Affordable Access

Access to the full text

Transcriptomic analysis of Macrobrachium rosenbergii (giant fresh water prawn) post-larvae in response to M. rosenbergii nodavirus (MrNV) infection: de novo assembly and functional annotation

Authors
  • Pasookhush, Phongthana1
  • Hindmarch, Charles2
  • Sithigorngul, Paisarn1, 3
  • Longyant, Siwaporn1, 3
  • Bendena, William G.4
  • Chaivisuthangkura, Parin1, 3
  • 1 Srinakharinwirot University, Department of Biology, Sukhumvit 23, Bangkok, 10110, Thailand , Bangkok (Thailand)
  • 2 Queen’s University, QCPU, Queen’s Cardiopulmonary Unit, Translational Institute of Medicine (TIME), Department of Medicine, Kingston, ON, K7L 3N6, Canada , Kingston (Canada)
  • 3 Srinakharinwirot University, Center of Excellence for Animal, Plant and Parasite Biotechnology, Sukhumvit 23, Bangkok, 10110, Thailand , Bangkok (Thailand)
  • 4 Queen’s University, Department of Biology, Kingston, ON, K7L 3N6, Canada , Kingston (Canada)
Type
Published Article
Journal
BMC Genomics
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Oct 22, 2019
Volume
20
Issue
1
Identifiers
DOI: 10.1186/s12864-019-6102-6
Source
Springer Nature
Keywords
License
Green

Abstract

BackgroundMacrobrachium rosenbergii, is one of a major freshwater prawn species cultured in Southeast Asia. White tail disease (WTD), caused by Macrobrachium rosenbergii nodavirus (MrNV), is a serious problem in farm cultivation and is responsible for up to 100% mortality in the post larvae stage. Molecular data on how M. rosenbergii post-larvae launches an immune response to an infection with MrNV is not currently available. We therefore compared the whole transcriptomic sequence of M. rosenbergii post-larvae before and after MrNV infection.ResultsTranscriptome for M. rosenbergii post-larvae demonstrated high completeness (BUSCO Complete: 83.4%, fragmentation: 13%, missing:3.3%, duplication:16.2%; highest ExN50 value: 94%). The assembled transcriptome consists of 96,362 unigenes with N50 of 1308 bp. The assembled transcriptome was successfully annotated against the NCBI non-redundant arthropod database (33.75%), UniProt database (26.73%), Gene Ontology (GO) (18.98%), Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups (EggNOG) (20.88%), and Kyoto Encyclopedia of Genes and Genome pathway (KEGG) (20.46%). GO annotations included immune system process, signaling, response to stimulus, and antioxidant activity. Differential abundance analysis using EdgeR showed 2413 significantly up-regulated genes and 3125 significantly down-regulated genes during the infection of MrNV.ConclusionsThis study reported a highly complete transcriptome from the post-larvae stage of giant river prawn, M. rosenbergii. Differential abundant transcripts during MrNV infection were identified and validated by qPCR, many of these differentially abundant transcripts as key players in antiviral immunity. These include known members of the innate immune response with the largest expression change occurring in the M. rosenbergii post-larvae after MrNV infection such as antiviral protein, C-type lectin, prophenol oxidase, caspase, ADP ribosylation factors, and dicer.

Report this publication

Statistics

Seen <100 times