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Data from: Characterisation of reproductive gene diversity in the endangered Tasmanian devil

Citation

Brandies, Parice et al. (2021), Data from: Characterisation of reproductive gene diversity in the endangered Tasmanian devil, Dryad, Dataset, https://doi.org/10.5061/dryad.t1g1jwt10

Abstract

Inter-individual variation at genes known to play a role in reproduction may impact reproductive fitness. The Tasmanian devil is an endangered Australian marsupial with low genetic diversity. Recent work has shown concerning declines in productivity in both wild and captive populations over time. Understanding whether functional diversity exists at reproductive genes in the Tasmanian devil is a key first step in identifying genes that may influence productivity. We characterised single nucleotide polymorphisms (SNPs) at 214 genes involved in reproduction in 37 Tasmanian devils. Twenty genes contained non-synonymous substitutions, with genes involved in embryogenesis, fertilisation and hormonal regulation of reproduction displaying greater numbers of nonsynonymous SNPs than synonymous SNPs. Two genes, ADAMTS9 and NANOG, showed putative signatures of balancing selection indicating that natural selection is maintaining diversity at these genes despite the species exhibiting low overall levels of genetic diversity. We will use this information in future to examine the interplay between reproductive gene variation and reproductive fitness in Tasmanian devil populations.

Methods

Two existing datasets comprising 37 resequenced genomes (SRA Accessions: SRX6096677- SRX6096696, ERS682204-ERS682210, ERS1202857-ERS1202861) were used to explore reproductive gene diversity in the Tasmanian devil. Reads were aligned to the Tasmanian devil reference genome assembly version 7.0 (GenBank Accession: GCA_000189315.1) using Burrows-Wheeler aligner v 0.7.15. SNPs were called within target reproductive genes of interest across the 37 individuals using SAMtools v 1.6 with minimum base and mapping quality of 30 and a coefficient for downgrading mapping quality for reads containing excessive mismatches of 50. Individual sample VCF files were then subset from the multisample VCF file and filtered to exclude variants below a filtered depth threshold using BCFtools v1.3.1. The remaining variants were then merged into a multisample VCF file using VCFtools v0.1.14.

Usage Notes

Please refer to the published paper for information regarding the target genes of interest, sample information, downstream analyses and references for associated datasets and software. The readme file contains a summary of information relating to this dataset 

Funding

Australian Research Council, Award: LP140100508

Save the Tasmanian Devil Program

Zoo and Aquarium Association Australasia

San Diego Zoo Global

Australian Research Council, Award: DP170101253

Save the Tasmanian Devil Program

Zoo and Aquarium Association Australasia

San Diego Zoo Global