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.

Codon usage bias of goose circovirus and its adaptation to host

“…CAI and expected CAI ( E-CAI ) values of the GoCV coding sequences were calculated using the CAIcal web-server ( http://genomes.urv.cat/CAIcal/ ), with the codon usage tables of A. cygnoides and A. anser ( https://www.kazusa.or.jp/codon/ ) used as reference sources ( Puigbo et al, 2008a ). If the CAI value is higher than the E-CAI value, it suggests that the virus adaptation to its host might be due to translational selection ( Puigbo et al, 2008b ; Ismail et al, 2019 ). The isoacceptor tRNA database was collected from the genome annotation of A. cygnoides ( https://www.ncbi.nlm.nih.gov/datasets/gene/taxon/8845/?gene-type=Small%20RNAs ).…”

The Mitogenome of Sedum plumbizincicola (Crassulaceae): Insights into RNA Editing, Lateral Gene Transfer, and Phylogenetic Implications

“…The GC12 and GC3 were calculated by using MEGA X 10.0.5 [ 55 ]. In addition, the ENC-GC3s plot analysis has proven to be a highly efficient tool for verifying the main driving factor of mutation pressure or natural selection [ 56 , 57 , 58 , 59 , 60 ]. Meanwhile, the neutrality plot (GC12 vs. GC3) can be used to estimate the extent of directional mutation pressure against natural selection in the codons.…”