A transcriptomic analysis of striped catfish (Pangasianodon hypophthalmus) in response to salinity adaptation: De novo assembly, gene annotation and marker discovery

Nguyen Minh Thanh, Jung, Hyungtaek, Lyons, Russell E., Chand, Vincent, Nguyen Viet Tuan, Vo Thi Minh Thu and Mather, Peter (2014) A transcriptomic analysis of striped catfish (Pangasianodon hypophthalmus) in response to salinity adaptation: De novo assembly, gene annotation and marker discovery. Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics, 10 1: 52-63. doi:10.1016/j.cbd.2014.04.001

Attached Files (Some files may be inaccessible until you login with your UQ eSpace credentials)
Name Description MIMEType Size Downloads

Author Nguyen Minh Thanh
Jung, Hyungtaek
Lyons, Russell E.
Chand, Vincent
Nguyen Viet Tuan
Vo Thi Minh Thu
Mather, Peter
Title A transcriptomic analysis of striped catfish (Pangasianodon hypophthalmus) in response to salinity adaptation: De novo assembly, gene annotation and marker discovery
Formatted title
A transcriptomic analysis of striped catfish (Pangasianodon hypophthalmus) in response to salinity adaptation: De novo assembly, gene annotation and marker discovery
Journal name Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics   Check publisher's open access policy
ISSN 1878-0407
1744-117X
Publication date 2014-06
Year available 2014
Sub-type Article (original research)
DOI 10.1016/j.cbd.2014.04.001
Open Access Status
Volume 10
Issue 1
Start page 52
End page 63
Total pages 12
Place of publication Philadelphia United States
Publisher Elsevier
Collection year 2015
Language eng
Formatted abstract
The striped catfish (Pangasianodon hypophthalmus) culture industry in the Mekong Delta in Vietnam has developed rapidly over the past decade. The culture industry now however, faces some significant challenges, especially related to climate change impacts notably from predicted extensive saltwater intrusion into many low topographical coastal provinces across the Mekong Delta. This problem highlights a need for development of culture stocks that can tolerate more saline culture environments as a response to expansion of saline water-intruded land. While a traditional artificial selection program can potentially address this need, understanding the genomic basis of salinity tolerance can assist development of more productive culture lines. The current study applied a transcriptomic approach using Ion PGM technology to generate expressed sequence tag (EST) resources from the intestine and swim bladder from striped catfish reared at a salinity level of 9 ppt which showed best growth performance. Total sequence data generated was 467.8 Mbp, consisting of 4,116,424 reads with an average length of 112 bp. De novo assembly was employed that generated 51,188 contigs, and allowed identification of 16,116 putative genes based on the GenBank non-redundant database. GO annotation, KEGG pathway mapping, and functional annotation of the EST sequences recovered with a wide diversity of biological functions and processes. In addition, more than 11,600 simple sequence repeats were also detected. This is the first comprehensive analysis of a striped catfish transcriptome, and provides a valuable genomic resource for future selective breeding programs and functional or evolutionary studies of genes that influence salinity tolerance in this important culture species.
Keyword Ion PGM
Pangasianodon hypophthalmus
Salinity tolerance
Simple sequence repeat
Transcriptome
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2015 Collection
School of Veterinary Science Publications
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 5 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 5 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Tue, 09 Dec 2014, 11:51:23 EST by System User on behalf of School of Veterinary Science