Mouse genome

Editor's Notes

• #3: Mice are extremely useful for studying complex diseases, such as atherosclerosis and hypertension, as many of the genes responsible for these diseases are shared between mice and humans. Research in mice provides insights into the genetic risk factors for these diseases in the human population. It is relatively easy to manipulate the mouse genome, for example, adding or removing a gene to better understand its role in the body. This provides a powerful tool for modelling specific diseases when a mutated gene is known to play a role in the disease. Immunodeficient mice can also be used as hosts to grow both normal and diseased human tissue. This has been a useful tool in cancer and AIDS research.  Inbred strains are well-characterized, genetically uniform mouse models that can be used for a wide variety of human biological and disease research.  
• #6: The haploid genome is about 3 billion base pairs long. (2818.97 Mb size) Mice have 20 chromosomes in their haploid genome. The current count of primary coding genes in lab mouse is 24,500. They have a GC % of about 41.95% N50 is defined as the sequence length of the shortest contig at 50% of the total genome length. For example, consider 9 contigs with the lengths 2,3,4,5,6,7,8,9,and 10; their sum is 54, half of the sum is 27, and the size of the genome also happens to be 54. 50% of this assembly would be 10 + 9 + 8 = 27 (half the length of the sequence). Thus the N50=8, which is the size of the contig which, along with the larger contigs, contain half of sequence of a particular genome. Note: When comparing N50 values from different assemblies, the assembly sizes must be the same size in order for N50 to be meaningful
• #8: A contig is the assembly of overlapping clones without a gap, i.e. the unbroken series of clones assembled using overlapping sequences. The N50 is defined as the minimum contig length needed to cover 50% of the genome.  ExampleFor an assembly fragmented into 4 contigs with lengths: 1, 2, 4, and 5 kb (total size = 12 kb), half of the genome length is covered by the two largest contigs, and hence N50=4kb is the minimum contig length required to cover 50 percent of the assembled genome sequence.  N10 is the minimum contig length to cover 10 percent of the genome. N90 is the minimum contig length to cover 90 percent of the genome. 
• #9: In fact, only about 300 genes are unique to either organism, which further supports the use of the mouse models for studying various diseases as well as testing novel treatments. The key differences lie in those areas of the genome governing immunity, detoxification, smell and sex, which makes sense considering where rodents usually live, how they find food and the number of offspring they can produce. the Broad Institute has been generating a map of single-nucleotide polymorphisms (SNPs) among mouse strains. The initial set contains ~340,000 SNPs and has been used to characterize the haplotype structure of the laboratory mouse. The current goal is a dense haplotype map (20 kb resolution) of 48 mouse strains, as well as an in-depth characterization of variation within 15 mouse strains.
• #10: This mixed strategy was designed to exploit the simpler organizational aspects of WGS assemblies in the initial phase, while still culminating in the complete high-quality sequence afforded by clone-based maps.
• #16: the mouse and human genomes have each been shuffled by chromosomal rearrangements. The rate of these changes, however, is low enough that local gene order remains largely intact. It is thus possible to recognize syntenic (literally ‘same thread’) regions in the two species that have descended relatively intact from the common ancestor.
• #18: Human chromosome 20 corresponds entirely to a portion of mouse chromosome 2, with nearly perfect conservation of order along almost the entire length, disrupted only by a small central segment (Fig. 4a, d). Human chromosome 17 corresponds entirely to a portion of mouse chromosome 11, but extensive rearrangements have divided it into at least 16 segments (Fig. 4b, e). Other chromosomes, however, show evidence of much more extensive interchromosomal rearrangement than these cases 
• #22: L1 seems to have remained highly active in mouse, whereas it has declined in the human lineage. only a single SINE (Alu) was active in the human lineage, the mouse lineage has been exposed to four distinct SINEs (B1, B2, ID, B4). Each is thought to rely on L1 for retroposition, although none share sequence similarity, as is the rule for other LINE–SINE pairs Only four lineage-specific DNA transposon families could be identified in mouse (the mariner element MMAR1, and the hAT elements URR1, RMER30 and RChar1), compared with 14 in the primate lineage.
• #24: Comparisons of sequence from inbred strains demonstrate that the level of sequence differences between any two inbred strains varies enormously between different regions of the genome [24–26]. In some regions, the frequency of SNPs is as high as 1 in 250 bp. Other regions are relatively devoid of sequence variants and the SNP frequency is as low as 1 in 20 kb – the so-called SNP deserts. It is assumed that these deserts represent ancestral regions shared by the founder mice that were used to estab-lish most inbred strains.