Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing
Background: The Antarctic clam, Laternula elliptica, is an infaunal stenothermal bivalve mollusc with a circumpolar distribution. It plays a significant role in bentho-pelagic coupling and hence has been proposed as a sentinel species for climate change monitoring. Previous studies have shown that t...
Published in: | BMC Genomics |
---|---|
Main Authors: | , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
BIOMED CENTRAL LTD
2010
|
Subjects: | |
Online Access: | http://nora.nerc.ac.uk/id/eprint/10567/ https://nora.nerc.ac.uk/id/eprint/10567/1/1471-2164-11-362.pdf |
id |
ftnerc:oai:nora.nerc.ac.uk:10567 |
---|---|
record_format |
openpolar |
spelling |
ftnerc:oai:nora.nerc.ac.uk:10567 2023-05-15T13:45:10+02:00 Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing Clark, Melody S Thorne, Michael A.S. Vieira, Florbela A. Cardoso, Joao C.R. Power, Deborah M. Peck, Lloyd S. 2010 text http://nora.nerc.ac.uk/id/eprint/10567/ https://nora.nerc.ac.uk/id/eprint/10567/1/1471-2164-11-362.pdf en eng BIOMED CENTRAL LTD https://nora.nerc.ac.uk/id/eprint/10567/1/1471-2164-11-362.pdf Clark, Melody S orcid:0000-0002-3442-3824 Thorne, Michael A.S. orcid:0000-0001-7759-612X Vieira, Florbela A.; Cardoso, Joao C.R.; Power, Deborah M.; Peck, Lloyd S. orcid:0000-0003-3479-6791 . 2010 Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing. BMC Genomics, 11, 362. 14, pp. https://doi.org/10.1186/1471-2164-11-362 <https://doi.org/10.1186/1471-2164-11-362> cc_by CC-BY Meteorology and Climatology Biology and Microbiology Ecology and Environment Publication - Article PeerReviewed 2010 ftnerc https://doi.org/10.1186/1471-2164-11-362 2023-02-04T19:26:49Z Background: The Antarctic clam, Laternula elliptica, is an infaunal stenothermal bivalve mollusc with a circumpolar distribution. It plays a significant role in bentho-pelagic coupling and hence has been proposed as a sentinel species for climate change monitoring. Previous studies have shown that this mollusc displays a high level of plasticity with regard to shell deposition and damage repair against a background of genetic homogeneity. The Southern Ocean has amongst the lowest present-day CaCO3 saturation rate of any ocean region, and is predicted to be among the first to become undersaturated under current ocean acidification scenarios. Hence, this species presents as an ideal candidate for studies into the processes of calcium regulation and shell deposition in our changing ocean environments. Results: 454 sequencing of L. elliptica mantle tissue generated 18,290 contigs with an average size of 535 bp (ranging between 142 bp-5.591 kb). BLAST sequence similarity searching assigned putative function to 17% of the data set, with a significant proportion of these transcripts being involved in binding and potentially of a secretory nature, as defined by GO molecular function and biological process classifications. These results indicated that the mantle is a transcriptionally active tissue which is actively proliferating. All transcripts were screened against an in-house database of genes shown to be involved in extracellular matrix formation and calcium homeostasis in metazoans. Putative identifications were made for a number of classical shell deposition genes, such as tyrosinase, carbonic anhydrase and metalloprotease 1, along with novel members of the family 2 G-Protein Coupled Receptors (GPCRs). A membrane transport protein (SEC61) was also characterised and this demonstrated the utility of the clam sequence data as a resource for examining cold adapted amino acid substitutions. The sequence data contained 46,235 microsatellites and 13,084 Single Nucleotide Polymorphisms(SNPs/INDELS), providing a resource ... Article in Journal/Newspaper Antarc* Antarctic Ocean acidification Southern Ocean Natural Environment Research Council: NERC Open Research Archive Antarctic Southern Ocean The Antarctic BMC Genomics 11 1 362 |
institution |
Open Polar |
collection |
Natural Environment Research Council: NERC Open Research Archive |
op_collection_id |
ftnerc |
language |
English |
topic |
Meteorology and Climatology Biology and Microbiology Ecology and Environment |
spellingShingle |
