Investigation of CaMV-host co-evolution through synonymous codon pattern.

Publisher: Wiley-VCH Verlag Country of Publication: Germany NLM ID: 8503885 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1521-4028 (Electronic) Linking ISSN: 0233111X NLM ISO Abbreviation: J Basic Microbiol Subsets: MEDLINE

Publication: <2005->: Weinheim, Germany : Wiley-VCH Verlag
Original Publication: Berlin : Akademie-Verlag, [1985-

Codon Usage* ; Phylogeny* ; Genome, Viral*/genetics ; Caulimovirus*/genetics ; Evolution, Molecular* ; Plant Diseases*/virology; Open Reading Frames/genetics ; Codon/genetics ; Genetic Variation ; Brassica rapa/genetics ; Brassica rapa/virology ; Host-Pathogen Interactions/genetics ; Brassica/genetics ; Brassica/virology ; Raphanus/genetics ; Raphanus/virology ; Iran

Cauliflower mosaic virus (CaMV) has a double-stranded DNA genome and is globally distributed. The phylogeny tree of 121 CaMV isolates was categorized into two primary groups, with Iranian isolates showing the greatest genetic variations. Nucleotide A demonstrated the highest percentage (36.95%) in the CaMV genome and the dinucleotide odds ratio analysis revealed that TC dinucleotide (1.34 ≥ 1.23) and CG dinucleotide (0.63 ≤ 0.78) are overrepresented and underrepresented, respectively. Relative synonymous codon usage (RSCU) analysis confirmed codon usage bias in CaMV and its hosts. Brassica oleracea and Brassica rapa, among the susceptible hosts of CaMV, showed a codon adaptation index (CAI) value above 0.8. Additionally, relative codon deoptimization index (RCDI) results exhibited the highest degree of deoptimization in Raphanus sativus. These findings suggest that the genes of CaMV underwent codon adaptation with its hosts. Among the CaMV open reading frames (ORFs), genes that produce reverse transcriptase and virus coat proteins showed the highest CAI value of 0.83. These genes are crucial for the creation of new virion particles. The results confirm that CaMV co-evolved with its host to ensure the optimal expression of its genes in the hosts, allowing for easy infection and effective spread. To detect the force behind codon usage bias, an effective number of codons (ENC)-plot and neutrality plot were conducted. The results indicated that natural selection is the primary factor influencing CaMV codon usage bias.
(© 2024 Wiley‐VCH GmbH.)

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Keywords: CaMV; codon adaptation; co‐evolution; phylogeography; virus–host interaction

0 (Codon)

Date Created: 20240304 Date Completed: 20240502 Latest Revision: 20240502

20240502

10.1002/jobm.202300664

38436477