cryptic species. DNA minibarcoding has and authentication of animal species in
been an effective tool in the investigation of traditional medicine. Evid Based
marketed food products. DNA Barcoding is one Complement Alternat Med. 2018;2018:
of the most effective tools for wildlife protection. 5160254.
However, depending on the condition of the DOI: 10.1155/2018/5160254
specimen available first-hand, the type of 7. Tan SC, Yiap BC. DNA, RNA, and protein
analysis can vary. A reference library can be extraction: the past and the present. J
developed for dried marine illegal specimens Biomed Biotechnol. 2009;2009:574398.
under the WPA (Wildlife Protection Act) DOI: 10.1155/2009/574398
Schedule list. 8. Ankola K, Mahadevegowda L, Melichar T,
Boregowda MH. DNA barcoding. In
ACKNOWLEDGEMENT Advances in Animal Genomics.2021;299–
308. Elsevier.
The author wishes to express his gratitude to the Available:https://doi.org/10.1016/B978-0-
Principal and Management of S.V.K.M's Mithibai 12-820595-2.00018-7.
College for their constant encouragement and 9. Hebert PDN, Ratnasingham S, deWaard
support. JR. Barcoding animal life: cytochrome c
oxidase subunit 1 divergences among
COMPETING INTERESTS closely related species. Proc R Soc Lond
B. 2003;270;Suppl 1(suppl_1):S96-9.
DOI: 10.1098/rsbl.2003.0025
Authors have declared that no competing
10. Wilson JJ. DNA barcodes for insects. In:
interests exist.
Kress WJ, Erickson DL, editors. Methods
in Molecular Biology (Clifton, N.J.). Vol.
REFERENCES 858. Humana Press; 2012.
DOI: 10.1007/978-1-61779-591-6_3
1. Ahmed S, Ibrahim M, Nantasenamat C, 11. CBOL Plant Working Group. A DNA
Nisar MF, Malik AA, Waheed R et al. barcode for land plants. Proc Natl Acad Sci
Pragmatic applications and universality of U S A. 2009;106(31):12794-7.
DNA barcoding for substantial organisms DOI: 10.1073/pnas.0905845106
at species level: a review to explore a way 12. Hollingsworth PM. Refining the DNA
forward. BioMed Res Int. 2022;2022: barcode for land plants. Proc Natl Acad Sci
1846485. U S A. 2011;108(49):19451-2.
DOI: 10.1155/2022/1846485 DOI: 10.1073/pnas.1116812108
2. Haldar C, Nath S. DNA bar coding for fish 13. Schoch CL, Seifert KA, Huhndorf S, Robert
species identification: current status and V, Spouge JL, Levesque CA, Chen W,
future prospective. Int J Fauna Biol Stud. Fungal Barcoding Consortium, Fungal
2020;7(4):73. Barcoding Consortium Author List,
3. Hellberg RS, Pollack SJ, Hanner RH. Bolchacova E, Voigt K. Nuclear ribosomal
Seafood Species Identification Using DNA internal transcribed spacer (ITS) region as
Sequencing. In Seafood Authenticity and a universal DNA barcode marker for Fungi.
Traceability. 2016;113–132. Elsevier. Proceedings of the national academy of
Available:https://doi.org/10.1016/B978-0- Sciences. 2012;109(16):6241-6..
12-801592-6.00006-1. Available:https://doi.org/10.1073/pnas.111
4. Kress WJ, Erickson DL. DNA barcodes: 7018109.
genes, genomics, and bioinformatics. Proc 14. Pawlowski J, Audic S, Adl S, Bass D,
Natl Acad Sci U S A. 2008;105(8):2761-2. Belbahri L, Berney C et al. Bar coding
DOI: 10.1073/pnas.0800476105 eukaryotic richness beyond the animal,
5. Centre for Biodiversity Genomics, plant, and fungal kingdoms. PLOS Biol.
University of Guelph : The Global 2012;10(11):e1001419.
Taxonomy Initiative 2020: A Step-by-Step DOI: 10.1371/journal.pbio.1001419
Guide for DNA Barcoding. Technical 15. Sanger F, Nicklen S, Coulson AR. DNA
Series No. 94. Secretariat of the sequencing with chain-terminating

