Genome-wide analysis of codon usage bias in Ascovirus: Insights into viral evolution and host adaptation

Aktürk Dizman Y.

MICROBIAL PATHOGENESIS, cilt.207, ss.1-9, 2025 (SCI-Expanded)

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 207
  • Basım Tarihi: 2025
  • Doi Numarası: 10.1016/j.micpath.2025.107892
  • Dergi Adı: MICROBIAL PATHOGENESIS
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Academic Search Premier, BIOSIS, CAB Abstracts, Environment Index, Food Science & Technology Abstracts, MEDLINE, Veterinary Science Database
  • Sayfa Sayıları: ss.1-9
  • Recep Tayyip Erdoğan Üniversitesi Adresli: Evet

Özet

Ascoviruses are circular double-stranded DNA viruses that infect lepidopterans, producing large enveloped virions

and causing a chronic, deadly disease with apoptosis-like cytopathology. Understanding the codon usage patterns

of ascoviruses could shed light on host-virus interactions, evolutionary pressure, gene expression optimization.

Nevertheless, thorough analyses of codon usage bias (CUB) within the genomes of Ascovirus (a genus in the

Ascoviridae family) have yet to be conducted. Herein, a systematic analysis was performed to clarify the codon usage

patterns in nine viruses of the Ascovirus genus, using their complete genomes. The results revealed a higher

average nucleotide composition for A and T compared to G and C, with a preference for A/T nucleotides, particularly

at the third codon position. Moreover, the results indicated that Ascovirus has a relatively low CUB. Dinucleotide

composition significantly influences the codon usage patterns in Ascovirus. Further analyses, including

ENC plot, neutrality plot, parity rule 2 (PR2) analysis, correspondence analysis, and correlation analysis, confirmed

that mutational pressure had a more significant influence than natural selection in shaping codon usage.

Codon adaptation index (CAI) analysis indicated that Ascovirus is strongly adapted to its hosts. The results of our

study illustrated the codon usage patterns in Ascovirus genomes and provided essential primary data for foundational

evolutionary research on these viruses.