Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database

Abstract

With more than 30,000 species, ray-finned fish represent approximately half of vertebrates. The evolution of ray-finned fish was impacted by several whole genome duplication (WGD) events including a teleost-specific WGD event (TGD) that occurred at the root of the teleost lineage about 350 million years ago (Mya) and more recent WGD events in salmonids, carps, suckers and others. In plants and animals, WGD events are associated with adaptive radiations and evolutionary innovations. WGD-spurred innovation may be especially relevant in the case of teleost fish, which colonized a wide diversity of habitats on earth, including many extreme environments. Fish biodiversity, the use of fish models for human medicine and ecological studies, and the importance of fish in human nutrition, fuel an important need for the characterization of gene expression repertoires and corresponding evolutionary histories of ray-finned fish genes. To this aim, we performed transcriptome analyses and developed the PhyloFish database to provide (i) de novo assembled gene repertoires in 23 different ray-finned fish species including two holosteans (i.e. a group that diverged from teleosts before TGD) and 21 teleosts (including six salmonids), and (ii) gene expression levels in ten different tissues and organs (and embryos for many) in the same species. This resource was generated using a common deep RNA sequencing protocol to obtain the most exhaustive gene repertoire possible in each species that allows between-species comparisons to study the evolution of gene expression in different lineages. The PhyloFish database described here can be accessed and searched using RNAbrowse, a simple and efficient solution to give access to RNA-seq de novo assembled transcripts.

De novo assembly and characterization of the Hucho taimen transcriptome

“…The transcript and protein sequences of brown trout, brook trout, and grayling were downloaded from the PhyloFish database (Pasquier et al., 2016). The eggNOG database (Huerta‐Cepas et al., 2016) was used to define the gene family, and eggNOG‐mapper was used to search the fiNOG dataset for orthologous groups (Huerta‐Cepas et al., 2017).…”

Evolutionary history of glucose-6-phosphatase encoding genes in vertebrate lineages: towards a better understanding of the functions of multiple duplicates

“…Since comparative studies of gene expression are critical for establishing links between divergent gene expression and divergence of a particular phenotype, we thus proposed to examine the evolution of the spatial g6pc expression pattern in vertebrates using the powerful PhyloFish database [16]. Indeed, this database provides a transcriptomic repertoire of 10 tissues and organs in 23 different ray-finned fish species including two holosteans (i.e.…”

Pattern of Nitrergic Neuronal System Organization in the Brain of Two Holostean Fishes (Actinopterygii: Ginglymodi)

“…1a). This lineage diverged from the lineage leading to teleosts before the teleost-specific round of whole genome duplication occurred more than 320-350 million years ago [Hoegg et al, 2004;Kikugawa et al, 2004;Amores et al, 2011;Near et al, 2012;Pasquier et al, 2016]. Thus, holosteans and teleosts are currently grouped in the "Neopterygii" (neopterygians).…”