Comparative Genomics - Initial sequencing and comparative analysis of the mouse genome

 At 2014-03-16 02:40:49 AM  |   95

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.

With the complete sequence of the human genome nearly in hand1, 2, the next challenge is to extract the extraordinary trove of information encoded within its roughly 3 billion nucleotides. This information includes the blueprints for all RNAs and proteins, the regulatory elements that ensure proper expression of all genes, the structural elements that govern chromosome function, and the records of our evolutionary history. Some of these features can be recognized easily in the human sequence, but many are subtle and difficult to discern. One of the most powerful general approaches for unlocking the secrets of the human genome is comparative genomics, and one of the most powerful starting points for comparison is the laboratory mouse, Mus musculus.

Metaphorically, comparative genomics allows one to read evolution's laboratory notebook. In the roughly 75 million years since the divergence of the human and mouse lineages, the process of evolution has altered their genome sequences and caused them to diverge by nearly one substitution for every two nucleotides (see below) as well as by deletion and insertion. The divergence rate is low enough that one can still align orthologous sequences, but high enough so that one can recognize many functionally important elements by their greater degree of conservation. Studies of small genomic regions have demonstrated the power of such cross-species conservation to identify putative genes or regulatory elements3, 4, 5, 6, 7, 8, 9, 10, 11, 12. Genome-wide analysis of sequence conservation holds the prospect of systematically revealing such information for all genes. Genome-wide comparisons among organisms can also highlight key differences in the forces shaping their genomes, including differences in mutational and selective pressures13, 14.

Literally, comparative genomics allows one to link laboratory notebooks of clinical and basic researchers. With knowledge of both genomes, biomedical studies of human genes can be complemented by experimental manipulations of corresponding mouse genes to accelerate functional understanding. In this respect, the mouse is unsurpassed as a model system for probing mammalian biology and human disease15, 16. Its unique advantages include a century of genetic studies, scores of inbred strains, hundreds of spontaneous mutations, practical techniques for random mutagenesis, and, importantly, directed engineering of the genome through transgenic, knockout and knockin techniques17, 18, 19, 20, 21, 22.

For these and other reasons, the Human Genome Project (HGP) recognized from its outset that the sequencing of the human genome needed to be followed as rapidly as possible by the sequencing of the mouse genome. In early 2001, the International Human Genome Sequencing Consortium reported a draft sequence covering about 90% of the euchromatic human genome, with about 35% in finished form1. Since then, progress towards a complete human sequence has proceeded swiftly, with approximately 98% of the genome now available in draft form and about 95% in finished form.

Here, we report the results of an international collaboration involving centres in the United States and the United Kingdom to produce a high-quality draft sequence of the mouse genome and a broad scientific network to analyse the data. The draft sequence was generated by assembling about sevenfold sequence coverage from female mice of the C57BL/6J strain (referred to below as B6). The assembly contains about 96% of the sequence of the euchromatic genome (excluding chromosome Y) in sequence contigs linked together into large units, usually larger than 50 megabases (Mb).

With the availability of a draft sequence of the mouse genome, we have undertaken an initial comparative analysis to examine the similarities and differences between the human and mouse genomes. Some of the important points are listed below.

• The mouse genome is about 14% smaller than the human genome (2.5 Gb compared with 2.9 Gb). The difference probably reflects a higher rate of deletion in the mouse lineage.

• Over 90% of the mouse and human genomes can be partitioned into corresponding regions of conserved synteny, reflecting segments in which the gene order in the most recent common ancestor has been conserved in both species.

• At the nucleotide level, approximately 40% of the human genome can be aligned to the mouse genome. These sequences seem to represent most of the orthologous sequences that remain in both lineages from the common ancestor, with the rest likely to have been deleted in one or both genomes.

• The neutral substitution rate has been roughly half a nucleotide substitution per site since the divergence of the species, with about twice as many of these substitutions having occurred in the mouse compared with the human lineage.

• By comparing the extent of genome-wide sequence conservation to the neutral rate, the proportion of small (50–100 bp) segments in the mammalian genome that is under (purifying) selection can be estimated to be about 5%. This proportion is much higher than can be explained by protein-coding sequences alone, implying that the genome contains many additional features (such as untranslated regions, regulatory elements, non-protein-coding genes, and chromosomal structural elements) under selection for biological function.

• The mammalian genome is evolving in a non-uniform manner, with various measures of divergence showing substantial variation across the genome.