365
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

inhibitors. Proc Natl Acad Sci U S A. 1977; DOI: 10.1016/j.cryobiol.2006.10.188

74(12):5463-7. 25. Sunagawa S, DeSantis TZ, Piceno YM,
DOI: 10.1073/pnas.74.12.5463 Brodie EL, DeSalvo MK, Voolstra CR et al.
16. Parveen I, Gafner S, Techen N, Murch SJ, Bacterial diversity and White Plague
Khan IA. DNA barcoding for the Disease-associated community changes in
identification of botanicals in herbal the Caribbean coral Montastraea
medicine and dietary supplements: faveolata. ISME J. 2009;3(5):512-21.
strengths and limitations. Planta Med. DOI: 10.1038/ismej.2008.131
2016;82(14):1225-35. 26. Gray MA, Pratte ZA, Kellogg CA.
DOI: 10.1055/s-0042-111208 Comparison of DNA preservation methods
17. Staats M, Arulandhu AJ, Gravendeel B, for environmental bacterial community
Holst-Jensen A, Scholtens I, Peelen T et samples. FEMS Microbiol Ecol.
al. Advances in DNA metabarcoding for 2013;83(2):468-77.
food and wildlife forensic species DOI: 10.1111/1574-6941.12008
identification. Anal Bioanal Chem. 27. Smith LM, Burgoyne LA. Collecting,
2016;408(17):4615-30. archiving and processing DNA from wildlife
DOI: 10.1007/s00216-016-9595-8 samples using FTA® databasing paper.
18. Elias M, Hill RI, Willmott KR, BMC Ecol. 2004;4(1):4.
Dasmahapatra KK, Brower AVZ, Mallet J DOI: 10.1186/1472-6785-4-4
et al. Limited performance of DNA 28. Beckett SM, Laughton SJ, Pozza LD,
barcoding in a diverse community of McCowage GB, Marshall G, Cohn RJ et al.
tropical butterflies. Proc Biol Sci. Buccal swabs and treated cards:
2007;274(1627):2881-9. methodological considerations for
DOI: 10.1098/rspb.2007.1035 molecular epidemiologic studies examining
19. Rodriguez-Ezpeleta N, Mendibil I, Álvarez pediatric populations. Am J Epidemiol.
P, Cotano U. Effect of fish sampling and 2008;167(10):1260-7.
tissue storage conditions in DNA quality: DOI: 10.1093/aje/kwn012
considerations for genomic studies. 29. Livia L, Antonella P, Hovirag L, Mauro N,
Revista de Investigaciones Marinas. Panara F. A nondestructive, rapid, reliable
2013;20:77-87. and inexpensive method to sample, store
20. Oosting T, Hilario E, Wellenreuther M, and extract high‐quality DNA from fish
Ritchie PA. DNA degradation in fish: body mucus and buccal cells. Mol Ecol
practical solutions and guidelines to Notes. 2006;6(1):257-60.
improve DNA preservation for genomic DOI: 10.1111/j.1471-8286.2005.01142.x.
research. Ecol Evol. 2020;10(16):8643-51. 30. Crabbe MJC. A novel method for the
DOI: 10.1002/ece3.6558 transport and analysis of genetic material
21. Van Der Heijden I, Beijnen JH, Nuijen B. from polyps and zooxanthellae of
Long term stability of lyophilized plasmid scleractinian corals. J Biochem Biophys
DNA pDERMATT. Int J Pharm. Methods. 2003;57(2):171-6.
2013;453(2):648-50. DOI: 10.1016/S0165-022X(03)00051-4.
DOI: 10.1016/j.ijpharm.2013.06.010 31. Lampel KA, Orlandi PA, Kornegay L.
22. Hirabayashi M, Kato M, Ito J, Hochi S. Improved template preparation for PCR-
Viable rat offspring derived from oocytes based assays for detection of food-borne
intracytoplasmically injected with freeze- bacterial pathogens. Appl Environ
dried sperm heads. Zygote. 2005;13(1):79- Microbiol. 2000;66(10):4539-42.
85. DOI: 10.1128/AEM.66.10.4539-4542.2000
DOI: 10.1017/S096719940500300X 32. Rajendram D, Ayenza R, Holder FM,
23. Nagy ZT. A hands-on overview of tissue Moran B, Long T, Shah HN. Long-term
preservation methods for molecular storage and safe retrieval of DNA from
genetic analyses. Org Divers Evol. microorganisms for molecular analysis
2010;10(1):91-105. using FTA matrix cards. J Microbiol
DOI: 10.1007/s13127-010-0012-4. Methods. 2006;67(3):582-92.
24. Stoycheva T, Venkov P, Tsvetkov Ts. DOI: 10.1016/j.mimet.2006.05.010
Mutagenic effect of freezing on 33. Gustavsson I, Lindell M, Wilander E,
mitochondrial DNA of Saccharomyces Strand A, Gyllensten U. Use of FTA card
cerevisiae. Cryobiology. 2007;54(3):243- for dry collection, transportation and
50. storage of cervical cell specimen to detect

