Codon adaptability index pipeline
The codon adaptation index (CAI) is a measure of the relative adaptability of the codon usage of a gene/viral gene towards that of highly expressed genes within a given host (Sharp et al, 1987). The maximum CAI is 1 and the minimum is 0. In general, the higher the CAI value, the more efficient the mRNA can be translated.
The CAI values of OROV genomes were analyzed in the context of the following: Homo sapiens as host (NCBI accession no. GCF_000001405.40), and several known reservoirs hosts species implicated in the transmission of OROV: nonhuman primates such as capuchin monkeys (Sarajus spp.; genome available for the Sapajus apella - GCF_009761245.1) and marmosets (genome available for the common marmoset Callithrix jacchus - GCF_011100555.1). The main vector responsible for the transmission of OROV in sylvatic and urban cycle are midges Culicoides paraensis; the mosquito species Coquillettidia venezuelensis, Aedes serratus, Culex quinquefasciatus have also been reported as potential secondary vectors in sylvatic and urban cycles (Cardoso et al., 2015; McGregor et al., 2021; Travassos et al., 2017). In absence of genomes for C. paraensis, C. sonorensis, C. venezuelensis, Ae. serratus, we have tested Culicoides brevitarsis (GCF_036172545.1) as potential sylvatic vector, Cx. quinquefasciatus (GCF_015732765.1) as cosmopolitan vector (rural, peri‑urban, and urban environments), and Ae. aegypti (GCF_002204515.2) as potential sylvatic and urban vector (de Mendonca et al., 2021).
Because eukaryotic viruses generally do not have their own translation machinery, they typically evolve codon usage in response to their host tRNA pools; thus, viruses evolved their increased translation efficiency to match the most abundant cognate tRNA. Gene expression is proportional to respective tRNA anticodon genome copy numbers (Chithambaram et al., 2014a; Chithambaram et al., 2014b; Prabhakaran et al., 2014; Prabhakaran et al., 2015; van Weringh et al., 2011). Therefore, we have identified the highly expressed genes for each host were inferred by calculating the tRNA adaptation index (dos Reis e al., 2003) of host CDS sequences at least 500 base pairs long: sequences with no start codon or having an internal stop codon were excluded; these filters were implemented in order to reduce the chance of pseudogenes being part of the dataset. Then, we have identified best tAI were considered highly expressed (Navon and Pilpel, 2011) from the top 500 genes. Single triplet amino acids (Met and Trp) were excluded to reduce bias analyses in favor of proteins rich in such amino acids, as they would get a high CAI (Xia, 2007). Afterwards, we have calculated CAI for each each target viral sequence.
Analyses were performed in R v.4.4 (R Core team) and RStudio (R Studio team, 2015). Fasta files were imported into R using the Biostring package (Pagès et al., 2020); tAI and CAI were calculated using the R package cubar (Zhang et al., 2024) and CAI plots were drawn with the ggplot2 R package (Wickham H., 2016).
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