Help Login Create account

Data released on August 04, 2017

Supporting data for "Novel transcriptome resources for three scleractinian coral species from the Indo-Pacific"

Bay, L, K; Kenkel, C, D (2017): Supporting data for "Novel transcriptome resources for three scleractinian coral species from the Indo-Pacific" GigaScience Database. http://dx.doi.org/10.5524/100328 RIS BibTeX Text

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 26,693-37,894 isogroups (~genes) with an average N50 of 2,254. Gene name and/or gene ontology annotations were possible for 58% of isogroups on average. Transcriptomes contained 93.1-94.3% of KOGs comprising the core eukaryotic gene set and 89.98-91.92% of the single-copy metazoan core gene set orthologs were complete, indicating fairly comprehensive assemblies.
This work expands the complement of transcriptomic resources available for scleractinian coral species, including the first reference for a representative of Goniopora spp. as well as species with novel morphology.

Contact Submitter

Related manuscripts:

doi:10.1093/gigascience/gix074

Additional information:

http://dornsife.usc.edu/labs/carlslab/data/

Accessions (data included in GigaDB):

BioProject: PRJNA350363
BioProject: PRJNA352640
BioProject: PRJNA352641

Keywords:

thermal stress functional genomics Coral 

Transcriptomic

http://gigadb.org/images/data/cropped/100328.jpg

Funding:

  • Funding body - National Science Foundation
  • Award ID - DBI-1401165
  • Comment - International Postdoctoral Research Fellowship
  • Awardee - CD Kenkel

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Gach1888344  Galaxea acrhelia Descriptions:RNA extracted from multiple pooled cl...
Analyte type:RNA
Isolate:Gach_R2
...
+
Gast154325  Galaxea astreata Description:RNA extracted from multiple pooled clo...
Analyte type:RNA
Isolate:Gast_R2
...
+
Gcol541198  Goniopora columna Description:RNA extracted from multiple pooled clo...
Analyte type:RNA
Isolate:Gcol_R2
...
+
Displaying 1-3 of 3 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
annotationTSV1.74 MB2017-07-10
protein sequenceFASTA52.82 MB2017-07-10
protein sequenceFASTA40.46 MB2017-07-10
transcriptome sequenceFASTA113.43 MB2017-07-10
BLASTTSV1.91 MB2017-07-10
protein sequenceFASTA18.4 MB2017-07-10
protein sequenceFASTA14.28 MB2017-07-10
annotationTSV1.52 MB2017-07-10
annotationTSV1.8 MB2017-07-10
annotationTSV146.03 KB2017-07-10
Displaying 11-20 of 34 File(s).

History:

+

Other datasets you might like: