title: Characterization of the Antarctic sea urchin (Sterechinus neumayeri) transcriptome and mitogenome: a molecular resource for phylogenetics, ecophysiology and global change biology.
abstract: 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.
authors.affiliation: Marine Science Institute, Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA.
authors.forename: G F
authors.initials: GF
authors.lastname: Dilly
authors.forename: J D
authors.initials: JD
authors.lastname: Gaitán-Espitia
authors.forename: G E
authors.initials: GE
authors.lastname: Hofmann
mesh_terms: D000818:Animals; D000864:Antarctic Regions; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics*; D017753:Ecosystem; D016678:Genome; D008969:Molecular Sequence Data; D010802:Phylogeny; D012617:Sea Urchins / Q000235:genetics*; D017422:Sequence Analysis, DNA; D059467:Transcriptome
chemical_list: D018076:DNA, Complementary; D004272:DNA, Mitochondrial
keywords: Antarctica; Sterechinus neumayeri; echinoids; mitogenome; ocean acidification; transcriptomics