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PcarnBase: development of a transcriptomic database for the brain coral Platygyra carnosus
Jin Sun1, Qian Chen, Janice C Y Lun
1Department of Biology, Hong Kong Baptist University, Hong Kong, China.
Marine Biotechnology (New York, N.Y.)
|August 10, 2012
Summary
Researchers sequenced the brain coral Platygyra carnosus transcriptome, creating a searchable database (PcarnBase). This resource aids functional genomic studies, including biomarker discovery for coral health and stress responses.
Area of Science:
- Marine Biology
- Genomics
- Bioinformatics
Background:
- Platygyra carnosus is a dominant reef-building coral in Southern China.
- Understanding its genetic makeup is crucial for coral reef conservation.
- Previous genomic data for this species was limited.
Purpose of the Study:
- To generate a comprehensive transcriptome dataset for Platygyra carnosus.
- To establish a searchable database (PcarnBase) for this data.
- To facilitate future functional genomic research on this coral species.
Main Methods:
- RNA extraction from healthy and tumorous coral tissues.
- cDNA library generation and Illumina paired-end sequencing.
- De novo assembly of sequence data and BLASTx analysis.
Main Results:
- Generated 59.6 million clean sequences, assembled into 162,468 unigenes.
- Largest transcriptome dataset for a coral species lacking a sequenced genome.
- Identified significant matches to Metazoa, Alveolata (Symbiodinium), and bacteria.
Conclusions:
- The PcarnBase database provides valuable genomic resources for Platygyra carnosus.
- Facilitates research into coral bleaching, tumor formation, and stress resistance.
- Enables investigation of symbiotic algae roles in host coral stress responses.
