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.

The transcriptional correlates of divergent electric organ discharges inParamormyropselectric fish

“…A second notable pattern in our results is the unusual degree to which mormyrid electrocytes retain expression of some sarcomeric genes, which has been noted in several studies [58,85,92,95,96]. The role these proteins serves in electrocytes is presently unknown; however, results indicate that they are highly differentially expressed between Parmormyrops with different EOD waveforms.…”

“…We used Trimmomatic v.0.32 [60] to remove library adaptors, low quality reads, and filter small reads; following the suggested settings of MacManes [61]: 2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25. After trimming, reads from each specimen were aligned to the predicted transcripts of the NCBI-annotated (Release 100) P. kingsleyae (N-type) genome [58] using bowtie 2 v2.3.4.1 [62]. Expression quantification was estimated at the gene level using RSEM v1.3.0 [63], followed by exploration of the data with a gene expression correlation matrix based on Euclidean distances and Pearson’s correlation coefficient (for genes with read counts >10, Trinity’s default parameters).…”

A review of the systematic biology of fossil and living bony-tongue fishes, Osteoglossomorpha (Actinopterygii: Teleostei)

“…With the development of high throughput sequencing technology and the near-future possibility to sequence whole genome at reasonable cost (and the concomitant progresses in computer-based comparative methods), we are entering in a new area in fish systematics which will complete traditional approaches (morphological examination and low efficiency sequencing technology) and refine our understanding of the phylogeny (and evolution) of Osteoglossomorpha (Braasch et al, 2015). Three draft genomes of Osteoglossomorpha are already available, Scleropages formosus (Austin et al, 2015;Bian et al, 2016), Paramormyrops kingsleyae (Gallant et al, 2017) and Arapaima gigas (Vialle et al, 2018) and there are plans to sequence additional ones, such as that of Hiodon and Pantodon (Bernardi et al, 2012). Although as promising as each (including this one) new technological step can be with the comparison of extremely large genetic datasets, it is not expected this will be the "panacea" as already evidenced by the incongruent results presented by several genomic studies on the phylogenetic position of the Osteoglossomorpha (Austin et al, 2015;Faircloth et al, 2013;Chen et al, 2015;Bian et al, 2016;Hughes et al, 2018;Vialle et al, 2018).…”

The Polycomb Orthologues in Teleost Fishes and Their Expression in the Zebrafish Model

“…Thus, consistent with the teleost cladogram, the two Osteoglossomorpha cbx6 ohnologues originate from the TGD but are less divergent to each other than cbx6a to cbx6b. Among the Osteoglossomorpha, the elephant fish (Paramormyrops kingsleyae) and the Asian bonytongue (Scleropages formosus) are so far the only two species that have fully sequenced genomes [59,60]. Like Ostariphysi and Clupeomorpha, the cbx6 gene exists as pairs of ohnologues in the elephant fish and in the Asian bonytongue genomes (Figure 2, Supplementary Table S1).…”