Data from: Characterization of the transcriptome and gene expression of four different tissues in the ecologically relevant sea urchin Arbacia lixula using RNA-seq

The sea urchin Arbacia lixula is a keystone species in Mediterranean ecosystems that drive landscape changes in littoral communities. However, genomic information available for the whole order Arbacioida is very limited. Using RNA-seq techniques, we have characterised the transcriptome of four different tissue types in A. lixula: the “somatic” tissues (coelomocytes and digestive tissue) and the “reproductive” tissues (ovary and testis), from two replicated cDNA libraries for each sample. Additionally, we performed a de novo assembly to build the “reference” transcriptome, pooling reads of the four tissues, to analyse the differential expression (DE) in pairwise comparisons between tissues. The complete de novo assembly yielded 186,084 transcripts, with a sequence size limit of 100 nt, being 31% of them spliced isoforms. Approximately 21% of the transcripts had blast hits against proteins of metazoans (E < 10-5), being less than 2.2% functionally annotated. Between coelomocytes and digestive, 30,794 transcripts showed DE (~11.8% of them with blast hit), and 19,567 transcripts did so between testis and ovary (~28.5 % of them with blast hit). Major GO term categories up-regulated in somatic tissues were those related to muscle contraction and energy generation in digestive, and lipid metabolism associated to immune response in coelomocytes. Between reproductive tissues the major up-regulated GO categories were related to energy generation in testis, and negative regulation of nucleotide metabolism in ovary. We particularly screened for a collection of target genes in each tissue because of their relevance for further studies on evolution and adaptation of echinoids.

疣海胆（Arbacia lixula）是地中海生态系统中的关键物种，能够驱动潮间带群落的景观格局演变。然而，目前针对整个拱齿海胆目（Arbacioida）的可用基因组信息仍极为匮乏。本研究采用RNA测序（RNA-seq）技术，对疣海胆（A. lixula）的四类不同组织的转录组进行了表征："体细胞"组织（体腔细胞与消化组织）以及"生殖"组织（卵巢与精巢），每个样本均设置两个重复cDNA文库。此外，本研究通过合并四类组织的测序读段开展从头组装，以构建参考转录组，用于分析组织间两两比较的差异表达（DE）情况。本次完整的从头组装共得到186084条转录本，序列长度下限为100 nt，其中31%为剪接异构体。约21%的转录本可与后生动物蛋白数据库实现BLAST比对命中（E值＜10^-5），其中仅不到2.2%得到了功能注释。体腔细胞与消化组织之间，共有30794条转录本呈现差异表达（其中约11.8%存在BLAST比对命中）；精巢与卵巢之间则有19567条转录本呈现差异表达（其中约28.5%存在BLAST比对命中）。体细胞组织中上调表达的主要基因本体（GO）术语类别包括：消化组织中与肌肉收缩及能量产生相关的类别，以及体腔细胞中与免疫应答相关的脂质代谢类别。生殖组织间上调表达的主要GO类别包括：精巢中与能量产生相关的类别，以及卵巢中与核苷酸代谢负调控相关的类别。鉴于这些靶标基因对于海胆纲动物的演化与适应性后续研究具有重要价值，本研究针对各组织中的一系列靶标基因开展了针对性筛选。