366
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

high-risk HPV. J Clin Virol. 2009;46(2):112- method for herbal molecular identification.
6. Front Plant Sci. 2019;10:987.
DOI: 10.1016/j.jcv.2009.06.021 DOI: 10.3389/fpls.2019.00987
34. Barrett MT, Glogovac J, Porter P, Reid BJ, 42. Taberlet P, Coissac E, Pompanon F, Gielly
Rabinovitch PS. High yields of RNA and L, Miquel C, Valentini A et al. Power and
DNA suitable for array analysis from cell limitations of the chloroplast trnL (UAA)
sorter purified epithelial cell and tissue intron for plant DNA barcoding. Nucleic
populations. Nat Genet. 1999;23;Suppl Acids Res. 2007;35(3):e14-.
3:32-40. DOI: 10.1093/nar/gkl938
DOI: 10.1038/14266. 43. Meusnier I, Singer GA, Landry JF, Hickey
35. Mutter GL, Zahrieh D, Liu C, Neuberg D, DA, Hebert PD, Hajibabaei M. A universal
Finkelstein D, Baker HE et al. Comparison DNA mini-barcode for biodiversity analysis.
of frozen and RNAlater solid tissue storage BMC Genomics. 2008;9(1):214.
methods for use in RNA expression DOI: 10.1186/1471-2164-9-214
microarrays. BMC Genomics. 44. Särkinen T, Staats M, Richardson JE,
2004;5(1):88. Cowan RS, Bakker FT. How to open the
DOI: 10.1186/1471-2164-5-88 treasure chest? Optimising DNA extraction
from herbarium specimens. PLOS ONE.
36. Nechvatal JM, Ram JL, Basson MD,
2012;7(8):e43808.
Namprachan P, Niec SR, Badsha KZ et al.
DOI: 10.1371/journal.pone.0043808
Fecal collection, ambient preservation, and
45. Li M, Hou X-F, Zhang J, Wang S-C, Fu Q,
DNA extraction for PCR amplification of
bacterial and human markers from human He L-C. Applications of HPLC/MS in the
feces. J Microbiol Methods. 2008;72(2) analysis of traditional Chinese medicines. J
Pharm Anal. 2011;1(2):81-91.
:124-32.
DOI: 10.1016/S2095-1779(11)70015-6.
DOI: 10.1016/j.mimet.2007.11.007
46. Booker A, Zhai L, Gkouva C, Li S, Heinrich
37. Wilkinson S, Law B, Whitney S, Coulon L, M. From traditional resource to global
Clement O, Shireen L et al. Innovative commodities: –A comparison of Rhodiola
technology to stabilize DNA at room species using NMR spectroscopy—
temperature in tissue and cells. FASEB J. metabolomics and HPTLC. Front
2010;24(S1);Suppl 1. Pharmacol. 2016;7:254.
DOI: DOI: 10.3389/fphar.2016.00254
10.1096/fasebj.24.1_supplement.650.4. 47. Barcaccia G, Lucchin M, Cassandro M.
38. Sharpe A, Barrios S, Gayer S, Allan- DNA barcoding as a molecular tool to track
Perkins E, Stein D, Appiah-Madson HJ et down mislabeling and food piracy.
al. DESS deconstructed: is EDTA solely Diversity. 2015;8(4):2.
responsible for protection of high DOI: 10.3390/d8010002.
molecular weight DNA in this common 48. Lalramliana S, Lalronunga S, Kumar S,
tissue preservative? PLOS ONE. Singh MDNA barcoding revealed a new
2020;15(8) :e0237356. species of Neolissochilus Rainboth, 1985
DOI: 10.1371/journal.pone.0237356 from the Kaladan River of Mizoram, North
39. Mohammed Abubakar B, Mohd Salleh F, East India. Mitochondrial DNA A DNA
Shamsir Omar MS, Wagiran A. Review: Mapp Seq Anal. 2019;30(1):52-9.
DNA barcoding and chromatography DOI: 10.1080/24701394.2018.1450398
fingerprints for the authentication of 49. Adler PH. Sibling Species. In Encyclopedia
botanicals in herbal medicinal products. of Entomology. Kluwer Academic
Evid Based Complement Alternat Med. Publishers. 2004;2004.
2017;2017:1352948. Available: https://doi.org/10.1007/0-306-
DOI: 10.1155/2017/1352948 48380-7_3899
40. Leray M, Knowlton N. DNA barcoding and 50. Rebijith KB, Asokan R, Kumar NKK,
metabarcoding of standardized samples Krishna V, Chaitanya BN, Ramamurthy
reveal patterns of marine benthic diversity. VV. DNA barcoding and elucidation of
Proc Natl Acad Sci U S A. cryptic aphid species (Hemiptera:
2015;112(7):2076-81. Aphididae) in India. Bull Entomol Res.
DOI: 10.1073/pnas.1424997112 2013;103(5):601-10.
41. Gao Z, Liu Y, Wang X, Wei X, Han J. DNA DOI: 10.1017/S0007485313000278
mini-barcoding: A derived barcoding 51. Inland Fisheries in India. (2023, April 17).

