An Evolutionary Perspective of Codon Usage Pattern, Dinucleotide Composition and Codon Pair Bias in Prunus Necrotic Ringspot Virus

Lingqi Wang; Haiting Zhao; Zhilei Wang; Shiwen Ding; Lang Qin; Runzhou Jiang; Xiaolong Deng; Zhen He; Liangjun Li

doi:10.3390/genes14091712

An Evolutionary Perspective of Codon Usage Pattern, Dinucleotide Composition and Codon Pair Bias in Prunus Necrotic Ringspot Virus

Genes (Basel). 2023 Aug 28;14(9):1712. doi: 10.3390/genes14091712.

Authors

Lingqi Wang^{1

2}, Haiting Zhao², Zhilei Wang², Shiwen Ding², Lang Qin², Runzhou Jiang², Xiaolong Deng², Zhen He^{2

3}, Liangjun Li^{1

3}

Affiliations

¹ College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China.
² College of Plant Protection, Yangzhou University, Yangzhou 225009, China.
³ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China.

Abstract

Prunus necrotic ringspot virus (PNRSV) is a significant virus of ornamental plants and fruit trees. It is essential to study this virus due to its impact on the horticultural industry. Several studies on PNRSV diversity and phytosanitary detection technology were reported, but the content on the codon usage bias (CUB), dinucleotide preference and codon pair bias (CPB) of PNRSV is still uncertain. We performed comprehensive analyses on a dataset consisting of 359 coat protein (CP) gene sequences in PNRSV to examine the characteristics of CUB, dinucleotide composition, and CPB. The CUB analysis of PNRSV CP sequences showed that it was not only affected by natural selection, but also affected by mutations, and natural selection played a more significant role compared to mutations as the driving force. The dinucleotide composition analysis showed an over-expression of the CpC/GpA dinucleotides and an under-expression of the UpA/GpC dinucleotides. The dinucleotide composition of the PNRSV CP gene showed a weak association with the viral lineages and hosts, but a strong association with viral codon positions. Furthermore, the CPB of PNRSV CP gene is low and is related to dinucleotide preference and codon usage patterns. This research provides reference for future research on PNRSV genetic diversity and gene evolution mechanism.

Keywords: codon pair bias; codon usage bias; dinucleotide preference; natural selection; phylogenetic analysis; prunus necrotic ringspot virus.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Sequence
Biological Evolution*
Codon Usage* / genetics
Evolution, Molecular

Supplementary concepts

Prunus necrotic ringspot virus

Grants and funding

This work was supported by grants from the National Natural Science Foundation of China (No. 32272485), the key intergovernmental special projects for international scientific and technological innovation cooperation (2022YFE0130900), the Natural Science Foundation of the Jiangsu Province (BK20211323), Project of “Vice President of Science and Technology” of Jiangsu Province (FZ20221535) and “Fengcheng Talent Plan” double innovation introduction special support program of Taizhou City, the High-Level Talent Support Program of Yangzhou University, Yangzhou University interdisciplinary high-level young talent Cultivation project.