TY  - JOUR
T1  - A Comprehensive Comparative Analysis on the Codon Usage Bias of DNA Polymerase Genes in Invertebrate Iridescent Viruses
TT  - Invertebrate Iridescent Virüslerdeki DNA Polimeraz Genlerinin Kodon Kullanım Eğilimi Üzerine Ayrıntılı Karşılaştırmalı Bir Analiz
AU  - Aktürk Dizman, Yeşim
PY  - 2024
DA  - June
Y2  - 2024
DO  - 10.53501/rteufemud.1416072
JF  - Recep Tayyip Erdogan University Journal of Science and Engineering
JO  - RTEÜ-FEMÜD
PB  - Recep Tayyip Erdoğan Üniversitesi
WT  - DergiPark
SN  - 2687-2315
SP  - 32
EP  - 48
VL  - 5
IS  - 1
LA  - en
AB  - 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.
KW  - DNA polymerase
KW  - Invertebrate iridescent viruses
KW  - Codon usage bias
KW  - Mutation pressure
KW  - Natural selection
N2  - 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.
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UR  - https://doi.org/10.53501/rteufemud.1416072
L1  - http://dergipark.org.tr/tr/download/article-file/3645147
ER  -