Characterization of the Antarctic sea urchin (Sterechinus neumayeri) transcriptome and mitogenome: A molecular resource for phylogenetics, ecophysiology and global change biology
© 2014 John Wiley & Sons Ltd. 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 id...
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ftunivhongkonghu:oai:hub.hku.hk:10722/253116 2023-05-15T13:43:10+02:00 Characterization of the Antarctic sea urchin (Sterechinus neumayeri) transcriptome and mitogenome: A molecular resource for phylogenetics, ecophysiology and global change biology Hofmann, G. E. Gaitán-Espitia, J. D. Dilly, G. F. 2015 https://doi.org/10.1111/1755-0998.12316 http://hdl.handle.net/10722/253116 eng eng Molecular Ecology Resources Molecular Ecology Resources, 2015, v. 15, n. 2, p. 425-436 doi:10.1111/1755-0998.12316 1755-0998 436 1755-098X 2 25143045 eid_2-s2.0-84922596914 425 http://hdl.handle.net/10722/253116 15 Ocean acidification Antarctica Mitogenome Transcriptomics Sterechinus neumayeri Echinoids Article 2015 ftunivhongkonghu https://doi.org/10.1111/1755-0998.12316 2023-01-14T16:24:51Z © 2014 John Wiley & Sons Ltd. 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 CO 2 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. Link_to_subscribed_fulltext Article in Journal/Newspaper Antarc* Antarctic Antarctica Ocean acidification University of Hong Kong: HKU Scholars Hub Antarctic The Antarctic Molecular Ecology Resources 15 2 425 436 |
institution |
Open Polar |
collection |
University of Hong Kong: HKU Scholars Hub |
op_collection_id |
ftunivhongkonghu |
language |
English |
topic |
Ocean acidification Antarctica Mitogenome Transcriptomics Sterechinus neumayeri Echinoids |
spellingShingle |
Ocean acidification Antarctica Mitogenome Transcriptomics Sterechinus neumayeri Echinoids Hofmann, G. E. Gaitán-Espitia, J. D. Dilly, G. F. Characterization of the Antarctic sea urchin (Sterechinus neumayeri) transcriptome and mitogenome: A molecular resource for phylogenetics, ecophysiology and global change biology |
topic_facet |
Ocean acidification Antarctica Mitogenome Transcriptomics Sterechinus neumayeri Echinoids |
description |
© 2014 John Wiley & Sons Ltd. 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 CO 2 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. Link_to_subscribed_fulltext |
format |
Article in Journal/Newspaper |
author |
Hofmann, G. E. Gaitán-Espitia, J. D. Dilly, G. F. |
author_facet |
Hofmann, G. E. Gaitán-Espitia, J. D. Dilly, G. F. |
author_sort |
Hofmann, G. E. |
title |
Characterization of the Antarctic sea urchin (Sterechinus neumayeri) transcriptome and mitogenome: A molecular resource for phylogenetics, ecophysiology and global change biology |
title_short |
Characterization of the Antarctic sea urchin (Sterechinus neumayeri) transcriptome and mitogenome: A molecular resource for phylogenetics, ecophysiology and global change biology |
title_full |
Characterization of the Antarctic sea urchin (Sterechinus neumayeri) transcriptome and mitogenome: A molecular resource for phylogenetics, ecophysiology and global change biology |
title_fullStr |
Characterization of the Antarctic sea urchin (Sterechinus neumayeri) transcriptome and mitogenome: A molecular resource for phylogenetics, ecophysiology and global change biology |
title_full_unstemmed |
Characterization of the Antarctic sea urchin (Sterechinus neumayeri) transcriptome and mitogenome: A molecular resource for phylogenetics, ecophysiology and global change biology |
title_sort |
characterization of the antarctic sea urchin (sterechinus neumayeri) transcriptome and mitogenome: a molecular resource for phylogenetics, ecophysiology and global change biology |
publishDate |
2015 |
url |
https://doi.org/10.1111/1755-0998.12316 http://hdl.handle.net/10722/253116 |
geographic |
Antarctic The Antarctic |
geographic_facet |
Antarctic The Antarctic |
genre |
Antarc* Antarctic Antarctica Ocean acidification |
genre_facet |
Antarc* Antarctic Antarctica Ocean acidification |
op_relation |
Molecular Ecology Resources Molecular Ecology Resources, 2015, v. 15, n. 2, p. 425-436 doi:10.1111/1755-0998.12316 1755-0998 436 1755-098X 2 25143045 eid_2-s2.0-84922596914 425 http://hdl.handle.net/10722/253116 15 |
op_doi |
https://doi.org/10.1111/1755-0998.12316 |
container_title |
Molecular Ecology Resources |
container_volume |
15 |
container_issue |
2 |
container_start_page |
425 |
op_container_end_page |
436 |
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1766185550299004928 |