Initial sequencing and comparative analysis of the mouse genome

Abstract

The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

Computational challenges in the analysis of ancient DNA

“…Neandertal data are well suited for investigating the potential effects of having a progressively more distantly related comparison genome, since complete genome sequences are available from three great apes and several more distantly related primates. By using only the increasingly more distantly related genome sequences of human [27], chimpanzee [28], orangutan, rhesus macaque [29], mouse lemur, bushbaby and mouse [30], we gauge how many Neandertal sequences could be identified if each of these genomes was the only one that was available. We also investigated the accuracy of the observed number of pairwise nucleotide differences in each of these comparisons ([31].…”

“…These genome sequences span a range from less than 1 million years (between Neandertal and human) [9,10] up to 87 million years of divergence (between mouse and human) [35]. Mouse-human genome divergence has been estimated to be, on average, 0.5 substitutions per site [30]. This constitutes the most diverged genome comparison in our test.…”

Genetic Susceptibility to Rhodococcus equi

“…Genome‐wide association studies (GWASs) rapidly gained popularity after the sequencing of the genomes of several animal species, including human beings 31, 32, 33, 34. The completion of the sequencing and assembly of these reference genomes (an assembly of the DNA sequence and its chromosomal locations representing the genetic baseline of a species) provided a tool that could be used as a map indicating where elements of the genome reside.…”

Exploring the selective constraint on the sizes of insertions and deletions in 5' untranslated regions in mammals

“…Insertion and deletion mutations (indels) frequently occur during the evolution of mammalian genomes [1-4]. Most of these indels are selectively neutral when they occur in noncoding genomic regions [5,6].…”