A Comprehensive Comparative Analysis on the Codon Usage Bias of DNA Polymerase Genes in Invertebrate Iridescent Viruses

Year 2024, Volume: 5 Issue: 1, 32 - 48, 30.06.2024

Yeşim Aktürk Dizman

https://doi.org/10.53501/rteufemud.1416072

Abstract

Invertebrate iridescent viruses (IIVs) are classified as double-stranded DNA viruses within the Iridoviridae family. IIVs are viruses that infect invertebrate hosts, causing symptoms that vary in intensity from slight reductions in host fitness to systemic disease. Numerous earlier investigations have provided insights into the genomic, proteomic, and transcriptional analyses of invertebrate iridescent viruses. However, the codon usage bias (CUB) of IIVs has yet to be fully understood. In order to gain a more profound insight into the evolutionary features of IIVs, we conducted an extensive analysis of the codon usage patterns in the DNA polymerase genes (DNA pol genes) of 12 invertebrate iridescent viruses. The analysis of both nucleotide composition and relative synonymous codon usage (RSCU) indicated a higher prevalence of AT-ended codons in the DNA pol genes of IIVs. Additionally, a low codon usage bias was determined from the effective number of codons (ENC) value. Analyses of ENC-GC3s plot, neutrality plot, and parity rule 2 plot illustrated that the codon usage patterns in IIVs DNA pol genes were influenced by both natural selection and mutational pressure. This investigation holds significance as it has delineated the codon usage patterns within the DNA pol genes of IIVs and has furnished crucial data for a foundational study of their evolutionary aspects.

Keywords

DNA polymerase, Invertebrate iridescent viruses, Codon usage bias, Mutation pressure, Natural selection

Invertebrate Iridescent Virüslerdeki DNA Polimeraz Genlerinin Kodon Kullanım Eğilimi Üzerine Ayrıntılı Karşılaştırmalı Bir Analiz

Abstract

Invertebrate iridescent virüsler (IIV’ler), Iridoviridae familyası içerinde yer alan çift sarmallı DNA virüsleri olarak sınıflandırılır. IIV’ler omurgasız konakçıları enfekte eden, konak hareketinde hafif azalmalardan sistemik hastalığa kadar değişen yoğunlukta semptomlara neden olan virüslerdir. Daha önce yapılan çok sayıda araştırma, invertebrate iridescent virüslerin genomik, proteomik ve transkripsiyonel analizlerine ilişkin bilgiler sağlamıştır. Bununla birlikte, IIV'lerin kodon kullanım eğilimi henüz tam olarak anlaşılamamıştır. IIV'lerin evrimsel özellikleri hakkında daha derin bir bilgi elde etmek için, 12 invertebrate iridescent virüsün DNA polimeraz genlerindeki kodon kullanım modellerinin kapsamlı bir analizini gerçekleştirdik. Hem nükleotid kompozisyonu hem de göreli sinonim kodon kullanımı (RSCU) analizi, IIV'lerin DNA pol genlerinde AT-uçlu kodonların daha yüksek bir yaygınlıkta bulunduğunu göstermiştir. Ayrıca, etkin kodon sayısı (ENC) değerinden düşük bir kodon kullanım yanlılığı tespit edilmiştir. ENC-GC3s grafiği, nötraliti grafiği ve parite kuralı 2 grafiği analizleri, IIV’lerin DNA pol genlerindeki kodon kullanım modellerinin hem doğal seçilim hem de mutasyon baskısından etkilendiğini göstermiştir. Bu araştırma, IIV'lerin DNA pol genlerindeki kodon kullanım modellerini tanımlaması ve evrimsel yönlerine ilişkin temel bir çalışma için önemli veriler sağlaması açısından önem taşımaktadır.

Keywords

DNA polimeraz, Invertebrate iridescent virüsler, Kodon kullanım eğilimi, Mutasyon baskısı, Doğal seçilim

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