Format

Send to

Choose Destination
BMC Genomics. 2019 May 17;20(1):387. doi: 10.1186/s12864-019-5744-8.

Development of a transcriptomic database for 14 species of scleractinian corals.

Author information

1
HKBU Institute of Research and Continuing Education, Virtual University Park, Gaoxin South 4th Road, Shenzhen, 518057, China.
2
Department of Biology, Hong Kong Baptist University, Hong Kong, China.
3
Department of Computer Science, Hong Kong Baptist University, Hong Kong, China.
4
Present address: Google China, Beijing, China.
5
Shenzhen Institute of Guangdong Ocean University, Shenzhen, China.
6
Department of Computer Science, Hong Kong Baptist University, Hong Kong, China. xujl@comp.hkbu.edu.hk.
7
HKBU Institute of Research and Continuing Education, Virtual University Park, Gaoxin South 4th Road, Shenzhen, 518057, China. qiujw@hkbu.edu.hk.
8
Department of Biology, Hong Kong Baptist University, Hong Kong, China. qiujw@hkbu.edu.hk.

Abstract

BACKGROUND:

Scleractinian corals are important reef builders, but around the world they are under the threat of global climate change as well as local stressors. Molecular resources are critical for understanding a species' stress responses and resilience to the changing environment, but such resources are unavailable for most scleractinian corals, especially those distributed in the South China Sea. We therefore aimed to provide transcriptome resources for 14 common species, including a few structure forming species, in the South China Sea.

DESCRIPTION:

We sequenced the transcriptome of 14 species of scleractinian corals using high-throughput RNA-seq and conducted de novo assembly. For each species, we produced 7.4 to 12.0 gigabases of reads, and assembled them into 271 to 762 thousand contigs with a N50 value of 629 to 1427 bp. These contigs included 66 to 114 thousand unigenes with a predicted open reading frame, and 74.3 to 80.5% of the unigenes were functionally annotated. In the azooxanthelate species Tubastraea coccinea, 41.5% of the unigenes had at least a best-hit sequence from corals. In the other thirteen species, 20.2 to 48.9% of the annotated unigenes had best-hit sequences from corals, and 28.3 to 51.6% from symbiotic algae belonging to the family Symbiodinaceae. With these resources, we developed a transcriptome database (CoralTBase) which features online BLAST and keyword search for unigenes/functional terms through a user friendly Internet interface.

SHORT CONCLUSION:

We developed comprehensive transcriptome resources for 14 species of scleractinian corals and constructed a publicly accessible database ( www.comp.hkbu.edu.hk/~db/CoralTBase ). CoralTBase will facilitate not only functional studies using these corals to understand the molecular basis of stress responses and adaptation, but also comparative transcriptomic studies with other species of corals and more distantly related cnidarians.

KEYWORDS:

Coral; Coral reef; Database; Scleractinia; Symbiotic algae; Transcriptome

PMID:
31101011
PMCID:
PMC6525400
DOI:
10.1186/s12864-019-5744-8
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center