Meteorology and Climatology Biology and Microbiology Ecology and Environment Clark, Melody S Thorne, Michael A.S. Vieira, Florbela A. Cardoso, Joao C.R. Power, Deborah M. Peck, Lloyd S. Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing |
topic_facet |
Meteorology and Climatology Biology and Microbiology Ecology and Environment |
description |
Background: The Antarctic clam, Laternula elliptica, is an infaunal stenothermal bivalve mollusc with a circumpolar distribution. It plays a significant role in bentho-pelagic coupling and hence has been proposed as a sentinel species for climate change monitoring. Previous studies have shown that this mollusc displays a high level of plasticity with regard to shell deposition and damage repair against a background of genetic homogeneity. The Southern Ocean has amongst the lowest present-day CaCO3 saturation rate of any ocean region, and is predicted to be among the first to become undersaturated under current ocean acidification scenarios. Hence, this species presents as an ideal candidate for studies into the processes of calcium regulation and shell deposition in our changing ocean environments. Results: 454 sequencing of L. elliptica mantle tissue generated 18,290 contigs with an average size of 535 bp (ranging between 142 bp-5.591 kb). BLAST sequence similarity searching assigned putative function to 17% of the data set, with a significant proportion of these transcripts being involved in binding and potentially of a secretory nature, as defined by GO molecular function and biological process classifications. These results indicated that the mantle is a transcriptionally active tissue which is actively proliferating. All transcripts were screened against an in-house database of genes shown to be involved in extracellular matrix formation and calcium homeostasis in metazoans. Putative identifications were made for a number of classical shell deposition genes, such as tyrosinase, carbonic anhydrase and metalloprotease 1, along with novel members of the family 2 G-Protein Coupled Receptors (GPCRs). A membrane transport protein (SEC61) was also characterised and this demonstrated the utility of the clam sequence data as a resource for examining cold adapted amino acid substitutions. The sequence data contained 46,235 microsatellites and 13,084 Single Nucleotide Polymorphisms(SNPs/INDELS), providing a resource ... |
format |
Article in Journal/Newspaper |
author |
Clark, Melody S Thorne, Michael A.S. Vieira, Florbela A. Cardoso, Joao C.R. Power, Deborah M. Peck, Lloyd S. |
author_facet |
Clark, Melody S Thorne, Michael A.S. Vieira, Florbela A. Cardoso, Joao C.R. Power, Deborah M. Peck, Lloyd S. |
author_sort |
Clark, Melody S |
title |
Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing |
title_short |
Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing |
title_full |
Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing |
title_fullStr |
Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing |
title_full_unstemmed |
Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing |
title_sort |
insights into shell deposition in the antarctic bivalve laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing |
publisher |
BIOMED CENTRAL LTD |
publishDate |
2010 |
url |
http://nora.nerc.ac.uk/id/eprint/10567/ https://nora.nerc.ac.uk/id/eprint/10567/1/1471-2164-11-362.pdf |
geographic |
Antarctic Southern Ocean The Antarctic |
geographic_facet |
Antarctic Southern Ocean The Antarctic |
genre |
Antarc* Antarctic Ocean acidification Southern Ocean |
genre_facet |
Antarc* Antarctic Ocean acidification Southern Ocean |
op_relation |
https://nora.nerc.ac.uk/id/eprint/10567/1/1471-2164-11-362.pdf Clark, Melody S orcid:0000-0002-3442-3824 Thorne, Michael A.S. orcid:0000-0001-7759-612X Vieira, Florbela A.; Cardoso, Joao C.R.; Power, Deborah M.; Peck, Lloyd S. orcid:0000-0003-3479-6791 . 2010 Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing. BMC Genomics, 11, 362. 14, pp. https://doi.org/10.1186/1471-2164-11-362 <https://doi.org/10.1186/1471-2164-11-362> |
op_rights |
cc_by |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1186/1471-2164-11-362 |
container_title |
BMC Genomics |
container_volume |
11 |
container_issue |
1 |
container_start_page |
362 |
_version_ |
1766214187423367168 |