A transcriptomic analysis of the kidney tissue of tra catfish (Pangasianodon hypophthalmus) reared in saline condition: de novo assembly, annotation, snp discovery

Authors

  • Nguyen Minh Thanh Trường ĐH Quốc tế, ĐHQG HCM
  • Vo Minh Thu
  • Hyungtaek Jung
  • Peter Mather

DOI:

https://doi.org/10.15625/0866-7160/v37n2.6427

Keywords:

Pangasianodon hypophthalmus, transcriptome, kidney, salinity tolerance

Abstract

Tra catfish (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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Published

07-08-2015

How to Cite

Thanh, N. M., Thu, V. M., Jung, H., & Mather, P. (2015). A transcriptomic analysis of the kidney tissue of tra catfish (Pangasianodon hypophthalmus) reared in saline condition: de novo assembly, annotation, snp discovery. Academia Journal of Biology, 37(2), 220–227. https://doi.org/10.15625/0866-7160/v37n2.6427

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Articles