367
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

Available:https://dof.gov.in/inland-fisheries. Africa reveals their phylogenetic

52. Pavan-Kumar A, Jaiswar AK, Gireesh- relationships. Afr J Aquat Sci.
Babu P, Chaudhari A, Krishna G. 2019;44(3):291-3.
Applications of DNA barcoding in fisheries. DOI: 10.2989/16085914.2019.1628703.
DNA barcoding and molecular phylogeny. 60. Masters G, Norgrove L. Climate change
2020:177-89. and invasive alien species. UK: CABI
DOI: 10.1007/978-3-030-50075-7_11. Working Paper. 2010;3.
53. Muschick M, Barluenga M, Salzburger W, 61. Fadli N, Mohd Nor SA, Othman AS, Sofyan
Meyer A. Adaptive phenotypic plasticity in H, Muchlisin ZA. DNA barcoding of
the Midas cichlid fish pharyngeal jaw and commercially important reef fishes in Weh
its relevance in adaptive radiation. BMC Island, Aceh, Indonesia. PeerJ. 2020;8:
Evol Biol. 2011;11(1):116. e9641.
DOI: 10.1186/1471-2148-11-116 DOI: 10.7717/peerj.9641
54. Barry J, Newton M, Dodd JA, Hooker OE, 62. Bakun A. Patterns in the ocean: ocean
Boylan P, Lucas MC et al. Foraging processes and marine population
specialisms influence space use and dynamics. California Sea Grant College
movement patterns of the European eel System, National Oceanic and
Anguilla anguilla. Hydrobiologia. 2016; Atmospheric Adminstration in cooperation
766(1):333-48. with Centro de Investigaciones Biológicas
DOI: 10.1007/s10750-015-2466-z. del Noroeste. 1996.
55. Alberts EC. Study Finds Major Brands 63. Cowen RK, Paris CB, Srinivasan A.
Selling Cat Food That Contain Protected Scaling of connectivity in marine
Sharks [Conservation]. Mongabay Series: populations. Science. 2006;311(5760):522-
Oceans; 2022. 7.
Available:https://news.mongabay.com/202 DOI: 10.1126/science.1122039
2/03/study-finds-major-brands-selling-cat- 64. Serafy JE, Cowen RK, Paris CB, Capo TR,
food-that-contain-protected- Luthy SA. Evidence of blue marlin, Makaira
sharks/#:~:text=Study%20finds%20major nigricans, spawning in the vicinity of
%20brands%20selling%20cat%20food%2 Exuma Sound, Bahamas. Mar Freshw
0that%20contain%20protected%20sharks, Res. 2003;54(4):299.
- DOI: 10.1071/MF01273.
by%20Elizabeth%20Claire&text=Research 65. Govoni JJ, Laban EH, Hare JA. The early
ers%20used%20DNA%20barcoding%20to life history of swordfish (Xiphias gladius) in
,protected%20under%20CITES%20Appen the western North Atlantic. Fish Bull.
dix%20II. 2003;101(4):778.
56. Galal-Khallaf A, Osman AGM, Carleos CE, 66. Ralston S, Bence JR, Eldridge MB, Lenarz
Garcia-Vazquez E, Borrell YJ. A case WH. An approach to estimating rockfish
study for assessing fish traceability in biomass based on larval production, with
Egyptian aquafeed formulations using application to Sebastes jordani*. Fish Bull.
Pyrosequencing and metabarcoding. Fish 2003;101:129-46.
Res. 2016;174:143-50. 67. Richardson DE, Cowen RK. Diversity of
DOI: 10.1016/j.fishres.2015.09.009. leptocephalus larvae around the island of
57. Gyamfua A, Shunkai H, Zhongdian D, Barbados (West Indies): relevance to
Yusong G, Felix KAK, Christian AL et al. regional distributions. Mar Ecol Prog Ser.
DNA barcoding of Ghanaian fish species: 2004;282:271-84.
status and prospects. Afr J Biotechnol. DOI: 10.3354/meps282271.
2019;18(27):659-63. 68. Panprommin D, Soontornprasit K,
DOI: 10.5897/AJB2019.16792. Tuncharoen S, Iamchuen N. Efficacy of
58. Van Ginneken M, Decru E, Verheyen E, DNA barcoding for the identification of
Snoeks J. Morphometry and DNA larval fish species in the Upper and Middle
barcoding reveal cryptic diversity in the Ing River, Thailand. Gene Rep.
genus Enteromius (Cypriniformes: 2021;23:101057.
Cyprinidae) from the Congo basin, Africa. DOI: 10.1016/j.genrep.2021.101057.
Eur J Taxon. 2017;(310). 69. Mohanty B, Mahanty A, Ganguly S, Sankar
DOI: 10.5852/ejt.2017.310. TV, Chakraborty K, Rangasamy A et al.
59. Van Der Bank F. A DNA barcoding study Amino acid compositions of 27 food fishes
of seven cichlid species from southern

