Suppression Subtractive Hybridization PCR Isolation of cDNAs from a Caribbean Soft Coral

Authors

Jose V. Lopez, Nova Southeastern UniversityFollow
Angela Ledger, Florida Atlantic University
Lory Z. Santiago-Vázquez, Florida Atlantic University
Mihai Pop, University of Maryland
Dan D. Sommer, University of Maryland
Llanie K. Ranzer, Florida Atlantic University
Robert A. Feldman, SymBio Corporation
Russell G. Kerr, Florida Atlantic University

ORCID

0000-0002-1637-4125

ResearcherID

F-8809-2011

Document Type

Article

Publication Title

Electronic Journal of Biotechnology

ISSN

0717-3458

Publication Date

1-15-2011

Keywords

cDNA, Erythropodium caribaeorum, EST, Gorgonia ventalina, Gorgonian, Sea fan

Abstract

Transcriptomic studies of marine organisms are still in their infancy. A partial, subtracted expressed sequence tag (EST) library of the Caribbean octocoral Erythropodium caribaeorum and the sea fan Gorgonia ventalina has been analyzed in order to find novel genes or differences in gene expression related to potential secondary metabolite production or symbioses. This approach entails enrichment for potential non-"housekeeping" genes using the suppression subtractive hybridization (SSH) polymerase chain reaction (PCR) method. More than 500 expressed sequence tags (ESTs) were generated after cloning SSH products, which yielded at least 53 orthologous groups of proteins (COGs) and Pfam clusters, including transcription factors (Drosophila Big Brother), catalases, reverse transcriptases, ferritins and various "hypothetical" protein sequences. A total of 591 EST sequences were deposited into GenBank [dbEST: FL512138 - FL512331, and GH611838]. The results represent proof of concept for enrichment of unique transcripts over housekeeping genes, such as actin or ribosomal genes, which comprised approximately 17% of the total dataset. Due to the gene and sequence diversity of some ESTs, such sequences can find utility as molecular markers in current and future studies of this species and other soft coral biogeography, chemical ecology, phylogenetics, and evolution.

DOI

10.2225/vol14-issue1-fulltext-3

Volume

14

Issue

1

Comments

©2011 by Pontificia Universidad Catolica de Valparaiso - Chile

Additional Comments

Florida Sea Grant grant #s: R/LR-MB-23, R/LR-MB-14; NSF grant #s: 0310283, 0514500; NIH grant #: R01-HG-0004885

NSUWorks Citation

Lopez, Jose V., Angela Ledger, Lory Z. Santiago-Vazquez, Mihai Pop, Dan D. Sommer, Llanie K. Ranzer, Robert A. Feldman, and Russell G. Kerr. "Suppression Subtractive Hybridization PCR Isolation of cDNAs from a Caribbean Soft Coral." Electronic Journal of Biotechnology. no. 1 (2011). 10.2225/vol14-issue1-fulltext-3.