The Genome and Adult Somatic Transcriptome of the Mormyrid Electric Fish Paramormyrops kingsleyae

Abstract

Several studies have begun to elucidate the genetic and developmental processes underlying major vertebrate traits. Few of these traits have evolved repeatedly in vertebrates, preventing the analysis of molecular mechanisms underlying these traits comparatively. Electric organs have evolved multiple times among vertebrates, presenting a unique opportunity to understand the degree of constraint and repeatability of the evolutionary processes underlying novel vertebrate traits. As there is now a completed genome sequence representing South American electric eels, we were motivated to obtain genomic sequence from a linage that independently evolved electric organs to facilitate future comparative analyses of the evolution and development of electric organs. We report here the sequencing and de novo assembly of the genome of the mormyrid Paramormyrops kingsleyae using short-read sequencing. In addition, we have completed a somatic transcriptome from 11 tissues to construct a gene expression atlas of predicted genes from this assembly, enabling us to identify candidate housekeeping genes as well as genes differentially expressed in the major somatic tissues of the mormyrid electric fish. We anticipate that this resource will greatly facilitate comparative studies on the evolution and development of electric organs and electroreceptors.

Keywords: Paramormyrops; electric fish; electric organs; mormyridae.

Fig. 1—

Atlas of gene expression based on 11 tissues from 3 P. kingsleyae specimens. (A) Heatmap matrix of differentially expressed genes between pairs of tissues (numbers indicated in each box). Warmer colors indicate larger numbers of differentially expressed genes between tissue pairs. (B) List of number of genes considered “expressed” (TPM reads > 1) in each tissue, and expressed as a percent of total genes expressed in at least one tissue. (C) Photograph of Paramormyrops kingsleyae overlayed with a colorized diagram indicating sources of tissues for transcriptome sequencing. HS,  head skin; FS, flank skin.