@article {630,
	title = {A new genome assembly of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha},
	volume = {24},
	year = {2023},
	month = {Mar-20-2023},
	abstract = {<p><jats title="">Abstract</jats><jats sec=""> <jats title="">Background</jats> <jats p="">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 <jats italic="">Campylomormyrus</jats> is mostly endemic to the Congo Basin. <jats italic="">Campylomormyrus</jats> 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 assembly and to use this to examine genome evolution in relation to other teleosts. This will facilitate further understanding of the evolution of the osteoglossomorpha fish in general and of electric fish in particular.</jats> </jats><jats sec=""> <jats title="">Results</jats> <jats p="">A high-quality weakly electric fish (<jats italic="">C. compressirostris</jats>) genome was produced from a single individual with a genome size of 862\&nbsp;Mb, consisting of 1,497 contigs with an N50 of 1,399\&nbsp;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 <jats italic="">Paramormyrops kingsleyae</jats> and <jats italic="">Scleropages formosus</jats>. A Computational Analysis of gene Family Evolution (CAFE5) 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 (<jats italic="">Cyprinus carpio</jats> and <jats italic="">Oncorhynchus mykiss</jats>)<jats italic="">.</jats> 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 <jats italic="">Kv1</jats> genes. We identified a tandem duplication in the <jats italic="">KCNA7a</jats> gene in the genome of <jats italic="">C. compressirostris</jats>.</jats> </jats><jats sec=""> <jats title="">Conclusions</jats> <jats p="">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 appear to exhibit rapid gene family evolution, with more gene family expansions than contractions. The curated <jats italic="">Kv1</jats> gene family showed seven gene clusters, which is more than in other analyzed fish genomes outside Osteoglossomorpha. The <jats italic="">KCNA7a</jats>, encoding for a potassium channel central for EOD production and modulation, is tandemly duplicated which may related to the diverse EOD observed among <jats italic="">Campylomormyrus</jats> species.</jats> </jats></p>
},
	issn = {1471-2164},
	doi = {10.1186/s12864-023-09196-6},
	url = {http://dx.doi.org/10.1186/s12864-023-09196-6},
	author = {Cheng, Feng and Dennis, Alice B. and Osuoha, Josephine Ijeoma and Canitz, Julia and Kirschbaum, Frank and Ralph Tiedemann}
}
@article {626,
	title = {Transcriptome-wide single nucleotide polymorphisms related to electric organ discharge differentiation among African weakly electric fish species.},
	journal = {PLoS One},
	volume = {15},
	year = {2020},
	month = {2020},
	pages = {e0240812},
	abstract = {<p>African weakly electric fish of the mormyrid genus Campylomormyrus generate pulse-type electric organ discharges (EODs) for orientation and communication. Their pulse durations are species-specific and elongated EODs are a derived trait. So far, differential gene expression among tissue-specific transcriptomes across species with different pulses and point mutations in single ion channel genes indicate a relation of pulse duration and electrocyte geometry/excitability. However, a comprehensive assessment of expressed Single Nucleotide Polymorphisms (SNPs) throughout the entire transcriptome of African weakly electric fish, with the potential to identify further genes influencing EOD duration, is still lacking. This is of particular value, as discharge duration is likely based on multiple cellular mechanisms and various genes. Here we provide the first transcriptome-wide SNP analysis of African weakly electric fish species (genus Campylomormyrus) differing by EOD duration to identify candidate genes and cellular mechanisms potentially involved in the determination of an elongated discharge of C. tshokwe. Non-synonymous substitutions specific to C. tshokwe were found in 27 candidate genes with inferred positive selection among Campylomormyrus species. These candidate genes had mainly functions linked to transcriptional regulation, cell proliferation and cell differentiation. Further, by comparing gene annotations between C. compressirostris (ancestral short EOD) and C. tshokwe (derived elongated EOD), we identified 27 GO terms and 2 KEGG pathway categories for which C. tshokwe significantly more frequently exhibited a species-specific expressed substitution than C. compressirostris. The results indicate that transcriptional regulation as well cell proliferation and differentiation take part in the determination of elongated pulse durations in C. tshokwe. Those cellular processes are pivotal for tissue morphogenesis and might determine the shape of electric organs supporting the observed correlation between electrocyte geometry/tissue structure and discharge duration. The inferred expressed SNPs and their functional implications are a valuable resource for future investigations on EOD durations.</p>
},
	keywords = {Animals, electric fish, electric organ, Electricity, Gene Expression, Gene Expression Profiling, Gene Expression Regulation, Phenotype, Polymorphism, Single Nucleotide, Species Specificity, transcriptome},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0240812},
	author = {Canitz, Julia and Kirschbaum, Frank and Ralph Tiedemann}
}
