[Coral-List] Acropora palmata transcriptome completed
baums at psu.edu
Mon Dec 19 09:21:16 EST 2011
We are pleased to announce the completion of a high quality Acropora palmata transcriptome.
A cDNA library from a sample enriched for symbiont free larval tissue was sequenced on the 454 GS-FLX platform. Over 960,000 reads were obtained and assembled into 42,630 contigs. Annotation data was acquired for 57% of the assembled sequences likely due to taxonomic limitations of currently available sequence databases. Analysis of the assembled sequences indicated that between 83 - 100% of all A. palmata transcripts were tagged, and provided a rough estimate of the total number genes expressed in our samples (ca 17,000 – 22,000). The annotation data showed that corals possess much of the diversity many of the same molecular tools found present in bilaterians, particularly in pathways associated with oxidative stress and DNA damage repair
Currently available transcriptome data now make comparative studies of the mechanisms underlying coral’s evolutionary success possible. Here we identified candidate genes that enable corals to maintain genomic integrity despite considerable exposure to genotoxic stress over long life spans, and showed conservation of important physiological pathways between corals and more complex animals. Molecular tools were also developed that will be useful for future studies of adaptive trait variation in corals. Assembled sequences were used to generate a NimbleGen Custom Gene Expression 12x135K Array (Roche Diagnostics, IN). Information on how to order this array from Roche-NimbleGen is available from the authors.
Polato N.R., Vera J.C., and Baums, I.B. (2011 – in press). Gene discovery in the threatened Elkhorn coral: 454 sequencing of the Acropora palmata transcriptome. PloS One
454 sequences and quality scores generated in this study are available from the NCBI short read archive (Accession #: SRP006958; http://www.ncbi.nlm.nih.gov/sra), and the assembled annotated sequences can be downloaded from https://homes.bio.psu.edu/people/faculty/baums/Links.htm. A 138-K feature microarray has been designed
Contributions: This study is part of Nick Polato’s PhD dissertation.. Nick prepared the samples, analyzed the data and wrote the manuscript. Chris Vera helped with data analysis and developed the annotation pipeline. Iliana Baums designed the study, obtained funding, gathered samples, and edited the manuscript.
Acknowledgements: We thank M. Medina and the members of her Lab at UC Merced for sharing their collection of A. palmata ESTs to include in our assembly. C. Praul and colleagues at the Penn State Genomic Core facility provided valuable advice regarding sample preparation and bioinformatic analysis. Transcriptome sequencing was performed at the Center for Genomics and Bioinformatics (CGB) at Indiana University, under the direction of J. Colbourne and K. Mockaitis. Assembly and bioinformatics support was provided by H. Tang and J.H. Choi. The CGB is supported in part by the METACyt Initiative of Indiana University, funded in part through a major grant from the Lilly Endowment, Inc. Thanks also to M. Matz and E. Meyer for providing A. millepora sequence data for comparison purposes. We thank M. Miller and A. Valdivia of NOAA and the members of SECORE for assistance with spawn collection and rearing, and R. Albright, B. Mason and C. Langdon for sharing samples raised under CO2 treatment conditions. Thanks also to the members of the Baums Lab at Penn State for assistance in the field and lab. This work was made possible with funding from an NSF GRFP grant to NP, NOAA Coral Reef Conservation Fund #NA08NMF4630462 to IBB and NSF grant OCE – 0825979 to IBB.
With best regards,
Iliana B. Baums, Ph.D.
Department of Biology
The Pennsylvania State University
208 Mueller Laboratory
University Park, PA, 16802
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