Comparative genome analysis reveals a distinct influence of nucleotide composition on virus–host species-specific interaction of prawn-infecting nodavirus

Siti Noor Fatimah Binti Ismail, Syarul Nataqain Baharum, Shazrul Fazry, Chen Fei Low

Research output: Contribution to journalArticle

Abstract

Discovery of species-specific interaction between the host and virus has drawn the interest of many researchers to study the evolution of the newly emerged virus. Comparative genome analysis provides insights of the virus functional genome evolution and the underlying mechanisms of virus–host interactions. The analysis of nucleotide composition signified the evolution of nodavirus towards host specialization in a host-specific mutation manner. GC-rich genome of betanodavirus was significantly deficient in UpA and UpU dinucleotides composition, whilst the AU-rich genome of gammanodavirus was deficient in CpG dinucleotide. The capsid of MrNV and PvNV of gammanodavirus retains the highest abundance of adenine and uracil at the second codon position, respectively, which were found to be very distinctive from the other genera. ENC-GC3 plot inferred the influence of natural selection and mutational pressure in shaping the evolution of MrNV RdRp and capsid, respectively. Furthermore, CAI/eCAI analysis predicts a comparable adaptability of MrNV in squid, Sepia officinalis than its natural host, Macrobrachium rosenbergii. Thus, further study is warranted to investigate the capacity of MrNV replication in S. officinalis owing to its high codon adaptation index.

Original languageEnglish
JournalJournal of Fish Diseases
DOIs
Publication statusAccepted/In press - 1 Jan 2019

Fingerprint

Nodaviridae
shrimp
Nucleotides
genome
nucleotides
Genome
virus
capsid
Capsid
Viruses
codons
Codon
viruses
Betanodavirus
Sepia
Palaemonidae
Sepia officinalis
Decapodiformes
uracil
Macrobrachium rosenbergii

Keywords

  • aquatic virus
  • comparative genomic
  • Nodaviridae
  • nodavirus

ASJC Scopus subject areas

  • Aquatic Science
  • veterinary (miscalleneous)

Cite this

@article{5a7667f86cd845a2aec0c9660f7feec2,
title = "Comparative genome analysis reveals a distinct influence of nucleotide composition on virus–host species-specific interaction of prawn-infecting nodavirus",
abstract = "Discovery of species-specific interaction between the host and virus has drawn the interest of many researchers to study the evolution of the newly emerged virus. Comparative genome analysis provides insights of the virus functional genome evolution and the underlying mechanisms of virus–host interactions. The analysis of nucleotide composition signified the evolution of nodavirus towards host specialization in a host-specific mutation manner. GC-rich genome of betanodavirus was significantly deficient in UpA and UpU dinucleotides composition, whilst the AU-rich genome of gammanodavirus was deficient in CpG dinucleotide. The capsid of MrNV and PvNV of gammanodavirus retains the highest abundance of adenine and uracil at the second codon position, respectively, which were found to be very distinctive from the other genera. ENC-GC3 plot inferred the influence of natural selection and mutational pressure in shaping the evolution of MrNV RdRp and capsid, respectively. Furthermore, CAI/eCAI analysis predicts a comparable adaptability of MrNV in squid, Sepia officinalis than its natural host, Macrobrachium rosenbergii. Thus, further study is warranted to investigate the capacity of MrNV replication in S. officinalis owing to its high codon adaptation index.",
keywords = "aquatic virus, comparative genomic, Nodaviridae, nodavirus",
author = "Ismail, {Siti Noor Fatimah Binti} and Baharum, {Syarul Nataqain} and Shazrul Fazry and Low, {Chen Fei}",
year = "2019",
month = "1",
day = "1",
doi = "10.1111/jfd.13093",
language = "English",
journal = "Journal of Fish Diseases",
issn = "0140-7775",
publisher = "Wiley-Blackwell",

}

TY - JOUR

T1 - Comparative genome analysis reveals a distinct influence of nucleotide composition on virus–host species-specific interaction of prawn-infecting nodavirus

AU - Ismail, Siti Noor Fatimah Binti

AU - Baharum, Syarul Nataqain

AU - Fazry, Shazrul

AU - Low, Chen Fei

PY - 2019/1/1

Y1 - 2019/1/1

N2 - Discovery of species-specific interaction between the host and virus has drawn the interest of many researchers to study the evolution of the newly emerged virus. Comparative genome analysis provides insights of the virus functional genome evolution and the underlying mechanisms of virus–host interactions. The analysis of nucleotide composition signified the evolution of nodavirus towards host specialization in a host-specific mutation manner. GC-rich genome of betanodavirus was significantly deficient in UpA and UpU dinucleotides composition, whilst the AU-rich genome of gammanodavirus was deficient in CpG dinucleotide. The capsid of MrNV and PvNV of gammanodavirus retains the highest abundance of adenine and uracil at the second codon position, respectively, which were found to be very distinctive from the other genera. ENC-GC3 plot inferred the influence of natural selection and mutational pressure in shaping the evolution of MrNV RdRp and capsid, respectively. Furthermore, CAI/eCAI analysis predicts a comparable adaptability of MrNV in squid, Sepia officinalis than its natural host, Macrobrachium rosenbergii. Thus, further study is warranted to investigate the capacity of MrNV replication in S. officinalis owing to its high codon adaptation index.

AB - Discovery of species-specific interaction between the host and virus has drawn the interest of many researchers to study the evolution of the newly emerged virus. Comparative genome analysis provides insights of the virus functional genome evolution and the underlying mechanisms of virus–host interactions. The analysis of nucleotide composition signified the evolution of nodavirus towards host specialization in a host-specific mutation manner. GC-rich genome of betanodavirus was significantly deficient in UpA and UpU dinucleotides composition, whilst the AU-rich genome of gammanodavirus was deficient in CpG dinucleotide. The capsid of MrNV and PvNV of gammanodavirus retains the highest abundance of adenine and uracil at the second codon position, respectively, which were found to be very distinctive from the other genera. ENC-GC3 plot inferred the influence of natural selection and mutational pressure in shaping the evolution of MrNV RdRp and capsid, respectively. Furthermore, CAI/eCAI analysis predicts a comparable adaptability of MrNV in squid, Sepia officinalis than its natural host, Macrobrachium rosenbergii. Thus, further study is warranted to investigate the capacity of MrNV replication in S. officinalis owing to its high codon adaptation index.

KW - aquatic virus

KW - comparative genomic

KW - Nodaviridae

KW - nodavirus

UR - http://www.scopus.com/inward/record.url?scp=85074370081&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85074370081&partnerID=8YFLogxK

U2 - 10.1111/jfd.13093

DO - 10.1111/jfd.13093

M3 - Article

C2 - 31637743

AN - SCOPUS:85074370081

JO - Journal of Fish Diseases

JF - Journal of Fish Diseases

SN - 0140-7775

ER -