A transcriptomic analysis of the kidney tissue of Tra catfish (pangasianodon hypophthalmus) reared in saline condition: De novo assembly, annotation, SNP discovery

Thanh, Nguyen Minh, Thu, Vo Thi Minh, Jung, Hyungtaek, & Mather, Peter (2015) A transcriptomic analysis of the kidney tissue of Tra catfish (pangasianodon hypophthalmus) reared in saline condition: De novo assembly, annotation, SNP discovery. TAP CHI SINH HOC, 37(2), pp. 220-227.

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Abstract

Pangasianodon hypophthalmus is a commercially important freshwater fish used in inland aquaculture in the Mekong Delta, Vietnam. The current study using Ion Torrent technology generated EST resources from the kidney for Tra catfish reared at a salinity level of 9 ppt. We obtained 2,623,929 reads after trimming and processing with an average length of 104 bp. De novo assemblies were generated using CLC Genomic Workbench, Trinity and Velvet/Oases with the best overall contig performance resulting from the CLC assembly. De novo assembly using CLC yielded 29,940 contigs, and allowing identification of 5,710 putative genes when comppared with NCBI non-redundant database. A large number of single nucleotide polymorphisms (SNPs) were also detected. The sequence collection generated in our study represents the most comprehensive transcriptomic resource for P. hypophthalmus available to date.

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ID Code: 92889
Item Type: Journal Article
Refereed: Yes
Keywords: Pangasianodon hypophthalmus, transcriptome, kidney, salinity tolerance
DOI: 10.15625/0866-7160/v37n2.6427
Subjects: Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000)
Australian and New Zealand Standard Research Classification > TECHNOLOGY (100000) > AGRICULTURAL BIOTECHNOLOGY (100100) > Agricultural Marine Biotechnology (100102)
Divisions: Current > Research Centres > Centre for Tropical Crops and Biocommodities
Current > Schools > School of Earth, Environmental & Biological Sciences
Current > Institutes > Institute for Future Environments
Current > QUT Faculties and Divisions > Science & Engineering Faculty
Copyright Owner: Copyright 2015 Vietnam Academy of Science and Technology
Deposited On: 18 Feb 2016 23:46
Last Modified: 22 Feb 2016 23:24

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