Comparative analysis of newly identified rodent arteriviruses and porcine reproductive and respiratory syndrome virus to characterize their evolutionary relationships

Zhao, Zhuang-Yan; Yu, De; Ji, Chun-Miao; Zheng, Qinfen; Huang, Yao‐Wei; Wang, Bin

doi:10.3389/fvets.2023.1174031

Cited by 4 publications

(1 citation statement)

References 28 publications

(31 reference statements)

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“…The usage of synonymous codons is not uniform or predictable across organisms, genes, or even within the same gene in different species. Certain codons are often favored for encoding specific amino acids ( Pakrashi et al, 2023 ; Wang et al, 2023 ; Zhao et al, 2023 ). Codon Usage Bias (CUB) refers to the phenomenon where synonymous codons are used with varying frequencies ( Iriarte et al, 2021 ; Alqahtani et al, 2022 ; Chen and Yang, 2022 ; Khandia et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of codon usage patterns of Plasmodium helical interspersed subtelomeric (PHIST) proteins

Yang,

Cheng,

Luo

et al. 2023

Front. Microbiol.

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BackgroundPlasmodium falciparum is a protozoan parasite that causes the most severe form of malaria in humans worldwide, which is predominantly found in sub-Saharan Africa, where it is responsible for the majority of malaria-related deaths. Plasmodium helical interspersed subtelomeric (PHIST) proteins are a family of proteins, with a conserved PHIST domain, which are typically located at the subtelomeric regions of the Plasmodium falciparum chromosomes and play crucial roles in the interaction between the parasite and its human host, such as cytoadherence, immune evasion, and host cell remodeling. However, the specific utilization of synonymous codons by PHIST proteins in Plasmodium falciparum is still unknown.MethodsCodon usage bias (CUB) refers to the unequal usage of synonymous codons during translation, resulting in over- or underrepresentation of certain nucleotide patterns. This imbalance in CUB can impact various cellular processes, including protein expression levels and genetic variation. To investigate this, the CUB of 88 PHIST protein coding sequences (CDSs) from 5 subgroups were analyzed in this study.ResultsThe results showed that both codon base composition and relative synonymous codon usage (RSCU) analysis identified a higher occurrence of AT-ended codons (AGA and UUA) in PHIST proteins of Plasmodium falciparum. The average effective number of codons (ENC) for these PHIST proteins was 36.69, indicating a weak codon preference among them, as it was greater than 35. Additionally, the correlation analysis among codon base composition (GC1, GC2, GC3, GCs), codon adaptation index (CAI), codon bias index (CBI), frequency of optimal codons (FOP), ENC, general average hydropathicity (GRAVY), aromaticity (AROMO), length of synonymous codons (L_sym), and length of amino acids (L_aa) revealed the influence of base composition and codon usage indices on codon usage bias, with GC1 having a significant impact in this study. Furthermore, the neutrality plot analysis, PR2-bias plot analysis, and ENC-GC3 plot analysis provided additional evidence that natural selection plays a crucial role in determining codon bias in PHIST proteins.ConclusionIn conclusion, this study has enhanced our understanding of the characteristics of codon usage and genetic evolution in PHIST proteins, thereby providing data foundation for further research on antimalarial drugs or vaccines.

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Section: Introductionmentioning

confidence: 99%

Comparative analysis of codon usage patterns of Plasmodium helical interspersed subtelomeric (PHIST) proteins

Yang,

Cheng,

Luo

et al. 2023

Front. Microbiol.

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Dissecting Genetic Diversity and Evolutionary Trends of Chinese PRRSV‐1 Based on Whole‐Genome Analysis

