Abstract
BackgroundThe number of species with completed genomes, including those with evidence for recent whole genome duplication events has exploded. The recently sequenced Atlantic salmon genome has been through two rounds of whole genome duplication since the divergence of teleost fish from the lineage that led to amniotes. This quadrupoling of the number of potential genes has led to complex patterns of retention and loss among gene families.ResultsMethods have been developed to characterize the interplay of duplicate gene retention processes across both whole genome duplication events and additional smaller scale duplication events. Further, gene expression divergence data has become available as well for Atlantic salmon and the closely related, pre-whole genome duplication pike and methods to describe expression divergence are also presented. These methods for the characterization of duplicate gene retention and gene expression divergence that have been applied to salmon are described.ConclusionsWith the growth in available genomic and functional data, the opportunities to extract functional inference from large scale duplicates using comparative methods have expanded dramatically. Recently developed methods that further this inference for duplicated genes have been described.Electronic supplementary materialThe online version of this article (doi:10.1186/s12575-016-0041-2) contains supplementary material, which is available to authorized users.
Highlights
Building gene families to study whole genome duplication (WGD) events Comparative genomics can be used to assess the interplay of gene retention and loss in WGDs by independently examining the fate of each gene duplicate within the genome
The findings from the analysis of the Atlantic salmon genome were surprising [3] and it is with new datasets and new methods for analysis with increasingly realistic assumptions that new findings will continue to emerge
Additional file 1: Pseudocode that summarizes the analysis presented here is available as an additional file for download from https://liberles. cst.temple.edu/public/BPO/Hermansen_et_al_2016_additional_file_1.pdf
Summary
Methods have been developed to characterize the interplay of duplicate gene retention processes across both whole genome duplication events and additional smaller scale duplication events. Gene expression divergence data has become available as well for Atlantic salmon and the closely related, pre-whole genome duplication pike and methods to describe expression divergence are presented. These methods for the characterization of duplicate gene retention and gene expression divergence that have been applied to salmon are described
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