关键词：
大麦黄矮病毒;株系;基因组序列;多序列比对;分子变异;亲缘关系;密码子偏好性
摘 要：
【目的】分析大麦黄矮病毒(BYDV)株系的生物学信息,为深入研究BYDV各株系的遗传特性及防治提供参考。【方法】从NCBI数据库搜索BYDV的全基因组序列,利用DNASTAR 7.1对其进行序列比对分析,并以MEGA 7.0构建BYDV系统发育进化树。用CodonW分析BYDV的密码子使用偏好性;运用NCBI中的E-Utilities工具搜索BYDV各株系的基因及蛋白,采用SWISS-MODEL预测BYDV蛋白的三级结构。【结果】BYDV各株系碱基序列相似性存在明显差异,其中PAV株系组内核苷酸序列最低相似性最低,仅为77.9%,表明该株系全基因组序列变异较多。PAV、KerII、GAV和RPV株系存在碱基突变,均以C—T碱基突变数目最多,且碱基变异倾向于碱基转换。BYDV各株系分为五大分支,其中分离地相近的株系或同一株系BYDV间亲缘关系较近,来自法国克尔格伦群岛的Ker-II株系与PAV株系亲缘关系较近,来自美国的MAV株系与来自我国的GAV株系亲缘关系较近,来自我国的GPV株系(NC-012931)与美国的RPV、RMV和RPS株系亲缘关系较近。BYDV密码子使用无明显的偏好性。PAS、MAV和GAV株系的基因组中均包含7个基因,而PAV株系基因组包含8个基因。在BYDV各株系gp1～gp4蛋白中,gp4蛋白的三级结构保守性最强,而gp1蛋白的空间结构发生一定变异,正是不同BYDV株系的传播媒介及对寄主植物侵染能力存在差异的原因。【结论】BYDV各株系普遍发生分子变异,但变异程度不同,以PAV株系变异程度最大;推测GPV和RMV株系隶属于马铃薯卷叶病毒属。
译 名：
Bioinformatics analysis of Barley yellow dwarf virus
作 者：
LIU Yan-li;WANG Yan-fang;ZHAO Yan-hong;BAI Xin-fu;LIU Lin-de;School of Life Sciences,Ludong University;Journal Editorial Department,Ludong University;
关键词：
Barley yellow dwarf virus(BYDV);;strain;;genome sequence;;multi-sequence comparison;;molecular mutation;;evolutionary relationship;;codon usage preference
摘 要：
【Objective】The biological information of the Barley yellow dwarf virus(BYDV)strains were analyzed to reveal hereditary characters of BYDV strains and provide useful references for control and prevention of barley yellow dwarf disease.【Method】Complete genome sequences of BYDV were searched from the NCBI databases. Sequence alignment was performed by DNA STAR 7.1 and the phylogenetic tree was constructed by MEGA 7.0. Codon usage preference was analyzed by CodonW. The genes and proteins from different BYDV strains were searched and downloaded by E-Utilities tools in NCBI. Tertiary structures of the proteins from BYDV were predicted by Protparam and SWISS-MODEL respectively.【Result】There were great differences in the similarity of base sequence of each BYDV strain. Among them,PAV strains had the lowest similarity(77.9%)in nucleotide sequence. So,it was concluded that PAV showed more whole genomic variation than other stains. Variation analysis showed that there were base mutations in strains PAV,Ker-II,GAV,and RPV. The number of C-T base mutation was the highest among all the mutations,and the base transition was the main form in the mutations. All BYDV strains were divided into five branches. The strains with the same origin or BYDV isolates from the same strain had close evolutionary relationships. It was also found that Ker-II from Kerguelens Islands,France and PAV had close genetic relationship,and MAV from America and GAV from China had close genetic relationship,and GPV peculiar to China(NC-012931)was closely related to RPV,RMV and RPS from America. The analysis of codon usage preference showed that there was no apparent bias in codon usage of BYDV. There were seven genes found from the genomes of MAV,GAV and PAS respectively,and eight genes contained in PAV genome. Among gp1-gp4 proteins,the tertiary structure of gp4 protein was the most conservative. There was certain mutation in the spatial structures of gp1 protein,which was responsible for the different transmission media and the different abilities to infect host plants among BYDV strains.【Conclusion】Molecular variation of each BYDV strain is common,but the variation degree is obviously different. Among them,PAV strain shows greater variation than other strains. GPV and RMV stains should be taxonomically classed into Polerovirus.
