Data from: A comprehensive transcriptome of early development in yellowtail kingfish (Seriola lalandi)

Seriola lalandi is an ecologically and economically important species that is globally distributed in temperate and subtropical marine waters. The aim of this study was to identify large numbers of genic single nucleotide polymorphisms (SNPs) and differential gene expression (DGE) related to the early development of normal and deformed S. lalandi larvae using high-throughput RNA-Seq data. A de novo assembly of reads generated 40,066 genes ranging from 300 bases to 64,799 bases with an N90 of 788 bases. Homology search and protein signature recognition assigned gene ontology (GO) terms to a total of 15,744 (39.34%) genes. A search against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) retrieved 6,808 KEGG Orthology (KO) identifiers for 10,520 genes (26.25%), and mapping of KO identifiers generated 337 KEGG pathways. Comparisons of annotated genes revealed that 1,262 genes were down-regulated and 1,047 genes were up-regulated in the deformed larvae group compared to the normal group of larvae. Additionally, we identified 6,989 high quality SNPs from the assembled transcriptome. These putative SNPs contain 4,415 transitions and 2,574 transversions, which will be useful for further ecological studies of S. lalandi. This is the first study to use a global transcriptomic approach in S. lalandi, and the resources generated can be used further for investigation of gene expression of marine teleosts to investigate larval developmental biology. The results of the GO enrichment analysis highlight the crucial role of the extracellular matrix in normal skeleton development, which could be important for future studies of skeletal deformities in S. lalandi and other marine species.

黄条鰤（Seriola lalandi）是一种兼具生态与经济价值的重要物种，广泛分布于全球温带及亚热带海域。本研究旨在利用高通量RNA测序（high-throughput RNA-Seq）数据，筛选与正常和畸形黄条鰤幼体早期发育相关的大量基因区域单核苷酸多态性（single nucleotide polymorphisms, SNPs）及差异基因表达（differential gene expression, DGE）信息。对测序读段进行从头组装后，共得到40066个基因，序列长度介于300 bp至64799 bp之间，N90值为788 bp。通过同源性搜索与蛋白质特征识别，共为15744个基因（占总基因数的39.34%）注释了基因本体（gene ontology, GO）术语。针对京都基因与基因组百科全书通路数据库（Kyoto Encyclopedia of Genes and Genomes Pathway database, KEGG）进行检索，共为10520个基因（占总基因数的26.25%）匹配到6808个KEGG同源分类（KEGG Orthology, KO）编号，基于KO编号的注释共得到337条KEGG通路。对注释基因的比较分析显示，与正常幼体组相比，畸形幼体组中有1262个基因表达下调、1047个基因表达上调。此外，本研究从组装得到的转录组中筛选得到6989个高质量SNPs，这些推定SNPs包含4415个转换突变与2574个颠换突变，可为后续黄条鰤的生态学研究提供宝贵资源。本研究首次在黄条鰤中采用全局转录组学分析方法，所产生的组学资源可进一步用于海洋硬骨鱼类的基因表达研究，以探索幼体发育生物学机制。GO富集分析结果揭示了细胞外基质在正常骨骼发育中的关键作用，这一发现可为黄条鰤及其他海洋物种的骨骼畸形相关研究提供重要参考。