368
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

and their importance in clinical nutrition. J barcoding identifies a cosmopolitan diet in

Amino Acids. 2014;2014:269797. the ocean sunfish. Sci Rep.
DOI: 10.1155/2014/269797 2016;6(1):28762.
70. Bogard JR, Thilsted SH, Marks GC, DOI: 10.1038/srep28762
Wahab MdA, Hossain MAR, Jakobsen J et 80. Nasren S, Basavaraja N, Shekar M, Al-
al. Nutrient composition of important fish Mamun MdA, Rathore SS, Abhiman PB et
species in Bangladesh and potential al. Use of DNA bar coding in the
contribution to recommended nutrient investigation of disputable meristic features
intakes. J Food Compos Anal. for Hypselobarbus jerdoni (DAY, 1870)
2015;42:120-33. fingerlings. J Exp Zool India.
DOI: 10.1016/j.jfca.2015.03.002. 2020;23(1):113-8.
71. Armani A, Castigliego L, Tinacci L, 81. Crab R, Defoirdt T, Bossier P, Verstraete
Gianfaldoni D, Guidi A. Molecular W. Biofloc technology in aquaculture:
characterization of icefish, (Salangidae beneficial effects and future challenges.
family), using direct sequencing of Aquaculture. 2012;356-357:351-6.
mitochondrial cytochrome b gene. Food DOI: 10.1016/j.aquaculture.2012.04.046.
Control. 2011;22(6):888-95. 82. Lebonah DE, Dileep A, Chandrasekhar K,
DOI: 10.1016/j.foodcont.2010.11.020. Sreevani S, Sreedevi B, Pramoda Kumari
72. Marko PB, Lee SC, Rice AM, Gramling JM, J. DNA barcoding on bacteria: a review.
Fitzhenry TM, McAlister JS et al. Fisheries: Adv Biol. 2014;2014:1-9.
Mislabelling of a depleted reef fish. Nature. DOI: 10.1155/2014/541787.
2004;430(6997):309-10. 83. Elsaied H, Soliman T, Abdelmageed AA,
DOI: 10.1038/430309b Abu-Taleb HT. Applications and
73. Shokralla S, Hellberg RS, Handy SM, King challenges of DNA barcoding and
I, Hajibabaei M. A DNA mini-barcoding metabarcoding in African fisheries. Egypt J
system for authentication of processed fish Aquat Res. 2021;47(1):1-12.
products. Sci Rep. 2015;5(1):15894. DOI: 10.1016/j.ejar.2021.02.003.
DOI: 10.1038/srep15894 84. Breitwieser FP, Lu J, Salzberg SL. A
74. Williamson M. Biological invasions. review of methods and databases for
Chapman & Hall, London. 1996;244. metagenomic classification and assembly.
75. Ghosh S. The cost of invasive species Brief Bioinform. 2019;20(4):1125-36.
bears heavy on Indian economy, finds DOI: 10.1093/bib/bbx120
study [Conservation]. The Cost of Invasive 85. Cruz-Laufer AJ, Artois T, Smeets K,
Species Bears Heavy on Indian Economy, Pariselle A, Vanhove MPM. The cichlid–
Finds Study; 2022. Cichlidogyrus network: A blueprint for a
Available:https://india.mongabay.com/2022 model system of parasite evolution.
/05/the-cost-of-invasive-species-bears- Hydrobiologia. 2021;848(16):3847-63.
heavy-on-indian-economy-finds-study/. DOI: 10.1007/s10750-020-04426-4.
76. Saitoh K, Takagaki M, Yamashita Y. 86. Nadler SA, De León GP-P. Integrating
Detection of Japanese flounder-specific molecular and morphological approaches
DNA from gut contents of potential for characterizing parasite cryptic species:
predators in the field. Fish Sci. implications for parasitology. Parasitology.
2003;69(3):473-7. 2011;138(13):1688-709.
DOI: 10.1046/j.1444-2906.2003.00647.x. DOI: 10.1017/S003118201000168X
77. Olden JD, LeRoy Poff N, Douglas MR, 87. Mandira S, PK, B. : First report of three
Douglas ME, Fausch KD. Ecological and species of Argulus (Crustacea: Branchiura)
evolutionary consequences of biotic infesting on redcan Oranda gold fish
homogenization. Trends Ecol Evol. (Carassius auratus auratus) in India.
2004;19(1):18-24. Biolife. 2015;3(4):813-9.
DOI: 10.1016/j.tree.2003.09.010 88. Mohanty S, Mausumee Mohanty S, Sarma
78. Côté I, Green S, Morris J, Akins J, Steinke K, Kumar T, Dey A, Das P et al. Classical
D. Diet richness of invasive Indo-Pacific morphology and DNA barcoding based
lionfish revealed by DNA barcoding. Mar identification of freshwater ectoparasite,
Ecol Prog Ser. 2013;472:249-56. Argulus foliaceus in rohu Labeo rohita:
DOI: 10.3354/meps09992. morphological and DNA barcoding based
79. Sousa LL, Xavier R, Costa V, Humphries identification of fish ectoparasite. Indian J
NE, Trueman C, Rosa R et al. DNA Fish. 2023;70(1).