Gong,

Xu,

Sun

et al. 2024

Transboundary and Emerging Diseases

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Porcine reproductive and respiratory syndrome (PRRS) poses a serious threat to the Chinese swine industry. The etiological agent PRRSV can be classified as either PRRSV‐1 or PRRSV‐2. Recent studies have revealed an increase in the rates of PRRSV‐1 detection and a wider PRRSV‐1 distribution. However, the PRRSV‐1 genome in China has yet to be fully characterized. In this study, 24 whole PRRSV‐1 genomes from different swine farms were assembled and subjected to whole‐genome analysis. A phylogenetic analysis based on the complete genome and ORF5 sequences revealed that the PRRSV‐1 strains from China belonged to Western European Subtype I and could be classified into seven subgroups. Statistical analysis revealed that BJEU06‐1‐Like PRRSV is currently the predominant PRRSV‐1 strain. Moreover, a similarity analysis showed low pairwise similarity between most PRRSV‐1 genomes from different pig farms. Amino acid alignments of the Nsp2 gene revealed that the BJEU06‐1‐Like subgroup had five discontinued aa deletions (4 + 1). The new subgroup 1 had 11 continued aa deletions and an aa insertion, the new subgroup 2 had two discontinued aa deletions (1 + 1), and, except for in the case of HKEU16, the HKEU16‐Like subgroup had five discontinuous aa deletions (1 + 4). Recombination analysis revealed that the BJEU06‐1‐Like and NMEU09‐1‐Like strains participated extensively in recent recombination events. The analysis of positive selection suggested that there were 15 positively selected codons in site model, and there were five sites under positive selection in the BJEU06‐1‐Like subgroup in the branch‐site model. The mean rate and tMRCA for PRRSV‐1 strains from China were 4.11 × 10−3 substitutions/site/year and 1,969.63, respectively. Thus, it is crucial to strengthen epidemiological surveys of PRRSV‐1 in China, especially those monitoring BJEU06‐1‐Like PRRSV.

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Analysis of codon usage bias of thioredoxin in apicomplexan protozoa

Wang,

Yang

2023

Parasites Vectors

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Background Apicomplexan protozoa are a diverse group of obligate intracellular parasites causing many diseases that affect humans and animals, such as malaria, toxoplasmosis, and cryptosporidiosis. Apicomplexan protozoa possess unique thioredoxins (Trxs) that have been shown to regulate various cellular processes including metabolic redox regulation, parasite survival, and host immune evasion. However, it is still unknown how synonymous codons are used by apicomplexan protozoa Trxs. Methods Codon usage bias (CUB) is the unequal usage of synonymous codons during translation which leads to the over- or underrepresentation of certain nucleotide patterns. This imbalance in CUB can impact a variety of cellular processes including protein expression levels and genetic variation. This study analyzed the CUB of 32 Trx coding sequences (CDS) from 11 apicomplexan protozoa. Results The results showed that both codon base composition and relative synonymous codon usage (RSCU) analysis revealed that AT-ended codons were more frequently used in Cryptosporidium spp. and Plasmodium spp., while the Eimeria spp., Babesia spp., Hammondia hammondi, Neospora caninum, and Toxoplasma gondii tended to end in G/C. The average effective number of codon (ENC) value of these apicomplexan protozoa is 46.59, which is > 35, indicating a weak codon preference among apicomplexan protozoa Trxs. Furthermore, the correlation analysis among codon base composition (GC1, GC2, GC3, GCs), codon adaptation index (CAI), codon bias index (CBI), frequency of optimal codons (FOP), ENC, general average hydropathicity (GRAVY), aromaticity (AROMO), length of synonymous codons (L_sym), and length of amino acids (L_aa) indicated the influence of base composition and codon usage indices on CUB. Additionally, the neutrality plot analysis, PR2-bias plot analysis, and ENC-GC3 plot analysis further demonstrated that natural selection plays an important role in apicomplexan protozoa Trxs codon bias. Conclusions In conclusion, this study increased the understanding of codon usage characteristics and genetic evolution of apicomplexan protozoa Trxs, which expanded new ideas for vaccine and drug research. Graphical Abstract

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Comparative analysis of newly identified rodent arteriviruses and porcine reproductive and respiratory syndrome virus to characterize their evolutionary relationships

Cited by 4 publications

References 28 publications

Comparative analysis of codon usage patterns of Plasmodium helical interspersed subtelomeric (PHIST) proteins

Comparative analysis of codon usage patterns of Plasmodium helical interspersed subtelomeric (PHIST) proteins

Dissecting Genetic Diversity and Evolutionary Trends of Chinese PRRSV‐1 Based on Whole‐Genome Analysis

Analysis of codon usage bias of thioredoxin in apicomplexan protozoa

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