Abstract
BackgroundTeleost fish play important roles in aquatic ecosystems and aquaculture. Threadfins (Perciformes: Polynemidae) show a range of interesting biology, and are of considerable importance for both wild fisheries and aquaculture. Additionally, the four-finger threadfin Eleutheronema tetradactylum is of conservation relevance since its populations are considered to be in rapid decline and it is classified as endangered. However, no genomic resources are currently available for the threadfin family Polynemidae.ResultsWe sequenced and assembled the first threadfin fish genome, the four-finger threadfin E. tetradactylum. We provide a genome assembly for E. tetradactylum with high contiguity (scaffold N50 = 56.3 kb) and high BUSCO completeness at 96.5%. The assembled genome size of E. tetradactylum is just 610.5 Mb, making it the second smallest perciform genome assembled to date. Just 9.07–10.91% of the genome sequence was found to consist of repetitive elements (standard RepeatMasker analysis vs custom analysis), making this the lowest repeat content identified to date for any perciform fish. A total of 37,683 protein-coding genes were annotated, and we include analyses of developmental transcription factors, including the Hox, ParaHox, and Sox families. MicroRNA genes were also annotated and compared with other chordate lineages, elucidating the gains and losses of chordate microRNAs.ConclusionsThe four-finger threadfin E. tetradactylum genome presented here represents the first available genome sequence for the ecologically, biologically, and commercially important clade of threadfin fish. Our findings provide a useful genomic resource for future research into the interesting biology and evolution of this valuable group of food fish.
Highlights
Teleost fish play important roles in aquatic ecosystems and aquaculture
The final assembly size was 610.5 Mb, which is close to the estimated genome size (~ 630 Mb, Supplementary Figure S1)
We found that 96.5% of BUSCO genes were detected (88.2% of which were complete, and 8.3% of which were fragmented) (Table 1, Supplementary Table S1)
Summary
Teleost fish play important roles in aquatic ecosystems and aquaculture. Threadfins (Perciformes: Polynemidae) show a range of interesting biology, and are of considerable importance for both wild fisheries and aquaculture. Teleostei is the most species-rich and diverse group of vertebrates, with ~ 30,000 species, accounting for around half of all extant vertebrate species [1] In addition to their great diversity, teleosts play important ecological roles in aquatic ecosystems, and are of great relevance as a source of protein in both wild fisheries and aquaculture. The teleost order Perciformes comprises more than 10,000 species and represents the single largest group of vertebrates, with representatives in almost every aquatic ecosystem on earth [2]. Many perciform fish are highly important commercially, and the group is fast becoming an important model system for vertebrate genomics, with the number of genome sequences available growing rapidly. E. tetradactylum is a protandrous hermaphrodite that can undergo sex change at different ages [4, 7]
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