School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, Exeter, TR10 9FE, UK.
BMC Genomics. 2020 Oct 19;21(1):726. doi: 10.1186/s12864-020-07145-1.
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. 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.
We 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.
The 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.
硬骨鱼在水生生态系统和水产养殖中发挥着重要作用。须鲷目（鲈形目： Polynemidae）表现出一系列有趣的生物学特征，对于野生渔业和水产养殖都具有重要意义。此外，四指须鲷 Eleutheronema tetradactylum 由于其种群数量迅速减少，被认为处于濒危状态，因此具有保护意义。然而，目前 Polynemidae 科的须鲷目还没有基因组资源。
我们测序并组装了第一个须鲷鱼类基因组，即四指须鲷 E. tetradactylum。我们提供了一个具有高连续性（支架 N50=56.3kb）和高 BUSCO 完整性（96.5%）的 E. tetradactylum 基因组组装。E. tetradactylum 的组装基因组大小仅为 610.5Mb，是迄今为止组装的第二小的鲈形目基因组。仅 9.07-10.91%的基因组序列由重复元件组成（标准 RepeatMasker 分析与定制分析），这是迄今为止在任何鲈形目鱼类中发现的最低重复含量。共注释了 37683 个蛋白质编码基因，我们还包括了发育转录因子的分析，包括 Hox、ParaHox 和 Sox 家族。还注释了 microRNA 基因，并与其他脊索动物谱系进行了比较，阐明了脊索动物 microRNA 的获得和丢失。
本文介绍的四指须鲷 E. tetradactylum 基因组代表了生态、生物和商业上重要的须鲷鱼类分支的第一个可用基因组序列。我们的研究结果为进一步研究这种有价值的食用鱼类的有趣生物学和进化提供了有用的基因组资源。
