Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Interspecific Introgressive Origin of Genomic Diversity in the House Mouse

ABSTRACT: We report on a genome-wide scan for introgression in the house mouse (Mus musculus domesticus) involving the Algerian mouse (Mus spretus), using 20 samples from the ranges of sympatry and allopatry. Our analysis reveals significant variability in introgression signatures along the genomes, as well as across the samples. We find that fewer than half of the chromosomes in each genome harbor all detectable introgression. Further, a surprising result is that European mice carry more M. spretus alleles than the sympatric African ones. Using the length distribution and sharing patterns of introgressed genomic tracts across the samples, we propose three hypotheses. First, at least three distinct hybridization events involving M. spretus have occurred, one of which is ancient, and the other two are recent. Second, several of the inferred introgressed tracts contain genes that are likely to confer adaptive advantage. Third, introgressed tracts might contain driver genes that determine the evolutionary fate of those tracts. Further, our analysis revealed introgressed genes of functional importance, including the Vkorc1 gene, which is implicated in rodenticide resistance, and olfactory receptor genes. Our findings highlight the extent and role of introgression in nature, and call for careful analysis and interpretation of house mouse data in evolutionary and genetic studies.

ORGANISM(S): Mus musculus domesticus Mus musculus

PROVIDER: GSE62906 | GEO | 2014/11/01

SECONDARY ACCESSION(S): PRJNA266014

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Interspecific Introgressive Origin of Genomic Diversity in the House Mouse

Project description:We report on a genome-wide scan for introgression in the house mouse (Mus musculus domesticus) involving the Algerian mouse (Mus spretus), using 20 samples from the ranges of sympatry and allopatry. Our analysis reveals significant variability in introgression signatures along the genomes, as well as across the samples. We find that fewer than half of the chromosomes in each genome harbor all detectable introgression. Further, a surprising result is that European mice carry more M. spretus alleles than the sympatric African ones. Using the length distribution and sharing patterns of introgressed genomic tracts across the samples, we propose three hypotheses. First, at least three distinct hybridization events involving M. spretus have occurred, one of which is ancient, and the other two are recent. Second, several of the inferred introgressed tracts contain genes that are likely to confer adaptive advantage. Third, introgressed tracts might contain driver genes that determine the evolutionary fate of those tracts. Further, our analysis revealed introgressed genes of functional importance, including the Vkorc1 gene, which is implicated in rodenticide resistance, and olfactory receptor genes. Our findings highlight the extent and role of introgression in nature, and call for careful analysis and interpretation of house mouse data in evolutionary and genetic studies. Six wild M. m. domesticus samples were genotyped using the Affymetrix Mouse Diversity Genotyping Array.

2014-11-01 | E-GEOD-62906 | biostudies-arrayexpress

Genome-wide analysis of alternative splicing evolution among Mus subspecies

Project description:We studied the evolution of alternative splicing in the early stages of species divergence in the house mouse. We sequenced the testis transcriptomes of three Mus musculus subspecies and Mus spretus using Illumina technology. On the basis of a genome-wide analysis of read coverage differences among subspecies, we identified several hundred candidate alternatively spliced regions.

2010-02-28 | E-GEOD-18905 | biostudies-arrayexpress

Contrasting patterns of expression divergence in early and late stages of population divergence in mice

2006-12-13 | GSE2597 | GEO

RNA-seq data from liver tissues of Mus spretus (SPRET/EiJ) and Mus caroli (Caroli/EiJ)

Project description:Illumina RNA-seq data of liver samples from Mus spretus (SPRET/EiJ) and Mus caroli (Caroli/EiJ)

2014-08-20 | E-MTAB-2483 | biostudies-arrayexpress

Comparison of the testicular transcriptome of chromosomes 2, X, Y and the mitochondrial genome between two mouse species

Project description:We used tiling arrays to compare the testicular expression of chromosomes 2, X, Y and the mitochondrial genome between Mus m. domesticus and Mus spretus. We found an excess of dysregulated non-coding RNAs on chromosome 2. This group consists of intronic antisense RNAs, intergenic RNAs and also premature forms of PIWI-interacting RNAs (piRNAs). The unique transcriptional regulation in spermatogenesis is a characteristic of chromosome X. It is subject to meiotic transcriptional silencing, which is accompanied by generating X-chromosomal retrogenes on autosomes. We found striking dysregulation of the G6pdx - G6pd2 parental-retrogene pair between the mouse species. The postmeiotic expression of G6pdx in Mus spretus points out the continuous evolution of X chromosome silencing and provides clue for regulatory changes, which accompanies the out-of-X gene flow. Comparison between 3 samples of Mus spretus and 3 samples of Mus m. domesticus (C57BL/6J, B6). The supplementary file 'GSE19633_Spr_v_B6.bed' contains the chromosomal localizations of the probes together with logFC and adjusted P values.

2011-02-16 | E-GEOD-19633 | biostudies-arrayexpress

Uterus and placenta gene expression at 10.5 days of pregnancies in control (B6 mice) and R3 IRCS mice

Project description:R3 IRCS have a 6 Mb fragment of mouse chromosome 1 originating from Mus spretus; they display a increase rate of embryonic mortality

2012-02-01 | GSE32640 | GEO

Transcription profiling of mouse interspecific recombinant testis

Project description:Analysis of the genomic expression profiles in Interspecific recombinant Congenic Strains starting from a Mus msuculus x mus spretus cross.

2008-08-31 | E-TABM-444 | biostudies-arrayexpress

ChIP-Seq analysis of CCCTC-binding factor (CTCF) binding in rodents

Project description:We explored the microevolutionary trends of CTCF binding evolution by preforming ChIP-seq experiments in five closely related Mus strains, subspecies and species: Mus musculus domesticus, Mus musculus castaneus, Mus spretus, Mus caroli and Mus pahari. All experiments were performed in adult male liver samples in 3 biological replicates and with an input control set. Complementary RNA-seq data from this same study have been deposited in ArrayExpress under accession numebr E-MTAB-5768 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5768 ).

2018-03-06 | E-MTAB-5769 | biostudies-arrayexpress

Environmental pollution assessment using Mus spretus

Project description:We evaluated the suitability of high-throughput transcriptomics approach to monitor terrestrial ecosystems. Free-living Mus spretus from several polluted sites of Huelva (Andalusia, SW Spain) were compared with mice from DoM-CM-1ana Biological Reserve (M-bM-^@M-^\Santa OlallaM-bM-^@M-^] lagoon (SOL) used as negative control). As most popular bioindicators, M. spretus is poorly represented in gene databases, therefore limiting the use of genomics in ecotoxicological studies. To solve this problem, we used microarrays produced from mRNAs of M. musculus. Specifically we used the One-Color Gene Expression Platform commercialized by Agilent. Gene expression in Mus spretus liver was assessed in mice from 5 sites of the Spanish Southwest. Five independent experiments were performed. The arrays were hybridized with labelled cRNA samples made from pooled livers of 9 mice per sampling site. We made 4 technichal repetitions per sample.

2013-12-31 | E-GEOD-33663 | biostudies-arrayexpress

Contrasting patterns of expression divergence in early and late stages of population divergence in mice

Project description:We compared gene expression differences in the polytypic species complex Mus musculus (Mus musculus musculus, Mus musculus domesticus, Mus musculus castaneus and Mus musculus ssp) with that of Mus spretus via oligonucleotide microarrays representing more than 20,000 genes. Analysis of the results by two way ANOVA statistics suggests that the most genes with significant differences in expression levels among the subspecies are found in liver and kidney and the least in testis. This picture is different when one compares with Mus spretus, where the largest number of differences is found in testis. The design we employed is a reference design. All tissues were hybridized against a pool of that same tissue from 9 C57BL6 mice. All mice were roughly 12 weeks of age. To control for biological variation, we have used several individual males from each sub-species. RNA was isolated from three different organs, namely brain, liver/kidney and testis.

2010-06-30 | E-GEOD-2597 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data