<i>De novo</i> assembly and characterization of the skeletal muscle and electric organ transcriptomes of the African weakly electric fish <i>Campylomormyrus compressirostris</i> (Mormyridae, Teleostei)

Lamanna, Francesco; Kirschbaum, Frank; Tiedemann, Ralph

doi:10.1111/1755-0998.12260

Cited by 23 publications

(18 citation statements)

References 45 publications

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“…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.…”

Section: Discussionsupporting

confidence: 76%

The transcriptional correlates of divergent electric organ discharges inParamormyropselectric fish

Losilla

Gallant

2019

Preprint

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12Background: Understanding the genomic basis of phenotypic diversity can be greatly facilitated 13 by examining adaptive radiations with hypervariable traits. In this study, we focus on a rapidly 14 diverged species group of mormyrid electric fish in the genus Paramormyrops, which are 15 characterized by extensive phenotypic variation in electric organ discharges (EODs). The main 16 components of EOD diversity are waveform duration, complexity and polarity. Using an RNA-17 sequencing based approach, we sought to identify gene expression correlates for each of these 18 EOD waveform features by comparing 11 specimens of Paramormyrops that exhibit variation in 19 these features. 20Results: Patterns of gene expression among Paramormyrops are highly correlated, and 3,274 21 genes (16%) were differentially expressed. Using our most restrictive criteria, we detected 71-22 144 differentially expressed genes correlated with each EOD feature, with little overlap between 23 them. The predicted functions of several of these genes are related to extracellular matrix, cation 24 homeostasis, lipid metabolism, and cytoskeletal and sarcomeric proteins. These genes are of 25 significant interest given the known morphological differences between electric organs that 26 underlie differences in the EOD waveform features studied. 27Conclusions: In this study, we identified plausible candidate genes that may contribute to 28 phenotypic differences in EOD waveforms among a rapidly diverged group of mormyrid electric 29 fish. These genes may be important targets of selection in the evolution of species-specific 30 differences in mate-recognition signals.Understanding the genomic basis of phenotypic diversity is a major goal of evolutionary 33 biology [1]. Adaptive radiations and explosive diversification of species [2] are frequently 34 characterized by interspecific phenotypic differences in divergence of few, hypervariable 35 phenotypic traits [3][4][5][6]. Such systems offer exceptional advantages to study the genomic bases of 36 phenotypic diversity: they can provide replication under a controlled phylogenetic framework 37 [7], and couple ample phenotypic differentiation with relatively "clean" genomic signals between 38 recently diverged species [8]. Study of the genomic mechanisms underlying hypervariable 39 phenotypic traits has identified, in some cases relatively simple genetic architectures [9][10][11][12][13]. 40 More often, the genetic architecture underlying such traits can be complex and polygenic [14-41 17]. It has long been recognized that changes in gene expression can affect phenotypic 42 differences between species [18], and RNA-seq based approaches have greatly facilitated the 43 study of this relationship [19]. A growing number of studies have examined differences in gene 44 expression in phenotypic evolution (e.g., [19][20][21][22][23][24][25][26][27]). While these studies do not implicate 45 mutational causes, analysis of differential gene expression (DGE) can be a useful approach in 46 examining the ...

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Section: Discussionsupporting

confidence: 76%

The transcriptional correlates of divergent electric organ discharges inParamormyropselectric fish

Losilla

Gallant

2019

Preprint

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“…C. compressirostrus -We downloaded the raw reads for skeletal muscle and electric organ tissue referenced in (44) with NCBI BioProject accession # (PRJNA192446 ).…”

Section: Additional Data Sourcesmentioning

confidence: 99%

Electrostatic Tuning of a Potassium Channel in Electric Fish

Swapna

Ghezzi

Markham

et al. 2017

Preprint

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Abstract:Molecular and biophysical variation contributes to the evolution of adaptive phenotypes, particularly behavior, though it is often difficult to understand precisely how. The adaptively significant electric organ discharge behavior of weakly electric fish is the direct result of biophysical membrane properties set by ion channels. Here we describe a voltage-gated potassium channel gene in African mormyrid electric fishes, that is under positive selection and highly expressed in the electric organ. The channel produced by this gene shortens electric organ action potentials by activating quickly and at hyperpolarized membrane potentials. Surprisingly, the source of these unique properties is a derived patch of negatively charged amino acids in an extracellular loop near the voltage sensor. Further, we demonstrate that this portion of the channel functions differently in vertebrates than the generally accepted model based on the . CC-BY-NC-ND 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/206243 doi: bioRxiv preprint first posted online Oct. 19, 2017; 2 shaker channel, and suggest a role for this loop in the evolutionary tuning of voltage-dependent channels.

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“…; Lamanna et al . ). Despite the high annotation success for Calligrapha testis libraries, there are still a large proportion of putative transcripts left out based on functional annotation analyses.…”

Section: Discussionmentioning

confidence: 97%

“…Moreover, annotation success depends on the efficiency of the initial BLAST step, so that functional annotation based on results of the blastx algorithm, as used here, consistently outperforms the same based on the blastn algorithm (e.g. Vidotto et al 2013;Lamanna et al 2014). Despite the high annotation success for Calligrapha testis libraries, there are still a large proportion of putative transcripts left out based on functional annotation analyses.…”

Section: Rna-seq and Male-biased Gene Annotationmentioning

confidence: 91%

Testis‐specific RNA‐Seq of Calligrapha (Chrysomelidae) as a transcriptomic resource for male‐biased gene inquiry in Coleoptera

Vizán‐Rico

Gómez‐Zurita

2016

Molecular Ecology Resources

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We report the architecture of testis transcriptomes of four closely related species of Calligrapha (Chrysomelidae) beetles, which diverged during the last 3 million years. Five cDNA libraries were sequenced using Illumina HiSeq technology, retrieving 102 884-176 514 assembled contigs, of which ~33-45% of these longer than 499 nt were functionally annotated. Annotation and sequence similarity comparisons of these libraries revealed high homogeneity in gene composition and the presence of several functional candidates related to reproduction or reproductive processes (0.72-1.08% of annotated sequences). Stringent sequence similarity analyses of these transcriptomes against empirically demonstrated male-biased genes in Drosophila melanogaster and Tribolium castaneum allowed the identification of 77 homologues in Calligrapha, possible candidates of male-biased expression. Some of these genes - including CG9313, Tektin-A or tomboy40 - were confirmed as orthologs of these male-biased genes using phylogenetic inference and available model insect data, increasing our confidence that they represent functional homologues too. Our transcriptomes are a valuable transcriptomic resource for the analysis of male-biased genes in Calligrapha, which has the added interest of including several female-only species. But it simultaneously represents a landmark for similar studies in Coleoptera, broadening the taxonomic diversity currently represented by the model species T. castaneum, and incipient genomic data in other herbivorous lineages, including weevils, longhorn beetles and leaf beetles.

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De novo assembly and characterization of the skeletal muscle and electric organ transcriptomes of the African weakly electric fish Campylomormyrus compressirostris (Mormyridae, Teleostei)

Cited by 23 publications

References 45 publications

The transcriptional correlates of divergent electric organ discharges inParamormyropselectric fish

The transcriptional correlates of divergent electric organ discharges inParamormyropselectric fish

Electrostatic Tuning of a Potassium Channel in Electric Fish

Testis‐specific RNA‐Seq of Calligrapha (Chrysomelidae) as a transcriptomic resource for male‐biased gene inquiry in Coleoptera

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