Marine Science Institute, Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA.
Mol Ecol Resour. 2015 Mar;15(2):425-36. doi: 10.1111/1755-0998.12316. Epub 2014 Sep 16.
This is the first de novo transcriptome and complete mitochondrial genome of an Antarctic sea urchin species sequenced to date. Sterechinus neumayeri is an Antarctic sea urchin and a model species for ecology, development, physiology and global change biology. To identify transcripts important to ocean acidification (OA) and thermal stress, this transcriptome was created pooling, and 13 larval samples representing developmental stages on day 11 (late gastrula), 19 (early pluteus) and 30 (mid pluteus) maintained at three CO2 levels (421, 652, and 1071 μatm) as well as four additional heat-shocked samples. The normalized cDNA pool was sequenced using emulsion PCR (pyrosequencing) resulting in 1.34M reads with an average read length of 492 base pairs. 40,994 isotigs were identified, averaging 1188 bp with a median coverage of 11×. Additional primer design and gap sequencing were required to complete the mitochondrial genome. The mitogenome of S. neumayeri is a circular DNA molecule with a length of 15 684 bp that contains all 37 genes normally found in metazoans. We detail the main features of the transcriptome and the mitogenome architecture and investigate the phylogenetic relationships of S. neumayeri within Echinoidea. In addition, we provide comparative analyses of S. neumayeri with its closest relative, Strongylocentrotus purpuratus, including a list of potential OA gene targets. The resources described here will support a variety of quantitative (genomic, proteomic, multistress and comparative) studies to interrogate physiological responses to OA and other stressors in this important Antarctic calcifier.
这是迄今为止测序的第一种南极海胆物种的从头转录组和完整线粒体基因组。Neumayer 海胆是一种南极海胆，也是生态学、发育、生理学和全球变化生物学的模式物种。为了鉴定对海洋酸化（OA）和热应激重要的转录本，本研究创建了一个转录组，汇集了 13 个幼虫样本，代表第 11 天（晚期原肠胚）、19 天（早期幼体）和 30 天（中期幼体）的发育阶段，这些样本在三个 CO2 水平（421、652 和 1071 μatm）以及四个额外的热休克样本下培养。使用乳液 PCR（焦磷酸测序）对归一化 cDNA 池进行测序，得到 1.34M 个reads，平均读长为 492 个碱基。鉴定出 40994 个同工基因，平均长度为 1188bp，中位数覆盖率为 11×。需要额外的引物设计和缺口测序来完成线粒体基因组。Neumayer 海胆的线粒体基因组是一个长度为 15684bp 的圆形 DNA 分子，包含所有 37 个通常在后生动物中发现的基因。我们详细介绍了转录组和线粒体基因组结构的主要特征，并研究了 Neumayer 海胆在海胆目中的系统发育关系。此外，我们还对 Neumayer 海胆与其最接近的亲缘种 Strongylocentrotus purpuratus 进行了比较分析，包括潜在的 OA 基因靶标列表。这里描述的资源将支持各种定量（基因组、蛋白质组、多应激和比较）研究，以研究 OA 和其他应激因子对这种重要南极钙化生物的生理反应。
