Don't throw the baby out with the bathwater: identifying and mapping paralogs in salmonids

Molecular Ecology Resources
France Dufresne

Abstract

Many eukaryotic genomes contain a large fraction of gene duplicates (or paralogs) as a result of ancient or recent whole-genome duplications (Ohno ; Jaillon et al. ; Kellis et al. ). Identifying paralogs with NGS data is a pervasive problem in both ancient polyploids and neopolyploids. Likewise, paralogs are often treated as a nuisance that has to be detected and removed (Everett et al. ). In this issue of Molecular Ecology Resources, Waples et al. () show that exclusion might not be necessary and how we may miss out on important genomic information in doing so. They present a novel statistical approach to detect paralogs based on the segregation of RAD loci in haploid offspring and test their method by constructing linkage maps with and without these duplicated loci in chum salmon, Oncorhynchus keta (Fig. ). Their linkage map including the resolved paralogs shows that these are mostly located in the distal regions of several linkage groups. Particularly intriguing is their finding that these homoeologous regions appear impoverished in transposable elements (TE). Given the role that TE play in genome remodelling, it is noteworthy that these elements are of low abundance in regions showing residual tetrasomic inheritance. This r...Continue Reading

References

Oct 15, 2008·PloS One·Nathan A BairdEric A Johnson
Jan 15, 2010·The New Phytologist·Christian ParisodChristian Brochmann
May 15, 2012·Cell·Kathleen H Burns, Jef D Boeke
Oct 4, 2012·BMC Genomics·Meredith V EverettJames E Seeb
Aug 22, 2014·Molecular Ecology Resources·V VersteirtW Van Bortel
Aug 27, 2014·Molecular Ecology Resources·Simon Y W HoDavid Duchêne

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