A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication

De-Kayne, Rishi; Feulner, Philine (2018). A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication. G3 Genes Genomes Genetics, 8(12), pp. 3745-3755. Genetics Society of America 10.1534/g3.118.200552

Preview	Text De-Kayne & Feulner 2018_G3_A European whitefish linkage map and its implications for understanding genome-wide synteny between salmonids following whole genome duplication.pdf - Accepted Version Available under License Creative Commons: Attribution (CC-BY). Download (2MB) | Preview
Preview	Text De-Kayne & Feulner 2018_G3_A European whitefish linkage map and its implications for understanding genome-wide synteny between salmonids following whole genome duplication_published ve.pdf - Published Version Available under License Creative Commons: Attribution (CC-BY). Download (1MB) | Preview

Genomic datasets continue to increase in number due to the ease of production for a wider selection of species including non-model organisms. For many of these species, especially those with large or polyploid genomes, highly contiguous and well-annotated genomes are still rare due to the complexity and cost involved in their assembly. As a result, a common starting point for genomic work in non-model species is the production of a linkage map. Dense linkage maps facilitate the analysis of genomic data in a variety of ways, from broad scale observations regarding genome structure e.g. chromosome number and type or sex-related structural differences, to fine scale patterns e.g. recombination rate variation and co-localization of differentiated regions. Here we present both sex-averaged and sex-specific linkage maps for Coregonus sp. “Albock”, a member of the European whitefish lineage (C. lavaretus spp. complex), containing 5395 single nucleotide polymorphism (SNP) loci across 40 linkage groups to facilitate future investigation into the genomic basis of whitefish adaptation and speciation. The map was produced using restriction-site associated digestion (RAD) sequencing data from two wild-caught parents and 156 F1 offspring. We discuss the differences between our sex
averaged and sex-specific maps and identify genome-wide synteny between C. sp. “Albock” and Atlantic Salmon (Salmo salar), which have diverged following the salmonid-specific whole genome duplication. Our analysis confirms that many patterns of synteny observed between Atlantic Salmon and Oncorhynchus and Salvelinus species are also shared by members of the Coregoninae subfamily. We also show that regions known for their species-specific rediploidization history can pose challenges for synteny identification since these regions have diverged independently in each salmonid species following the salmonid-specific whole genome duplication. The European whitefish map provided here will enable future studies to understand the distribution of loci of interest, 47 e.g. FST outliers, along the whitefish genome as well as assisting with the de novo assembly of a whitefish reference genome.

Interest & Impact

Downloads

323 since deposited on 02 Nov 2018
18 in the past 12 months

Citations

5 Citations in Web of Science ®
6 Citations in Scopus

Search

in Google Scholar™

Services

Actions (login required)

Edit item

Actions (login required)

Edit item