Genome cloning and genetic diversity of Apple chlorotic leaf spot virus

Abstract

Apple chlorotic leaf spot virus (ACLSV) with a wide distribution and variability is great threat to apple yield and quality. The systematic research on the occurrence, genetic structure and evolutionary mechanism is important for the prevention of ACLSV. In this study, 360 apple leaf samples were collected from Shanxi province and tested by RT-PCR, and the result showed that the incidence of ACLSV in Shanxi was ranged from 43.59% in Linfen to 68.18% in Wanrong. One new ACLSV isolate (shanxi14-MK368727) was collected from the positive samples, of which the genome (including the 5' and 3' ends) was 7507 bp and encoded 2536 amino acids. Compared with online database, the highest nd identity was between shanxi14 and KJ522693.1, and the lowest was shanxi14 and M58152.1. Phylogenetic analyzed based on genome showed that 25 isolated of ACLSV were divided two groups (Group I and II), which showed that was no significant correlation with geographic location. The selection pressures of POL, MP and CP were tested, the result proved the three genes were under negative selection pressure. The knowledge presented in this study will be useful in for the design of long-term, sustainable management strategies for controlling these viruses.