• The mouse and human genomes each seem to contain about 30,000 protein-coding genes. These refined estimates have been derived from both new evidence-based analyses that produce larger and more complete sets of gene predictions, and new de novo gene predictions that do not rely on previous evidence of transcription or homology. The proportion of mouse genes with a single identifiable orthologue in the human genome seems to be approximately 80%. The proportion of mouse genes without any homologue currently detectable in the human genome (and vice versa) seems to be less than 1%.

• Dozens of local gene family expansions have occurred in the mouse lineage. Most of these seem to involve genes related to reproduction, immunity and olfaction, suggesting that these physiological systems have been the focus of extensive lineage-specific innovation in rodents.

• Mouse–human sequence comparisons allow an estimate of the rate of protein evolution in mammals. Certain classes of secreted proteins implicated in reproduction, host defence and immune response seem to be under positive selection, which drives rapid evolution.

• Despite marked differences in the activity of transposable elements between mouse and human, similar types of repeat sequences have accumulated in the corresponding genomic regions in both species. The correlation is stronger than can be explained simply by local (G+C) content and points to additional factors influencing how the genome is moulded by transposons.

• By additional sequencing in other mouse strains, we have identified about 80,000 single nucleotide polymorphisms (SNPs). The distribution of SNPs reveals that genetic variation among mouse strains occurs in large blocks, mostly reflecting contributions of the two subspecies Mus musculus domesticusand Mus musculus musculus to current laboratory strains.

The mouse genome sequence is freely available in public databases (GenBank accession number CAAA01000000) and is accessible through various genome browsers (https://ensembl.org/Mus_musculus/https://genome.ucsc.edu/and https://ncbi.nlm.nih.gov/genome/guide/mouse/).

In this paper, we begin with information about the generation, assembly and evaluation of the draft genome sequence, the conservation of synteny between the mouse and human genomes, and the landscape of the mouse genome. We then explore the repeat sequences, genes and proteome of the mouse, emphasizing comparisons with the human. This is followed by evolutionary analysis of selection and mutation in the mouse and human lineages, as well as polymorphism among current mouse strains. A full and detailed description of the methods underlying these studies is provided as Supplementary Information. In many respects, the current paper is a companion to the recent paper on the human genome sequence1. Extensive background information about many of the topics discussed below is provided there.

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Background to the mouse genome sequencing project

Origins of the mouse

The precise origin of the mouse and human lineages has been the subject of recent debate. Palaeontological evidence has long indicated a great radiation of placental (eutherian) mammals about 65 million years ago (Myr) that filled the ecological space left by the extinction of the dinosaurs, and that gave rise to most of the eutherian orders23. Molecular phylogenetic analyses indicate earlier divergence times of many of the mammalian clades. Some of these studies have suggested a very early date for the divergence of mouse from other mammals (100–130 Myr23, 24, 25) but these estimates partially originate from the fast molecular clock in rodents (see below). Recent molecular studies that are less sensitive to the differences in evolutionary rates have suggested that the eutherian mammalian radiation took place throughout the Late Cretaceous period (65–100 Myr), but that rodents and primates actually represent relatively late-branching lineages26, 27. In the analyses below, we use a divergence time for the human and mouse lineages of 75 Myr for the purpose of calculating evolutionary rates, although it is possible that the actual time may be as recent as 65 Myr.

Origins of mouse genetics

The origin of the mouse as the leading model system for biomedical research traces back to the start of human civilization, when mice became commensal with human settlements. Humans noticed spontaneously arising coat-colour mutants and recorded their observations for millennia (including ancient Chinese references to dominant-spotting, waltzing, albino and yellow mice). By the 1700s, mouse fanciers in Japan and China had domesticated many varieties as pets, and Europeans subsequently imported favourites and bred them to local mice (thereby creating progenitors of modern laboratory mice as hybrids among M. m. domesticusM. m. musculus and other subspecies). In Victorian England, ‘fancy’ mice were prized and traded, and a National Mouse Club was founded in 1895 (refs 2829).

With the rediscovery of Mendel's laws of inheritance in 1900, pioneers of the new science of genetics (such as Cuenot, Castle and Little) were quick to recognize that the discontinuous variation of fancy mice was analogous to that of Mendel's peas, and they set out to test the new theories of inheritance in mice. Mating programmes were soon established to create inbred strains, resulting in many of the modern, well-known strains (including C57BL/6J)30.

