Data

Development of a genetic method to assess bleaching tolerance in corals (MTSRF Project 2.5i.2c)

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Souter, Petra B, Dr ; van Oppen, Madeleine JH, Dr
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ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=https://eatlas.org.au/data/uuid/6d6ba4c8-6b23-4f2b-91ac-83e063fc141e&rft.title=Development of a genetic method to assess bleaching tolerance in corals (MTSRF Project 2.5i.2c)&rft.identifier=https://eatlas.org.au/data/uuid/6d6ba4c8-6b23-4f2b-91ac-83e063fc141e&rft.publisher=eAtlas&rft.description=Next generation DNA sequencing was used to scan a large proportion of the transcribed coding DNA in Acropora millepora for polymorphisms. Transcribed coding DNA (messenger RNA - mRNA) was extracted from 8 colonies sampled at three thermally distinct habitats along the GBR (Wilke Island Reef in Princess Charlotte Bay, Nelly Bay at Magnetic Island, and Miall Island in the Keppel Islands). The mRNA extractions from each population were pooled and translated back to the complementary DNA (cDNA), which was sequenced using 454 pyrosequencing by the Australian Genome Research Facility. This transcriptome consists of over 500 000 DNA sequences that are assembled into 55 000 contigs, of which over 11 000 aligned to known genes (8 000 unique genes). A database was generated consisting of almost 90 000 SNPs (Single Nucleotide Polymorphisms/gene variants). 26 SNPs from 16 genes were investigated, from which one SNP from each of 15 genes were deemed suitable for large scale genotyping and a genotyping assay was developed. 20 individuals from 17 reefs throughout the Great Barrier Reef were genotyped. Four from the 15 show a geographic pattern. The relative frequency of each of the nucleotides was measured in each SNP (A, T, C, G).&rft.creator=Souter, Petra B, Dr &rft.creator=van Oppen, Madeleine JH, Dr &rft.date=2007&rft.coverage=northlimit=-11.45; southlimit=-23.08333; westlimit=143.04167; eastLimit=151.4&rft.coverage=northlimit=-11.45; southlimit=-23.08333; westlimit=143.04167; eastLimit=151.4&rft_rights=All AIMS data, products and services are provided as is and AIMS does not warrant their fitness for a particular purpose or non-infringement. While AIMS has made every reasonable effort to ensure high quality of the data, products and services, to the extent permitted by law the data, products and services are provided without any warranties of any kind, either expressed or implied, including without limitation any implied warranties of title, merchantability, and fitness for a particular purpose or non-infringement. AIMS make no representation or warranty that the data, products and services are accurate, complete, reliable or current. To the extent permitted by law, AIMS exclude all liability to any person arising directly or indirectly from the use of the data, products and services.&rft_rights=Ownership of all Intellectual Property Rights in the data remains with the Australian Institute of Marine Science (AIMS) and all use of the data must acknowledge AIMS.&rft_rights=All users of AIMS data must acknowledge the source of the material in the following manner:&rft_rights=Format for citation of data sourced from Australian Institute of Marine Science (AIMS) in a list of reference is as follows: Australian Institute of Marine Science. [year-of-data-download], [Title], [data-access-URL], accessed (date-of-access].&rft_rights=The data is under exclusive access period. Contact the AIMS Data Centre (adc@aims.gov.au) for possible access to the data within this period.&rft_subject=oceans&rft_subject=biota&rft_subject=environment&rft.type=dataset&rft.language=English Access the data
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All AIMS data, products and services are provided "as is" and AIMS does not warrant their fitness for a particular purpose or non-infringement. While AIMS has made every reasonable effort to ensure high quality of the data, products and services, to the extent permitted by law the data, products and services are provided without any warranties of any kind, either expressed or implied, including without limitation any implied warranties of title, merchantability, and fitness for a particular purpose or non-infringement. AIMS make no representation or warranty that the data, products and services are accurate, complete, reliable or current. To the extent permitted by law, AIMS exclude all liability to any person arising directly or indirectly from the use of the data, products and services.

Ownership of all Intellectual Property Rights in the data remains with the Australian Institute of Marine Science (AIMS) and all use of the data must acknowledge AIMS.

All users of AIMS data must acknowledge the source of the material in the following manner:

Format for citation of data sourced from Australian Institute of Marine Science (AIMS) in a list of reference is as follows: "Australian Institute of Marine Science. [year-of-data-download], [Title], [data-access-URL], accessed (date-of-access]".

The data is under exclusive access period. Contact the AIMS Data Centre (adc@aims.gov.au) for possible access to the data within this period.

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Brief description

Next generation DNA sequencing was used to scan a large proportion of the transcribed coding DNA in Acropora millepora for polymorphisms. Transcribed coding DNA (messenger RNA - mRNA) was extracted from 8 colonies sampled at three thermally distinct habitats along the GBR (Wilke Island Reef in Princess Charlotte Bay, Nelly Bay at Magnetic Island, and Miall Island in the Keppel Islands). The mRNA extractions from each population were pooled and translated back to the complementary DNA (cDNA), which was sequenced using 454 pyrosequencing by the Australian Genome Research Facility. This transcriptome consists of over 500 000 DNA sequences that are assembled into 55 000 contigs, of which over 11 000 aligned to known genes (8 000 unique genes). A database was generated consisting of almost 90 000 SNPs (Single Nucleotide Polymorphisms/gene variants). 26 SNPs from 16 genes were investigated, from which one SNP from each of 15 genes were deemed suitable for large scale genotyping and a genotyping assay was developed. 20 individuals from 17 reefs throughout the Great Barrier Reef were genotyped. Four from the 15 show a geographic pattern. The relative frequency of each of the nucleotides was measured in each SNP (A, T, C, G).

Notes

To investigate the variation in gene coding regions and their frequency distributions along a themal gradient on the Great Barrier Reef with the aim of using such genes as markers to map thermal tolerance across the Great Barrier Reef. To describe DNA sequences for genes that are likely to be involved in thermal stress responses. To describe gene variants and their potential function in the coral host. To map allele frequencies of these genes at select locations on the GBR.
Souter, PB: AIMS (Principal Investigator)
van Oppen, MJH: AIMS
Vera, C: Pennsylvania State University
Thumbnail Image: Google Earth Mapping Service.

Issued: 20070201

Data time period: 02 2007

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151.4,-11.45 151.4,-23.08333 143.04167,-23.08333 143.04167,-11.45 151.4,-11.45

147.220835,-17.266665

text: northlimit=-11.45; southlimit=-23.08333; westlimit=143.04167; eastLimit=151.4

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biota | environment | oceans |

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