Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Highly Accessed Database

Production of a reference transcriptome and transcriptomic database (PocilloporaBase) for the cauliflower coral, Pocillopora damicornis

Nikki Traylor-Knowles1, Brian R Granger23, Tristan J Lubinski2, Jignesh R Parikh23, Sara Garamszegi3, Yu Xia345, Jarrod A Marto67, Les Kaufman2 and John R Finnerty23*

Author Affiliations

1 Department of Biology, Stanford University, Hopkins Marine Station, Ocean View Blvd., Pacific Grove, CA, 93950, USA

2 Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215, USA

3 Bioinformatics Program, Boston University, 24 Cummington Street, Boston, MA 02215, USA

4 Department of Chemistry, Boston University, 24 Cummington Street, Boston, MA 02215, USA

5 Department of Biomedical Engineering, Boston University, 24 Cummington Street, Boston, MA 02215, USA

6 Department of Cancer Biology and Blais Proteomics Center, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA

7 Department of Biological Chemistry and Molecular Pharmacology, 44 Binney Street, Harvard Medical School, Boston, MA 02115, USA

For all author emails, please log on.

BMC Genomics 2011, 12:585  doi:10.1186/1471-2164-12-585

Published: 29 November 2011

Abstract

Background

Motivated by the precarious state of the world's coral reefs, there is currently a keen interest in coral transcriptomics. By identifying changes in coral gene expression that are triggered by particular environmental stressors, we can begin to characterize coral stress responses at the molecular level, which should lead to the development of more powerful diagnostic tools for evaluating the health of corals in the field. Furthermore, the identification of genetic variants that are more or less resilient in the face of particular stressors will help us to develop more reliable prognoses for particular coral populations. Toward this end, we performed deep mRNA sequencing of the cauliflower coral, Pocillopora damicornis, a geographically widespread Indo-Pacific species that exhibits a great diversity of colony forms and is able to thrive in habitats subject to a wide range of human impacts. Importantly, P. damicornis is particularly amenable to laboratory culture. We collected specimens from three geographically isolated Hawaiian populations subjected to qualitatively different levels of human impact. We isolated RNA from colony fragments ("nubbins") exposed to four environmental stressors (heat, desiccation, peroxide, and hypo-saline conditions) or control conditions. The RNA was pooled and sequenced using the 454 platform.

Description

Both the raw reads (n = 1, 116, 551) and the assembled contigs (n = 70, 786; mean length = 836 nucleotides) were deposited in a new publicly available relational database called PocilloporaBase http://www.PocilloporaBase.org webcite. Using BLASTX, 47.2% of the contigs were found to match a sequence in the NCBI database at an E-value threshold of ≤.001; 93.6% of those contigs with matches in the NCBI database appear to be of metazoan origin and 2.3% bacterial origin, while most of the remaining 4.1% match to other eukaryotes, including algae and amoebae.

Conclusions

P. damicornis now joins the handful of coral species for which extensive transcriptomic data are publicly available. Through PocilloporaBase http://www.PocilloporaBase.org webcite, one can obtain assembled contigs and raw reads and query the data according to a wide assortment of attributes including taxonomic origin, PFAM motif, KEGG pathway, and GO annotation.