TY - JOUR
T1 - Gene discovery in the threatened elkhorn coral
T2 - 454 sequencing of the acropora palmata transcriptome
AU - Polato, Nicholas R.
AU - Vera, J. Cristobal
AU - Baums, Iliana B.
N1 - Funding Information:
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 CO treatment conditions. Thanks also to the members of the Baums Lab at Penn State for assistance in the field and lab. 2
PY - 2011/12/28
Y1 - 2011/12/28
N2 - Background: Cnidarians, including corals and anemones, offer unique insights into metazoan evolution because they harbor genetic similarities with vertebrates beyond that found in model invertebrates and retain genes known only from non-metazoans. Cataloging genes expressed in Acropora palmata, a foundation-species of reefs in the Caribbean and western Atlantic, will advance our understanding of the genetic basis of ecologically important traits in corals and comes at a time when sequencing efforts in other cnidarians allow for multi-species comparisons. Results: 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. Analysis of the assembled sequences indicated that 83-100% of all A. palmata transcripts were tagged, and provided a rough estimate of the total number genes expressed in our samples (~18,000-20,000). The coral annotation data contained many of the same molecular components as in the Bilateria, particularly in pathways associated with oxidative stress and DNA damage repair, and provided evidence that homologs of p53, a key player in DNA repair pathways, has experienced selection along the branch separating Cnidaria and Bilateria. Transcriptome wide screens of paralog groups and transition/transversion ratios highlighted genes including: green fluorescent proteins, carbonic anhydrase, and oxidative stress proteins; and functional groups involved in protein and nucleic acid metabolism, and the formation of structural molecules. These results provide a starting point for study of adaptive evolution in corals. Conclusions: 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 bilaterians.
AB - Background: Cnidarians, including corals and anemones, offer unique insights into metazoan evolution because they harbor genetic similarities with vertebrates beyond that found in model invertebrates and retain genes known only from non-metazoans. Cataloging genes expressed in Acropora palmata, a foundation-species of reefs in the Caribbean and western Atlantic, will advance our understanding of the genetic basis of ecologically important traits in corals and comes at a time when sequencing efforts in other cnidarians allow for multi-species comparisons. Results: 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. Analysis of the assembled sequences indicated that 83-100% of all A. palmata transcripts were tagged, and provided a rough estimate of the total number genes expressed in our samples (~18,000-20,000). The coral annotation data contained many of the same molecular components as in the Bilateria, particularly in pathways associated with oxidative stress and DNA damage repair, and provided evidence that homologs of p53, a key player in DNA repair pathways, has experienced selection along the branch separating Cnidaria and Bilateria. Transcriptome wide screens of paralog groups and transition/transversion ratios highlighted genes including: green fluorescent proteins, carbonic anhydrase, and oxidative stress proteins; and functional groups involved in protein and nucleic acid metabolism, and the formation of structural molecules. These results provide a starting point for study of adaptive evolution in corals. Conclusions: 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 bilaterians.
UR - http://www.scopus.com/inward/record.url?scp=84555203214&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84555203214&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0028634
DO - 10.1371/journal.pone.0028634
M3 - Article
C2 - 22216101
AN - SCOPUS:84555203214
SN - 1932-6203
VL - 6
JO - PloS one
JF - PloS one
IS - 12
M1 - e28634
ER -