http://rna-seqblog.com/transcrioptome-sequenced/a-reference-transcriptome-for-the-cauliflower-coral-pocillopora-damicornis/
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.
With the goal of identifying genetic variants that are more or less resilient in the face of particular stressors, a team led by researchers at Boston & Stanford Universities 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. They 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 (www.PocilloporaBase.org).
P. damicornis now joins the handful of coral species for which extensive transcriptomic data are publicly available. Through PocilloporaBase (www.PocilloporaBase.org), 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.
- Traylor-Knowles N et al. (2011) Production of a reference transcriptome and a transcriptomic database (PocilloporaBase) for the cauliflower coral, Pocillopora damicornis. BMC Genomics 12, 585. [article]
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