369
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

DOI: 10.21077/ijf.2023.70.1.132415-16. 97. Ballard JWO, Whitlock MC. The

89. Ogawa K, Bondad-Reantaso MG, incomplete natural history of mitochondria.
Fukudome M, Wakabayashi H. Mol Ecol. 2004;13(4):729-44.
Neobenedenia girellae (Hargis, 1955) DOI: 10.1046/j.1365-294X.2003.02063.x
Yamaguti, 1963 (Monogenea: Capsalidae) 98. Rourke ML, Fowler AM, Hughes JM,
from cultured marine fishes of Japan. J Broadhurst MK, DiBattista JD, Fielder S et
Parasitol. 1995;81(2):223-7. doi: al. Environmental DNA (eDNA) as a tool
10.2307/3283923, PMID 7707197. for assessing fish biomass: a review of
90. Ogawa K, Shirakashi S, Ishitani H. approaches and future considerations for
Insemination of the monogenean resource surveys. Environ DNA.
Neobenedenia girellae (Capsalidae, 2022;4(1):9-33.
Benedeniinae). Parasitol Int. DOI: 10.1002/edn3.185.
2014;63(2):473-8. 99. Davis J. Environmental DNA: what is it and
DOI: 10.1016/j.parint.2013.10.009 how can it help us protect wildlife?, (2021,
91. Reyes‐Becerril M, Alamillo E, Trasviña A, May 23), British Wildlife.
Hirono I, Kondo H, Jirapongpairoj W et al. https://www.nhm.ac.uk/discover/what-is-
In vivo and in vitro studies using larval and environmental-dna-edna.html.
adult antigens from Neobenedenia melleni 100. Ruppert KM, Kline RJ, Rahman MS. Past,
on immune response in yellowtail (Seriola present, and future perspectives of
lalandi). J Fish Dis. 2017;40(11):1497-509. environmental DNA (eDNA)
DOI: 10.1111/jfd.12620 metabarcoding: A systematic review in
92. Argüello-Guevara W, Apolinario W, methods, monitoring, and applications of
Bohórquez-Cruz M, Reinoso S, Rodríguez global eDNA. Glob Ecol Conserv.
S, Sonnenholzner S. Effects of intermittent 2019;17:e00547.
feeding on water quality, skin parasites, DOI: 10.1016/j.gecco.2019.e00547.
feed consumption, and growth 101. Hansen BK, Bekkevold D, Clausen LW,
performance of juvenile longfin yellowtail Nielsen EE. The sceptical optimist:
Seriola rivoliana (Valenciennes, 1833). challenges and perspectives for the
Aquacult Res. 2018;49(11):3586-94. application of environmental DNA in
DOI: 10.1111/are.13825. marine fisheries. Fish Fish.
93. Brazenor AK, Bertozzi T, Miller TL, 2018;19(5):751-68.
Whittington ID, Hutson KS. DNA profiling DOI: 10.1111/faf.12286.
reveals Neobenedenia girellae as the 102. Strickler KM, Fremier AK, Goldberg CS.
primary parasitic monogenean in global Quantifying effects of UV-B, temperature,
