Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
Sci Data. 2018 Oct 8;5:180200. doi: 10.1038/sdata.2018.200.
Chondrichthyans (cartilaginous fishes) exhibit highly variable reproductive styles, categorized as viviparity and oviparity. Among these, species with oviparity provide an enormous potential of molecular experimentation with stable sample supply which does not demand the sacrifices of live mothers. Cartilaginous fishes are divided into two subclasses, chimaeras (Holocephali) and elasmobranchs (Elasmobranchii), and the latter consists of two monophyletic groups, Batoidea (rays, skates and torpedoes) and Selachimorpha (sharks). Here we report transcriptome assemblies of the ocellate spot skate Okamejei kenojei, produced by strand-specific RNA-seq of its embryonic tissues. We obtained a total of 325 million illumina short reads from libraries prepared using four different tissue domains and assembled them all together. Our assembly result confirmed the species authenticity and high continuity of contig sequences. Also, assessment of its coverage of pre-selected one-to-one orthologs supported high diversity of transcripts in the assemblies. Our products are expected to provide a basis of comparative molecular studies encompassing other chondrichthyan species with emerging genomic and transcriptomic sequence information.
软骨鱼类（软骨鱼）表现出高度可变的生殖方式，分为胎生和卵生。其中，卵生物种提供了巨大的分子实验潜力，具有稳定的样本供应，不需要牺牲活母鱼。软骨鱼类分为两个子类，即嵌合体（全头亚纲）和板鳃亚纲（板鳃亚纲），后者由两个单系群组成，即鳐形目（射线、鳐鱼和电鳐）和鲨形目（鲨鱼）。在这里，我们报告了小眼星鲨 Okamejei kenojei 的转录组组装，这是通过对其胚胎组织的链特异性 RNA-seq 产生的。我们从使用四个不同组织区域制备的文库中总共获得了 3.25 亿个 illumina 短读段，并将它们全部组装在一起。我们的组装结果证实了物种的真实性和连续体序列的高度连续性。此外，对预先选择的一对一直系同源物的评估支持了组装中转录本的高度多样性。我们的产品有望为涵盖其他具有新兴基因组和转录组序列信息的软骨鱼类的比较分子研究提供基础。
