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Marine Biotechnology

, Volume 15, Issue 2, pp 244–251 | Cite as

PcarnBase: Development of a Transcriptomic Database for the Brain Coral Platygyra carnosus

  • Jin Sun
  • Qian Chen
  • Janice C. Y. Lun
  • Jianliang Xu
  • Jian-Wen Qiu
Original Article

Abstract

The aims of this study were to sequence the transcriptome and organize the sequence data into a searchable database for the brain coral Platygyra carnosus, a structure-forming dominant species along the coast of southern China. We collected healthy and tumorous coral tissues from two locations, extracted RNA from each tissue sample, pooled the RNA from all tissue samples, generated a cDNA library from the pooled samples, and conducted paired-end sequencing of the cDNA library using the Illumina platform to produce 59.6 M clean sequences with a read length of 90 bp. De novo assembly of the sequence data resulted in 162,468 unigenes with an average length of 606 bp (range, 201 to 23,923 bp). This is the largest transcriptome dataset for a species of coral whose genome has not been sequenced. A BLASTx search against the NCBI protein database showed that 55,355 of the unigenes matched at least a sequence with an E-value of < 0.00001; 59 % of the matched sequences are from Metazoa, 13 % are from Alveolata to which the symbiont Symbiodinium belongs, and 7 % are from bacteria. A database (PcarnBase) was constructed to provide easy access to the unigenes with attributes such as NCBI protein annotation, GO annotation, and KEGG pathway. It will facilitate functional genomic studies of P. carnosus, such as biomarker discovery for bleaching, tumor formation, and disease development at the gene or protein level, involvement of coral symbiotic algae in the host coral’s stress responses, and genetic basis of stress resistance.

Keywords

Coral Platygyra Transcriptome Database Next-generation sequencing 

Notes

Acknowledgments

This paper is the result of a collaboration between Agriculture, Fisheries and Conservation Department, Hong Kong SAR Government, and Department of Biology, Hong Kong Baptist University (HKBU). A grant to JX from HKBU supported the database construction. Transcriptome sequencing was conducted by Beijing Genomics Institute, Shenzhen, China.

Supplementary material

10126_2012_9482_MOESM1_ESM.docx (56 kb)
ESM 1 Map showing the location of Hong Kong in the southeastern coast of China and the two collection sites (Hoi Ha Wan, Sharp Island) for P. carnosus in eastern Hong Kong (DOCX 56.1 kb)
10126_2012_9482_MOESM2_ESM.doc (266 kb)
ESM 2 A total of 242 KEGG pathways found in the transcriptome of P. carnosus (DOC 266 kb)
10126_2012_9482_MOESM3_ESM.xlsx (169 kb)
ESM 3 A total of 5,656 non-sea anemone genes shared by P. carnosus and Porites digitifera showing the gene names, the best-matched NCBI protein accession numbers, annotations, and species (XLSX 169 kb)
10126_2012_9482_MOESM4_ESM.docx (286 kb)
ESM 4 Human p38 MAPK pathway deduced from KEGG. Genes framed in a red box are found in our P. carnosus transcriptome database (DOCX 285 kb)

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of BiologyHong Kong Baptist UniversityHong KongChina
  2. 2.Department of Computer ScienceHong Kong Baptist UniversityHong KongChina
  3. 3.Agriculture, Fisheries and Conservation DepartmentThe Government of the Hong Kong Special Administrative RegionHong KongChina

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