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Quantification of loss of haplotype diversity in the highly inbred Scandinavian wolf population

ABSTRACT: Quantification of loss of haplotype diversity in the highly inbred Scandinavian wolf population

PROVIDER: PRJEB44869 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR5903374_1.fastq.gz	Fastqsanger.gz
	ERR5903374_2.fastq.gz	Fastqsanger.gz
	ERR5906614_1.fastq.gz	Fastqsanger.gz
	ERR5906614_2.fastq.gz	Fastqsanger.gz
	ERR5906615_1.fastq.gz	Fastqsanger.gz

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Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population.

Project description:Genetic drift can dramatically change allele frequencies in small populations and lead to reduced levels of genetic diversity, including loss of segregating variants. However, there is a shortage of quantitative studies of how genetic diversity changes over time in natural populations, especially on genome-wide scales. Here, we analyzed whole-genome sequences from 76 wolves of a highly inbred Scandinavian population, founded by only one female and two males, sampled over a period of 30 yr. We obtained chromosome-level haplotypes of all three founders and found that 10%-24% of their diploid genomes had become lost after about 20 yr of inbreeding (which approximately corresponds to five generations). Lost haplotypes spanned large genomic regions, as expected from the amount of recombination during this limited time period. Altogether, 160,000 SNP alleles became lost from the population, which may include adaptive variants as well as wild-type alleles masking recessively deleterious alleles. Although not sampled, we could indirectly infer that the two male founders had megabase-sized runs of homozygosity and that all three founders showed significant haplotype sharing, meaning that there were on average only 4.2 unique haplotypes in the six copies of each autosome that the founders brought into the population. This violates the assumption of unrelated founder haplotypes often made in conservation and management of endangered species. Our study provides a novel view of how whole-genome resequencing of temporally stratified samples can be used to visualize and directly quantify the consequences of genetic drift in a small inbred population.

| S-EPMC8896455 | biostudies-literature

Analysis of structural diversity in wolf-like canids reveals post-domestication variants

Project description:This study uses a custom made Nimblegen aCGH chip that targeted all segmental duplications in the canine genome to identify associated CNVs. A total of 23 hybridizations were performed in a panel of diverse dogs and a single wolf. This study focuses on the use a custom made Nimblegen aCGH chip to genotype 1,611 dog CNVs in 23 wolf-like canids (4 purebred dogs, one dingo, 15 gray wolves, one red wolf, one coyote and one golden jackal) to identify CNVs that may have arisen after domestication

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The brain transcriptome of the wolf spider, Schizocosa ocreata

Project description:The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a non-model organism of the pyhlum Euarthropoda, by generating transcriptomes and analyzing gene expression. To examine differences in sex-differential gene expression, short read transcript sequencing and de novo transcriptome assembly were performed. Messenger RNA (mRNA) was isolated from dissected brain tissue of male and female subadult and mature wolf spiders (Schizocosa ocreata). The data consist of short read sequences for the two different life stages in each sex. Computational analyses on these data include de novo transcriptome assembly, using Trinity and CAP3 assembly suites, and differential expression analysis using the edgeR package. Sample-specific and combined transcriptomes, gene annotations, and differential expression results are described in this data note and are available from associated database submissions.

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2014-06-05 | GSE58195 | GEO

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Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration

Project description: Not available

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Highly parallel quantification and compartment localization of transcription factors and nuclear proteins

Project description:Transcription factors and other chromatin-associated proteins are difficult to quantify comprehensively. Here we combine facile nuclear sub-fractionation with data-independent acquisition mass spectrometry to achieve rapid, sensitive, and highly-parallel quantification of the nuclear proteome in human cells. We apply this approach to quantify the response to acute degradation of BET bromodomains, revealing unexpected chromatin regulatory dynamics. The method is simple and enables systems-level study of previously inaccessible chromatin and genome regulators.

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Highly sensitive amplicon-based transcript quantification by semi-conductor sequencing

2014-07-15 | GSE58737 | GEO

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