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


Autoria(s): Thanh, Nguyen Minh; Thu, Vo Thi Minh; Jung, Hyungtaek; Mather, Peter
Data(s)

01/10/2015

Resumo

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.

Formato

application/pdf

Identificador

http://eprints.qut.edu.au/92889/

Publicador

Vietnam Academy of Science and Technology

Relação

http://eprints.qut.edu.au/92889/1/Thanh_Kidney%20NGS%20%26%20SNP_Vietnam.pdf

DOI:10.15625/0866-7160/v37n2.6427

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.

Direitos

Copyright 2015 Vietnam Academy of Science and Technology

Fonte

Centre for Tropical Crops and Biocommodities; School of Earth, Environmental & Biological Sciences; Institute for Future Environments; Science & Engineering Faculty

Palavras-Chave #060000 BIOLOGICAL SCIENCES #100102 Agricultural Marine Biotechnology #Pangasianodon hypophthalmus #transcriptome #kidney #salinity tolerance
Tipo

Journal Article