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A comparative transcriptome approach for identification of molecular changes in Aphanomyces invadans infected Channa striatus

  • Venkatesh Kumaresan
  • Mukesh Pasupuleti
  • Mariadhas Valan Arasu
  • Naif Abdullah Al-Dhabi
  • Aziz Arshad
  • S. M. Nurul Amin
  • Fatimah Md. Yusoff
  • Jesu Arockiaraj
Original Article

Abstract

Snakehead murrel, Channa striatus is an economically important aquatic species in Asia and are widely cultured and captured because of its nutritious and medicinal values. Their growth is predominantly affected by epizootic ulcerative syndrome (EUS) which is primarily caused by an oomycete fungus, Aphanomyces invadans. However, the molecular mechanism of immune response in murrel against this infection is still not clear. In this study, transcriptome technique was used to understand the molecular changes involved in C. striatus during A. invadans infection. RNA from the control (CF) and infected fish (IF) groups were sequenced using Illumina Hi-seq sequencing technology. For control group, 28,952,608 clean reads were generated and de novo assembly was performed to produce 60,753 contigs. For fungus infected group, 25,470,920 clean reads were obtained and assembled to produce 58,654 contigs. Differential gene expression analysis revealed that a total of 146 genes were up-regulated and 486 genes were down regulated. Most of the differentially expressed genes were involved in innate immune mechanism such as pathogen recognition, signalling and antimicrobial mechanisms. Interestingly, few adaptive immune genes, especially immunoglobulins were also significantly up regulated during fungal infection. Also, the results were validated by qRT-PCR analysis. These results indicated the involvement of various immune genes involved in both innate and adaptive immune mechanism during fungal infection in C. striatus which provide new insights into murrel immune mechanisms against A. invadans.

Keywords

Snakehead Murrel Aphanomyces invadans Epizootic ulcerative syndrome Transcriptome Gene expression 

Abbreviations

EUS

Epizootic ulcerative syndrome

CF

Control fish

IF

Infected fish

OIE

World Organisation for Animal Health

MG

Mycotic granulomatosis

RSD

Red spot disease

UM

Ulcerative mycosis

NGS

Next generation sequencing

FPKM

Fragments per kilobase of exon per million fragments mapped

GO

Gene ontology

MF

Molecular function

CC

Cellular component

BP

Biological process

qRT-PCR

Quantitative real-time polymerase chain reaction

Cq

Quantification cycle

PRRs

Pattern recognition receptors

PAMPs

Pathogen-associated molecular patterns

PGRPs

Peptidoglycan recognition proteins

PGNs

Peptidoglycans

NCC

Nonspecific cytotoxic cells

NK

Natural killer

PGC 1α

Peroxisome proliferator-activated receptor gamma co-activator 1 alpha

OXPHOS

Oxidative phosphorylation

CPT I

Carnitine palmitoyl transferase I

Ig

Immunoglobulin

LITR

Leukocyte immune-type receptor

IgSF

Immunoglobulin superfamily

AP

Alternate pathway

Notes

Acknowledgements

This research is supported by Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India, New Delhi under the program of Aquaculture and Marine Biotechnology (No. BT/PR13183/AAQ/3/723/2015). The authors also grateful to the Deanship of Scientific Research, King Saud University for partial funding through Vice Deanship of Scientific Research Chairs. Moreover, the corresponding author would like to acknowledge Institute of Bioscience, Universiti Putra Malaysia, Malaysia for providing him visiting professor Award (UPM/PEND/500-3/4/10) to complete this study under the HICoE and SATREPS-COSMOS programs, Ministry of Higher Education Malaysia.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Research involving human and animal participants

This experiment does not contain any human participants. The animal, striped murrel Channa striatus used in this experiment was treated with care following the ethical procedures of the SRM Institute of Science and Technology (SRMIST) guidelines and regulations. All the experimental protocols were approved by the research committee of SRMIST.

Supplementary material

11033_2018_4418_MOESM1_ESM.docx (285 kb)
Supplementary material 1 (DOCX 284 KB)

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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  1. 1.Department of Biotechnology, Faculty of Science and HumanitiesSRM Institute of Science and TechnologyChennaiIndia
  2. 2.Lab PCN 206, Microbiology DivisionCSIR-Central Drug Research InstituteLucknowIndia
  3. 3.Addiriyah Research Chair for Environmental Studies, Department of Botany and Microbiology, College of ScienceKing Saud UniversityRiyadhSaudi Arabia
  4. 4.International Institute of Aquaculture and Aquatic Sciences (I-AQUAS), Universiti Putra MalaysiaSi Rusa Port DicksonMalaysia
  5. 5.Department of Aquaculture, Faculty of AgricultureUniversiti Putra MalaysiaSerdangMalaysia
  6. 6.Laboratory of Marine Biotechnology, Institute of BioscienceUniversiti Putra MalaysiaSerdangMalaysia
  7. 7.SRM Research InstituteSRM Institute of Science and TechnologyChennaiIndia

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