Suppression subtractive hybridization PCR isolation of cDNAs from a Caribbean soft coral

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 r...

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Autores principales:	Lopez,Jose V, Ledger,Angela, Santiago-Vázquez,Lory Z, Pop,Mihai, Sommer,Dan D, Ranzer,Llanie K, Feldman,Robert A, Russell,G. Kerr
Lenguaje:	English
Publicado:	Pontificia Universidad Católica de Valparaíso 2011
Materias:	cDNA Erythropodium caribaeorum EST Gorgonia ventalina gorgonian sea fan
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582011000100008
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spelling	oai:scielo:S0717-345820110001000082011-05-24Suppression subtractive hybridization PCR isolation of cDNAs from a Caribbean soft coralLopez,Jose VLedger,AngelaSantiago-Vázquez,Lory ZPop,MihaiSommer,Dan DRanzer,Llanie KFeldman,Robert ARussell,G. Kerr cDNA Erythropodium caribaeorum EST Gorgonia ventalina gorgonian sea fan 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, GH611838, and HO061755-HO062154]. 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.info:eu-repo/semantics/openAccessPontificia Universidad Católica de ValparaísoElectronic Journal of Biotechnology v.14 n.1 20112011-01-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582011000100008en
institution	Scielo Chile
collection	Scielo Chile
language	English
topic	cDNA Erythropodium caribaeorum EST Gorgonia ventalina gorgonian sea fan
spellingShingle	cDNA Erythropodium caribaeorum EST Gorgonia ventalina gorgonian sea fan Lopez,Jose V Ledger,Angela Santiago-Vázquez,Lory Z Pop,Mihai Sommer,Dan D Ranzer,Llanie K Feldman,Robert A Russell,G. Kerr Suppression subtractive hybridization PCR isolation of cDNAs from a Caribbean soft coral
description	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, GH611838, and HO061755-HO062154]. 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.
author	Lopez,Jose V Ledger,Angela Santiago-Vázquez,Lory Z Pop,Mihai Sommer,Dan D Ranzer,Llanie K Feldman,Robert A Russell,G. Kerr
author_facet	Lopez,Jose V Ledger,Angela Santiago-Vázquez,Lory Z Pop,Mihai Sommer,Dan D Ranzer,Llanie K Feldman,Robert A Russell,G. Kerr
author_sort	Lopez,Jose V
title	Suppression subtractive hybridization PCR isolation of cDNAs from a Caribbean soft coral
title_short	Suppression subtractive hybridization PCR isolation of cDNAs from a Caribbean soft coral
title_full	Suppression subtractive hybridization PCR isolation of cDNAs from a Caribbean soft coral
title_fullStr	Suppression subtractive hybridization PCR isolation of cDNAs from a Caribbean soft coral
title_full_unstemmed	Suppression subtractive hybridization PCR isolation of cDNAs from a Caribbean soft coral
title_sort	suppression subtractive hybridization pcr isolation of cdnas from a caribbean soft coral
publisher	Pontificia Universidad Católica de Valparaíso
publishDate	2011
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582011000100008
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_version_	1718441831452114944

Suppression subtractive hybridization PCR isolation of cDNAs from a Caribbean soft coral

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