fisheries and aquaculture. Mol Phylogenet and pH on eDNA degradation in aquatic
Evol. 2018;129:130-7. microcosms. Biol Conserv. 2015;183:85-
DOI: 10.1016/j.ympev.2018.05.012 92.
94. Sepúlveda FA, González MT. DNA DOI: 10.1016/j.biocon.2014.11.038.
barcoding evidence for the first recorded 103. Lorenz MG, Wackernagel W. Bacterial
transmission of Neobenedenia sp. From gene transfer by natural genetic
wild fish species to Seriola lalandi cultured transformation in the environment.
in an open recirculating system on the Microbiol Rev. 1994;58(3):563-602.
Coast of Northern Chile. Aquaculture. DOI: 10.1128/mr.58.3.563-602.1994
2019;501:239-46. 104. Pietramellara G, Ascher J, Borgogni F,
DOI: 10.1016/j.aquaculture.2018.11.037. Ceccherini MT, Guerri G, Nannipieri P.
95. Naz S, Chatha AMM, Khan RU. Pragmatic Extracellular DNA in soil and sediment:
applications of DNA barcoding markers in fate and ecological relevance. Biol Fertil
identification of fish species – a review. Soils. 2009;45(3):219-35.
Ann Anim Sci. 2023;23(2):363-89. DOI: 10.1007/s00374-008-0345-8.
DOI: 10.2478/aoas-2022-0073. 105. Tsuji S, Ushio M, Sakurai S, Minamoto T,
96. Hajibabaei M, Smith MA, Janzen DH, Yamanaka H. Water temperature-
Rodriguez JJ, Whitfield JB, Hebert PDN. A dependent degradation of environmental
minimalist barcode can identify a specimen DNA and its relation to bacterial
whose DNA is degraded. Mol Ecol Notes. abundance. PLOS ONE.
2006;6(4):959-64. 2017;12(4):e0176608.
DOI: 10.1111/j.1471-8286.2006.01470.x. DOI: 10.1371/journal.pone.0176608

370
 Shetty and Shingadia; Uttar Pradesh J. Zool., vol. 44, no. 23, pp. 351-371, 2023; Article no.UPJOZ.3014

106. Salter I. Seasonal variability in the eutrophic lake. Int J Environ Res Public
persistence of dissolved environmental Health. 2019;16(18):3339.
DNA (eDNA) in a marine system: the role DOI: 10.3390/ijerph16183339
of microbial nutrient limitation. PLOS ONE. 108. Ramírez-Amaro S, Bassitta M, Picornell A,
2018;13(2):e0192409. Ramon C, Terrasa B. Environmental DNA:
DOI: 10.1371/journal.pone.0192409 state-of-the-art of its application for
107. Zulkefli NS, Kim KH, Hwang SJ. Effects of fisheries assessment in marine
microbial activity and environmental environments. Front Mar Sci.
parameters on the degradation of 2022;9:1004674.
extracellular environmental DNA from a DOI: 10.3389/fmars.2022.1004674.

© Copyright MB International Media and Publishing House. All rights reserved.

371

View publication stats