ST-2021-Cobia-transcriptome.xlsx

Cobia (<i>Rachycentron canadum</i>) is a marine teleost species with great productive potential worldwide. However, the genomic information currently available for this species in public databases is limited. Such lack of information hinders gene expression assessments that might bring forward novel insights into the physiology, ecology, evolution, and genetics of this potential aquaculture species. In this study, we report the first <i>de novo</i> transcriptome assembly of <i>R. canadum</i> liver, improving the availability of novel gene sequences for this species. Illumina sequencing of liver transcripts generated 1,761,965,794 raw reads, which were filtered into 1,652,319,304 high-quality reads. De novo assembly resulted in 101,789 unigenes and 163,096 isoforms, with an average length of 950.61 and 1617.34 nt, respectively. Moreover, we found that 126,013 of these transcripts bear potentially coding sequences, and 125,993 of these elements (77.3%) correspond to functionally annotated genes found in six different databases. We also identified 701 putative ncRNA and 35,414 putative lncRNA. Interestingly, homologues for 410 of these putative lncRNAs have already been observed in previous analyzes with <i>Danio rerio</i>, <i>Lates calcarifer</i>, <i>Seriola lalandi dorsalis</i>, <i>Seriola dumerili</i> or <i>Echeneis naucrates</i>. Finally, we identified 7894 microsatellites related to cobia's putative lncRNAs. Thus, the information derived from the transcriptome assembly described herein will likely assist future nutrigenomics and breeding programs involving this important fish farming species.<i></i>

军曹鱼（*Rachycentron canadum*）是一种在全球范围内具备极高养殖生产潜力的海水硬骨鱼类。然而，当前公共数据库中可获取的该物种基因组信息仍较为有限。这种信息匮乏阻碍了基因表达相关研究的推进，而这类研究本可为这一潜在养殖物种的生理学、生态学、进化及遗传学研究带来全新的见解。
本研究首次报道了军曹鱼肝脏的从头（de novo）转录组组装，提升了该物种新型基因序列的可获得性。对肝脏转录本进行Illumina测序后，共获得1,761,965,794条原始读段，经过滤处理后得到1,652,319,304条高质量读段。从头组装共得到101,789个单基因（unigene）和163,096个转录本异构体（isoform），二者的平均长度分别为950.61 nt和1617.34 nt。
此外，研究发现其中126,013条转录本携带潜在编码序列，且其中125,993个序列（占比77.3%）可在6个不同数据库中匹配到带有功能注释的同源基因。本研究还鉴定出701个潜在非编码RNA（ncRNA）以及35,414个潜在长链非编码RNA（lncRNA）。
值得注意的是，在这些潜在lncRNA中，有410个的同源序列已在先前针对斑马鱼（*Danio rerio*）、尖吻鲈（*Lates calcarifer*）、黄条𫚕加州亚种（*Seriola lalandi dorsalis*）、杜氏𫚕（*Seriola dumerili*）以及䲟鱼（*Echeneis naucrates*）的相关分析中被报道。
最后，本研究还鉴定出7,894个与军曹鱼潜在lncRNA相关的微卫星标记（microsatellites）。综上，本研究报道的转录组组装相关数据，将有望为未来涉及这一重要养殖鱼类的营养基因组学（nutrigenomics）及育种计划提供有力支撑。