A transcriptomic analysis of striped catfish (Pangasianodon hypophthalmus) in response to salinity adaptation: De novo assembly, gene annotation and marker discovery.
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 9ppt which showed best growth performance. Total sequence data generated was 467.8Mbp, consisting of 4,116,424 reads with an average length of 112bp. 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.
International University, VNU HCMC, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam. Electronic address: nmthanh@hcmiu.edu.vn.
Nguyen Minh
NM
Thanh
Institute for Future Environment, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia; Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia. Electronic address: h7.jung@qut.edu.au.
Hyungtaek
H
Jung
CSIRO Livestock Industries, Queensland Biosciences Precinct, QLD 4057, Australia. Electronic address: russell.lyons@csiro.au.
Russell E
RE
Lyons
Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia. Electronic address: v.chand@qut.edu.au.
Vincent
V
Chand
Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia. Electronic address: viettuan.nguyen@student.qut.edu.au.
Nguyen Viet
NV
Tuan
International University, VNU HCMC, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam. Electronic address: vtmthu@hcmiu.edu.vn.
Vo Thi Minh
VT
Thu
Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia. Electronic address: p.mather@qut.edu.au.
Peter
P
Mather
D000222:Adaptation, Physiological / Q000235:genetics; D000818:Animals; D015415:Biomarkers; D002397:Catfishes / Q000235:genetics*; D020224:Expressed Sequence Tags / Q000378:metabolism*; D018895:Microsatellite Repeats / Q000235:genetics; D058977:Molecular Sequence Annotation; D054712:Salinity; D059467:Transcriptome
D015415:Biomarkers
Ion PGM; Pangasianodon hypophthalmus; Salinity tolerance; Simple sequence repeat; Transcriptome