DOI: 10.5061/dryad.c59zw3rcj
title: A new genome of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha

description: Background Teleost fishes comprise more than half of the vertebrate
 species. Within teleosts, most phylogenies consider the split between
 Osteoglossomorpha and Euteleosteomorpha/Otomorpha as basal, preceded only
 by the derivation of the most primitive group of teleosts, the
 Elopomorpha. While Osteoglossomorpha are generally species-poor, the taxon
 contains the African weakly electric fish (Mormyroidei), which have
 radiated into numerous species. Within the mormyrids, the genus
 Campylomormyrus is mostly endemic to the Congo
 Basin. Campylomormyrus serves as a model to understand mechanisms
 of adaptive radiation and ecological speciation, especially with regard to
 its highly diverse species-specific electric organ discharges (EOD).
 Currently, there are few well-annotated genomes available for electric
 fish in general and mormyrids in particular. Our study aims at producing a
 high-quality genome and to use this to examine genome evolution in
 relation to other teleosts. This will facilitate further understanding of
 the evolution of the osteoglossomorph fish in general and of electric fish
 in particular. Results A high-quality weakly electric fish (C.
 compressirostris) genome was produced from a single individual with a
 genome size of 862Mb, consisting of 1,497 contigs with an N50 of 1,399 kb
 and a GC-content of 43.69%. Gene predictions identified 34,492
 protein-coding genes, which is a higher number than in the two other
 available Osteoglossomorpha genomes of Paramormyrops
 kingsleyae and Scleropages formosus. A CAFE5 analysis of
 gene family evolution comparing 33 teleost fish genomes suggests an
 overall faster gene family turnover rate in Osteoglossomorpha than in
 Otomorpha and Euteleosteomorpha. Moreover, the ratios of
 expanded/contracted gene family numbers in Osteoglossomorpha are
 significantly higher than in the other two taxa, except for species that
 had undergone an additional genome duplication (Cyprinus
 carpio and Oncorhynchus mykiss). As potassium channel
 proteins are hypothesized to play a key role in EOD diversity among
 species, we put a special focus on them, and manually curated 16 Kv1
 genes. We identified a tandem duplication in the KCNA7a gene in the genome
 of C. compressirostris. Conclusions We present the fourth genome
 of an electric fish and the third well-annotated genome for
 Osteoglossomorpha, enabling us to compare gene family evolution among
 major teleost lineages. Osteoglossomorpha appears to exhibit rapid gene
 family evolution, with more gene family expansions than contractions. The
 curated Kv1 gene family showed seven gene clusters, which is more than in
 other analyzed fish genomes outside Osteoglossomorpha. The KCNA7a,
 encoding for a potassium channel central for EOD production and
 modulation, is tandemly duplicated which may related to the diverse EOD
 observed among Campylomormyrus species.
description: <strong>Samples</strong> Genomic
 DNA was isolated from available frozen fin clips, which had been
 previously taken in the course of another study from an adult <em>C.
 compressirostris</em> artificially bred and raised at University
 Potsdam, Germany. The CTAB protocol was used to obtain high molecular
 weight genomic DNA. The concentration and quality were further verified
 with Nanodrop spectrophotometer and Agilent TapeStation before
 sequencing. <strong>Genome sequencing
 </strong> For Pacbio sequencing, a 15-kb SMRT
 cell DNA library was prepared and sequenced on a PacBio Sequel platform
 with one SMRT cell by a commercial company (Novogene). This produced 294
 Gb long reads, which were used to generate the HiFi long reads using
 circular consensus sequencing (CCS) mode (Pacific Biosciences,
 USA). <strong>De novo genome
 assembly</strong> The genome size and
 heterozygosity were estimated by GenomeScope 2.0 using a k-mer value of
 32. The genome was further assembled by hifiasm with the HiFi reads as
 input. The separated primary haplotigs were visualized in Bandage. This
 showed that some of the contigs contain two forks, which are likely
 homozygous breakpoints. Therefore, the program purge_dups was additionally
 applied for haplotig purging in the primary haplotigs. The mitochondrial
 DNA was separately assembled with the MitoHiFi.