Publication:
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

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Issued Date

2019

Resource Type

Article

File Type

application/pdf

ISSN

14712164

DOI

10.1186/s12864-019-6102-6

Other identifier(s)

2-s2.0-85073719139

Rights Holder(s)

มหาวิทยาลัยศรีนครินทรวิโรฒ

Bibliographic Citation

BMC Genomics. Vol 20, No.1 (2019)

Suggested Citation

Pasookhush P., Hindmarch C., Sithigorngul P., Longyant S., Bendena W.G., Chaivisuthangkura P. 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. BMC Genomics. Vol 20, No.1 (2019). doi:10.1186/s12864-019-6102-6 Retrieved from: https://hdl.handle.net/20.500.14740/5107

Title

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

Author(s)

Pasookhush P.
 Hindmarch C.
 Sithigorngul P.
 Longyant S.
 Bendena W.G.
 Chaivisuthangkura P.

Abstract

Background: Macrobrachium 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. Results: Transcriptome 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. Conclusions: This 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. © 2019 The Author(s).

Subject(s)

Adenosine diphosphate ribosylation factor
 Caspase
 Dicer
 Lectin
 Oxidoreductase
 Transcriptome
 Fresh water
 Transcriptome
 Article
 Controlled study
 Down regulation
 Gene expression
 Gene identification
 Gene ontology
 Innate immunity
 Macrobrachium rosenbergii
 Molecular genetics
 Nodaviridae
 Nonhuman
 Population abundance
 Postlarva
 Principal component analysis
 Quantitative analysis
 Reverse transcription polymerase chain reaction
 RNA extraction
 RNA sequence
 Signal transduction
 Stimulus response
 Transcriptomics
 Upregulation
 Virus immunity
 Virus infection
 Animal
 Aquaculture
 Gene expression profiling
 Genetics
 Immunity
 Immunology
 Palaemonidae
 Physiology
 RNA virus infection
 Veterinary medicine
 Virology
 Animals
 Aquaculture
 Fresh Water
 Gene Expression Profiling
 Gene Ontology
 Immunity
 Molecular Sequence Annotation
 Nodaviridae
 Palaemonidae
 RNA Virus Infections
 Transcriptome

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URI

https://hdl.handle.net/20.500.14740/5107

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Scopus: Year 1983-2021

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