Genetic mapping in the mouse began with Haldane's report31 in 1915 of linkage between the pink-eye dilution and albino loci on the linkage group that was eventually assigned to mouse chromosome 7, just 2 years after the first report of genetic linkage in Drosophila. The genetic map grew slowly over the next 50 years as new loci and linkage groups were added—chromosome 7 grew to three loci by 1935 and eight by 1954. The accumulation of serological and enzyme polymorphisms from the 1960s to the early 1980s began to fill out the genome, with the map of chromosome 7 harbouring 45 loci by 1982 (refs 29,31).

The real explosion, however, came with the development of recombinant DNA technology and the advent of DNA-sequence-based polymorphisms. Initially, this involved the detection of restriction-fragment length polymorphisms (RFLPs)32; later, the emphasis shifted to the use of simple sequence length polymorphisms (SSLPs; also called microsatellites), which could be assayed easily by polymerase chain reaction (PCR)33, 34, 35, 36 and readily revealed polymorphisms between inbred laboratory strains.

Origins of mouse genomics

When the Human Genome Project (HGP) was launched in 1990, it included the mouse as one of its five central model organisms, and targeted the creation of genetic, physical and eventually sequence maps of the mouse genome.

By 1996, a dense genetic map with nearly 6,600 highly polymorphic SSLP markers ordered in a common cross had been developed34, providing the standard tool for mouse genetics. Subsequent efforts filled out the map to over 12,000 polymorphic markers, although not all of these loci have been positioned precisely relative to one another. With these and other loci, Haldane's original two-marker linkage group on chromosome 7 had now swelled to about 2,250 loci.

Physical maps of the mouse genome also proceeded apace, using sequence-tagged sites (STS) together with radiation-hybrid panels37, 38 and yeast artificial chromosome (YAC) libraries to construct dense landmark maps39. Together, the genetic and physical maps provide thousands of anchor points that can be used to tie clones or DNA sequences to specific locations in the mouse genome.

Other resources included large collections of expressed-sequence tags (EST)40, a growing number of full-length complementary DNAs41, 42 and excellent bacterial artificial chromosome (BAC) libraries43. The latter have been used for deriving large sets of BAC-end sequences37 and, as part of this collaboration, to generate a fingerprint-based physical map44. Furthermore, key mouse genome databases were developed at the Jackson (https://informatics.jax.org/), Harwell (https://har.mrc.ac.uk/) and RIKEN (https://genome.rtc.riken.go.jp/) laboratories to provide the community with access to this information.

With these resources, it became straightforward (but not always easy) to perform positional cloning of classic single-gene mutations for visible, behavioural, immunological and other phenotypes. Many of these mutations provide important models of human disease, sometimes recapitulating human phenotypes with uncanny accuracy. It also became possible for the first time to begin dissecting polygenic traits by genetic mapping of quantitative trait loci (QTL) for such traits.

Continuing advances fuelled a growing desire for a complete sequence of the mouse genome. The development of improved random mutagenesis protocols led to the establishment of large-scale screens to identify interesting new mutants, increasing the need for more rapid positional cloning strategies. QTL mapping experiments succeeded in localizing more than 1,000 loci affecting physiological traits, creating demand for efficient techniques capable of trawling through large genomic regions to find the underlying genes. Furthermore, the ability to perform directed mutagenesis of the mouse germ line through homologous recombination made it possible to manipulate any gene given its DNA sequence, placing an increasing premium on sequence information. In all of these cases, it was clear that genome sequence information could markedly accelerate progress.

Origin of the Mouse Genome Sequencing Consortium

With the sequencing of the human genome well underway by 1999, a concerted effort to sequence the entire mouse genome was organized by a Mouse Genome Sequencing Consortium (MGSC). The MGSC originally consisted of three large sequencing centres—the Whitehead/Massachusetts Institute of Technology (MIT) Center for Genome Research, the Washington University Genome Sequencing Center, and the Wellcome Trust Sanger Institute—together with an international database, Ensembl, a joint project between the European Bioinformatics Institute and the Sanger Institute.

In addition to the genome-wide efforts of the MGSC, other publicly funded groups have been contributing to the sequencing of the mouse genome in specific regions of biological interest. Together, the MGSC and these programmes have so far yielded clone-based draft sequence consisting of 1,859 Mb (74%, although there is redundancy) and finished sequence of 477 Mb (19%) of the mouse genome. Furthermore, Mural and colleagues45 recently reported a draft sequence of mouse chromosome 16 containing 87 Mb (3.5%).

To analyse the data reported here, the MGSC was expanded to include the other publicly funded sequencing groups and a Mouse Genome Analysis Group consisting of scientists from 27 institutions in 6 countries.

Source: https://nature.com/nature/journal/v420/n6915/full/nature01262.html

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