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J Invertebr Pathol. 2016 May;136:10-22. doi: 10.1016/j.jip.2016.01.002. Epub 2016 Feb 12.

A transcriptome study on Macrobrachium rosenbergii hepatopancreas experimentally challenged with white spot syndrome virus (WSSV).

Author information

1
Animal Genetics and Evolutionary Biology Laboratory and Terra-Aqua Lab, Centre for Research in Biotechnology for Agriculture (CEBAR), Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia. Electronic address: ra2rulz_2004@yahoo.com.
2
Animal Genetics and Evolutionary Biology Laboratory and Terra-Aqua Lab, Centre for Research in Biotechnology for Agriculture (CEBAR), Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia. Electronic address: subhabhassu@gmail.com.
3
Beijing Genomics Institute, Shenzhen, 11th Floor, Main Building, Beishan, Industrial Zone, Yantian District, Shenzhen 518083, China. Electronic address: robin.zhu@bgitechsolutions.com.
4
Animal Genetics and Evolutionary Biology Laboratory and Terra-Aqua Lab, Centre for Research in Biotechnology for Agriculture (CEBAR), Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia. Electronic address: talinejad698@gmail.com.
5
Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Building 3, Jalan Lagoon Selatan, Bandar Sunway, 47500 Selangor Darul Ehsan, Malaysia. Electronic address: sharifah.syedhassan@monash.edu.
6
Animal Genetics and Evolutionary Biology Laboratory and Terra-Aqua Lab, Centre for Research in Biotechnology for Agriculture (CEBAR), Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia. Electronic address: wangjun30@gmail.com.

Abstract

The world production of shrimp such as the Malaysian giant freshwater prawn, Macrobrachium rosenbergii is seriously affected by the white spot syndrome virus (WSSV). There is an urgent need to understand the host pathogen interaction between M. rosenbergii and WSSV which will be able to provide a solution in controlling the spread of this infectious disease and lastly save the aquaculture industry. Now, using Next Generation Sequencing (NGS), we will be able to capture the response of the M. rosenbergii to the pathogen and have a better understanding of the host defence mechanism. Two cDNA libraries, one of WSSV-challenged M. rosenbergii and a normal control one, were sequenced using the Illumina HiSeq™ 2000 platform. After de novo assembly and clustering of the unigenes from both libraries, 63,584 standard unigenes were generated with a mean size of 698bp and an N50 of 1137bp. We successfully annotated 35.31% of all unigenes by using BLASTX program (E-value <10-5) against NCBI non-redundant (Nr), Swiss-Prot, Kyoto Encyclopedia of Genes and Genome pathway (KEGG) and Orthologous Groups of proteins (COG) databases. Gene Ontology (GO) assessment was conducted using BLAST2GO software. Differentially expressed genes (DEGs) by using the FPKM method showed 8443 host genes were significantly up-regulated whereas 5973 genes were significantly down-regulated. The differentially expressed immune related genes were grouped into 15 animal immune functions. The present study showed that WSSV infection has a significant impact on the transcriptome profile of M. rosenbergii's hepatopancreas, and further enhanced the knowledge of this host-virus interaction. Furthermore, the high number of transcripts generated in this study will provide a platform for future genomic research on freshwater prawns.

KEYWORDS:

De novo assembly; Host–pathogen interaction; Immune genes; Macrobrachium rosenbergii; Transcriptomics; WSSV

PMID:
26880158
DOI:
10.1016/j.jip.2016.01.002
[Indexed for MEDLINE]

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