Codon Usage in the Iflaviridae Family Is Not Diverse Though the Family Members Are Isolated from Diverse Host Taxa

Abstract

All iflavirus members belong to the unique genus, Iflavirus, of the family, Iflaviridae. The host taxa and sequence identities of these viruses are diverse. A codon usage bias, maintained by a balance between selection, mutation, and genetic drift, exists in a wide variety of organisms. We characterized the codon usage patterns of 44 iflavirus genomes that were isolated from the classes, Insecta, Arachnida, Mammalia, and Malacostraca. Iflaviruses lack a strong codon usage bias when they are evaluated using an effective number of codons. The odds ratios of the majority of dinucleotides are within the normal range. However, the dinucleotides at the 1st–2nd codon positions are more biased than those at the 2nd–3rd codon positions. Plots of effective numbers of codons, relative neutrality analysis, and PR2 bias analysis all indicate that selection pressure dominates mutations in shaping codon usage patterns in the family, Iflaviridae. When these viruses were grouped into their host taxa, we found that the indices, including the nucleotide composition, effective number of codons, relative synonymous codon usage, and the influencing factors behind the codon usage patterns, all show that there are non-significant differences between the six host-taxa-groups. Our results disagree with our assumption that diverse viruses should possess diverse codon usage patterns, suggesting that the nucleotide composition and codon usage in the family, Iflaviridae, are not host taxa-specific signatures.

Natural Selection Plays an Important Role in Shaping the Codon Usage of Structural Genes of the Viruses Belonging to the Coronaviridae Family

“…The RSCU values for the different gene sets were calculated using CodonW software v.1.4.2 and used for further analysis. For the RSCU values < 0.6, the codon is considered as under-represented and >1.6; it is considered as over-represented [ 21 , 22 , 23 ].…”

Virus Diversity, Abundance, and Evolution in Three Different Bat Colonies in Switzerland

“…Indeed, no single virus species has been detected at two time points, although the diversity of viruses from invertebrates detected in each colony in our study was vast and several members of Iflaviridae and Parvoviridae were present in all years and all colonies (Figure 1). Viruses belonging to the family Iflaviridae can infect members of the orders Lepidoptera, Hymenoptera, Hemiptera, and Diptera [60][61][62][63][64][65][66]. Members of Parvoviridae, subfamily Densovirinae, infect invertebrates of six orders, including Blattodea, Diptera, Hymenoptera, Hemiptera, Lepidoptera, and Orthoptera [67], which are the main source of food for the bat species analyzed here [27].…”

Chloroplast Genomes of Vitis flexuosa and Vitis amurensis: Molecular Structure, Phylogenetic, and Comparative Analyses for Wild Plant Conservation

“…An RSCU < 1 indicates less usage, RSCU = 1 suggests unbiased usage, and RSCU > 1 indicates high usage [ 28 ]. Additionally, RSCU values below 0.6 signify very low usage, whereas those exceeding 1.6 suggest very high usage [ 29 , 30 , 31 ]. Simple sequence repeats (SSRs) were identified using MISA [ 32 ], with mono-, di-, tri-, tetra-, penta-, and hexa-nucleotide sets of 10, 5, 4, 3, 3, and 3, respectively.…”