| Apple chlorotic leaf spot virus（ACLSV）is a representative species of the genus Trichovirus,single-stranded justice RNA,linear,with a genome about 7.4 Kb.The ACLSV genome includes three partially overlapping open reading frames（ORFs）,of which ORF3 encodes a coat protein（CP）with a size of about 21 k Da,which has large N-terminal variation and relatively conserved C-terminus.ACLSV is an important economic virus on apple and pear nuts,as well as stone fruit trees such as peaches,plums and cherries.ACLSV generally does not produce obvious symptoms on the natural host,and is a latent virus,but when mixed with other viruses,it can cause a variety of symptoms such as pear ring mosaic disease,plum pox,plum pseudopox disease,plum schizoderma,apricot ring spot disease,cherry peach ring spot disease,etc.Apple,peach and other perennials,under the influence of grafting,cuttings,pollination and other factors,will be infected with a variety of viruses including latent viruses such as ACLSV,resulting in the widespread occurrence of viral diseases,thereby significantly reducing fruit yield and seriously affecting the development of fruit industry.In order to clarify the host and geographic specificity of ACLSV common in various fruit trees,codon use preferences,spatiotemporal evolution,origin,lineage geography and evolutionary dynamics.In this study,the ACLSV cultivated in Shihezi,Xinjiang was sequenced by long-stranded non-coding RNA（Lnc RNA）sequencing,and then the latent virus ACLSV CP and whole genome sequences were analyzed by bioinformatics,genomics,lineage geography and other strategies,and the main results were as follows:（1）The full-length or near-full-length sequences of four ACLSV Xinjiang isolates from Shihezi Peach Orchard,Xinjiang,China,were identified by HTS（high-throughput sequencing）and de novo assembly.The ACLSV recombination and variation in Xinjiang were evaluated,and phylogenetic analysis of CP sequence ensembles showed obvious host and geographic adaptive clustering.ACLSV CP nucleotides exhibited significant differences in sequence consistency with amino acids and could be mapped to the two-dimensional and tertiary structure of proteins,which were related to the presence and length ofβ-turn,beta strand,coil and alpha helix.（2）Selection pressure analysis shows that ACLSV may appear more rapidly in new geographies or hosts over time.Further analysis shows that ACLSV CP codon usage preferences are influenced by adaptive responses by host and geographic sources.These comprehensive analyses allow us to further understand the underlying evolutionary dynamics of the virus,which will enable opportunities for proactive and effective prevention in the future（3）Approximately 101 ACLSV whole genome sequences were obtained from NCBI for exploration of the evolutionary dynamics of ACLSV.The ACLSV recent common ancestor（t MRCA）based on BEAST analysis dates from apple hosts that appeared in Canada in 1918 and then spread around the world in three ways,simultaneously across host transmissions.（4）The maximum clade confidence（MCC）tree of ACLSV showed that the average evolutionary rate was 4.92×10-4 subs/site/year,and it was found that the evolution rate was mostly 2.31×10-4subs/site/year—2.72×10-4 subs/site/year.The geographic rate of evolution is 5.51×10-4 subs/site/year—6.17×10-4 subs/site/yearIn summary,these studies not only reveal the adaptive response of ACLSV host,geographic adaptive clustering differences and CP codon use preferences by host and geographic source,but also reveal the changes of ACLSV in the past 30 years,and further elucidate the potential evolutionary dynamics of ACLSV.This is also the first report on the potential evolutionary dynamics of ACLSV,and it also provides new insights into the epidemic trends and control of fruit tree viruses. |
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