The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes

Adams, David J.; Doran, Anthony; Lilue, Jingtao; Keane, Thomas M.

doi:10.1007/s00335-015-9579-6

Cited by 79 publications

(98 citation statements)

References 43 publications

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“…The casual gene within this region is unknown, but the narrowed locus harbors multiple promising candidates, including testis- and ovary-expressed genes, a cluster of uncharacterized microRNAs, and several genes of unknown function. Patterns of diversity across this genomic locus are also consistent with the presence of structural mutations differentiating subspecies (Keane et al 2011; Adams et al 2015). …”

Section: Discussionsupporting

confidence: 60%

X-Chromosome Control of Genome-Scale Recombination Rates in House Mice

Dumont

2017

Genetics

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Sex differences in recombination are widespread in mammals, but the causes of this pattern are poorly understood. Previously, males from two interfertile subspecies of house mice, Mus musculus musculus and M. m. castaneus, were shown to exhibit a ∼30% difference in their global crossover frequencies. Much of this crossover rate divergence is explained by six autosomal loci and a large-effect locus on the X chromosome. Intriguingly, the allelic effects at this X-linked locus are transgressive, with the allele conferring increased crossover rate being transmitted by the low crossover rate M. m. castaneus parent. Despite the pronounced divergence between males, females from these subspecies exhibit similar crossover rates, raising the question of how recombination is genetically controlled in this sex. Here, I analyze publicly available genotype data from early generations of the Collaborative Cross, an eight-way panel of recombinant inbred strains, to estimate crossover frequencies in female mice with sex-chromosome genotypes of diverse subspecific origins. Consistent with the transgressive influence of the X chromosome in males, I show that females inheriting an M. m. castaneus X possess higher average crossover rates than females lacking the M. m. castaneus X chromosome. The differential inheritance of the X chromosome in males and females provides a simple genetic explanation for sex-limited evolution of this trait. Further, the presence of X-linked and autosomal crossover rate modifiers with antagonistic effects hints at an underlying genetic conflict fueled by selection for distinct crossover rate optima in males and females.

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Section: Discussionsupporting

confidence: 60%

X-Chromosome Control of Genome-Scale Recombination Rates in House Mice

Dumont

2017

Genetics

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“…Whole genome sequencing of key laboratory mouse strains has been ongoing over the last several years (5,41). Following a transition of the Mouse Genomes Project from a resequencing to de novo assembly strategy for a core set of 16 inbred mouse strains and subspecies, these mouse assemblies now fit Ensembl's data model and were introduced in Ensembl release 86 (October 2016) (Figure 2).…”

Section: Comparative Genomics and Non-human Speciesmentioning

confidence: 99%

“…These efforts include the 1000 Genomes Project (1), ENCODE (2), the Gene-Tissue Expression (GTEx) project (3), the Exome Aggregation Consortium (ExAC) (4), the Mouse Genomes Project (5) and the various component projects of the International Human Epigenome Consortium (IHEC). The data and results from these projects have created a strong foundation on which genomics research can build.…”

Section: Introductionmentioning

confidence: 99%

Ensembl 2017

et al. 2016

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Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes. We import, analyse, curate and integrate a diverse collection of large-scale reference data to create a more comprehensive view of genome biology than would be possible from any individual dataset. Our extensive data resources include evidence-based gene and regulatory region annotation, genome variation and gene trees. An accompanying suite of tools, infrastructure and programmatic access methods ensure uniform data analysis and distribution for all supported species. Together, these provide a comprehensive solution for large-scale and targeted genomics applications alike. Among many other developments over the past year, we have improved our resources for gene regulation and comparative genomics, and added CRISPR/Cas9 target sites. We released new browser functionality and tools, including improved filtering and prioritization of genome variation, Manhattan plot visualization for linkage disequilibrium and eQTL data, and an ontology search for phenotypes, traits and disease. We have also enhanced data discovery and access with a track hub registry and a selection of new REST end points. All Ensembl data are freely released to the scientific community and our source code is available via the open source Apache 2.0 license.

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“…Furthermore, if users wish to ‘browse’ additional genomes then transcript models can be ‘projected’ from the main assembly. Projection is part of the annotation strategy of the Mouse Genomes Project (MGP) — who have released 36 genome sequences of laboratory mice and wild-derived strains — in combination with ab initio modelling 32 .…”

Section: What Is Gene Annotation?mentioning

confidence: 99%

The state of play in higher eukaryote gene annotation

Mudge

Harrow

2016

Nat Rev Genet

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A genome sequence is worthless if it cannot be deciphered, therefore efforts to describe — or ‘annotate’ — genes began as soon as DNA sequences became available. Whereas early work focused on individual protein-coding genes, the modern genomic ocean is a complex maelstrom of alternative splicing, non-coding transcription and pseudogenes. Scientists — from clinicians to evolutionary biologists — need to navigate these waters, and this has led to the design of high-throughput, computationally driven annotation projects. The catalogues produced are key resources for genome exploration, especially as they become integrated with expression, epigenomic and variation datasets. Their creation, however, remains challenging.

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The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes

Cited by 79 publications

References 43 publications

X-Chromosome Control of Genome-Scale Recombination Rates in House Mice

X-Chromosome Control of Genome-Scale Recombination Rates in House Mice

Ensembl 2017

The state of play in higher eukaryote gene annotation

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