Data

de novo transcriptomes of Goniopora columna, Galaxea astreata and Galaxea acrhelia

Australian Institute of Marine Science
Australian Institute of Marine Science (AIMS) ; The University of Southern California
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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://apps.aims.gov.au/metadata/view/3c2d31c9-b921-491c-ae27-0d169fa98c84&rft.title=de novo transcriptomes of Goniopora columna, Galaxea astreata and Galaxea acrhelia&rft.identifier=https://apps.aims.gov.au/metadata/view/3c2d31c9-b921-491c-ae27-0d169fa98c84&rft.publisher=Australian Institute of Marine Science (AIMS)&rft.description=Transcriptomic resources for coral species can provide insight into coral evolutionary history and stress-response physiology. Goniopora columna, Galaxea astreata and Galaxea acrhelia are scleractinian corals of the Indo-Pacific, representing a diversity of morphologies and life-history traits. G. columna and G. astreata are common and cosmopolitan, while G. acrhelia is largely restricted to the coral triangle and Great Barrier Reef. Reference transcriptomes for these species were assembled from replicate colony fragments exposed to elevated (31°C) and ambient (27°C) temperature.Trinity was used to create de novo assemblies for each species from 92-102 million raw Illumina Hiseq 2 x 150 bp reads. Host-specific assemblies contained 65,460-72,405 contigs, representing 20,093-31,693 isogroups (~genes) with an average N50 of 2,254. Gene name and/or gene ontology annotations were possible for 61% of isogroups on average and transcriptomes contained 93.1-94.3% of KOGs comprising the core eukaryotic gene set, indicating fairly comprehensive assemblies.This work expands the complement of transcriptomic resources available for scleractinian coral species, including the first the first reference for a representative of Goniopora spp. as well as species with novel morphology. Data collected during these periods: 01 Aug 2016Maintenance and Update Frequency: notPlannedStatement: Statement: Bioinformatic scripts used to prune and annotate transcriptomes can be found on GitHub: https://github.com/Eli-Meyer/transcriptome_utilities https://github.com/z0on/annotatingTranscriptomes&rft.creator=Australian Institute of Marine Science (AIMS) &rft.creator=The University of Southern California &rft.date=2024&rft.coverage=westlimit=147.05466; southlimit=-19.26772; eastlimit=147.05466; northlimit=-19.26772&rft.coverage=westlimit=147.05466; southlimit=-19.26772; eastlimit=147.05466; northlimit=-19.26772&rft_rights= http://creativecommons.org/licenses/by-nc/3.0/au/&rft_rights=http://i.creativecommons.org/l/by-nc/3.0/au/88x31.png&rft_rights=WWW:LINK-1.0-http--related&rft_rights=License Graphic&rft_rights=Creative Commons Attribution-NonCommercial 3.0 Australia License&rft_rights=http://creativecommons.org/international/au/&rft_rights=WWW:LINK-1.0-http--related&rft_rights=WWW:LINK-1.0-http--related&rft_rights=License Text&rft_rights=Use Limitation: 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=Attribution: Format for citation of metadata sourced from Australian Institute of Marine Science (AIMS) in a list of reference is as follows: The University of Southern California. (2017). de novo transcriptomes of Goniopora columna, Galaxea astreata and Galaxea acrhelia. https://apps.aims.gov.au/metadata/view/3c2d31c9-b921-491c-ae27-0d169fa98c84, accessed[date-of-access].&rft_rights=Resource Usage:Security classification code: unclassifiedMetadata Usage:Security classification code: unclassified&rft_rights=Creative Commons Attribution-NonCommercial 3.0 Australia License http://creativecommons.org/licenses/by-nc/3.0/au&rft_subject=oceans&rft.type=dataset&rft.language=English Access the data
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Use Limitation: 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.

Attribution: Format for citation of metadata sourced from Australian Institute of Marine Science (AIMS) in a list of reference is as follows: "The University of Southern California. (2017). de novo transcriptomes of Goniopora columna, Galaxea astreata and Galaxea acrhelia. https://apps.aims.gov.au/metadata/view/3c2d31c9-b921-491c-ae27-0d169fa98c84, accessed[date-of-access]".

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Brief description

Transcriptomic resources for coral species can provide insight into coral evolutionary history and stress-response physiology. Goniopora columna, Galaxea astreata and Galaxea acrhelia are scleractinian corals of the Indo-Pacific, representing a diversity of morphologies and life-history traits. G. columna and G. astreata are common and cosmopolitan, while G. acrhelia is largely restricted to the coral triangle and Great Barrier Reef. Reference transcriptomes for these species were assembled from replicate colony fragments exposed to elevated (31°C) and ambient (27°C) temperature.Trinity was used to create de novo assemblies for each species from 92-102 million raw Illumina Hiseq 2 x 150 bp reads. Host-specific assemblies contained 65,460-72,405 contigs, representing 20,093-31,693 isogroups (~genes) with an average N50 of 2,254. Gene name and/or gene ontology annotations were possible for 61% of isogroups on average and transcriptomes contained 93.1-94.3% of KOGs comprising the core eukaryotic gene set, indicating fairly comprehensive assemblies.This work expands the complement of transcriptomic resources available for scleractinian coral species, including the first the first reference for a representative of Goniopora spp. as well as species with novel morphology. Data collected during these periods: 01 Aug 2016

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Maintenance and Update Frequency: notPlanned
Statement: Statement: Bioinformatic scripts used to prune and annotate transcriptomes can be found on GitHub: https://github.com/Eli-Meyer/transcriptome_utilities https://github.com/z0on/annotatingTranscriptomes

Notes

Credit
Carly Kenkel (Principal Investigator)

Modified: 17 10 2024

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147.05466,-19.26772

147.05466,-19.26772

text: westlimit=147.05466; southlimit=-19.26772; eastlimit=147.05466; northlimit=-19.26772

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oceans |

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Other Information
Kenkel CD, Bay LK (2017) Novel transcriptome resources for three scleractinian coral species from the Indo-Pacific. GigaScience 6(9): 1-4

local : 11068/11262

Identifiers
  • global : 3c2d31c9-b921-491c-ae27-0d169fa98c84
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