JIA-2019-11

2555 LI Liu et al. Journal of Integrative Agriculture 2019, 18(11): 2549–2560 two AGCaV isolates obtained from GenBank revealed that the N-terminal part (about 190 aa) of CP was highly variable (Fig. 2) and the reminded region near the C-terminal part of CP was relatively conserved (data not shown). Whilst, it was noticed that as compared with most ASPV isolates, ASPV-LYC, twoAGCaV isolatesAurora-1 and CYD, and the isolate FJ-12, shared two common deletions at aa 49–51 and 117–121 (Fig. 2). Additionally, isolates KL9 and YN-MRS had one and two large deletions, respectively (Fig. 2). The trees based on the sequences of ORFs 2–4 (TGB-encoding genes) showed similar topology structures to the CP-based tree (data not shown). Based on the genome structure and phylogenetic position, ASPV-LYC should be considered as a novel ASPV molecular variant. 3.3. Recombination detection Recombination events occurred frequently in genomes of ASPV and other foveaviruses (Boulila 2010; Dhir et al . 2011; Villamor and Eastwell 2013). Genome sequences of ASPV-LYC together withAGCaV (Aurora-1 and CYD) and 16 ASPV isolates available in GenBank were scanned and the possible recombination events in ASPV-LYC genome were detected using seven programs implemented in the software RDP version 3.44 (Martin 2009). One recombination event was detected by all seven methods with P -values ranging from 5.137×10 –73 to 4.379×10 –16 (Table 3). The recombination junction located at 1 955–2 782 nt of ORF1 of ASPV-LYC (Appendix B), withAurora-1 and KL9 identified as the major and minor parents by sharing 80.5 and 96.4% Fig. 2 Multiple alignment of the amino acid sequences of coat proteins from Apple stem pitting virus (ASPV) isolate ASPV-LYC and selected ASPV isolates and two apple green crinkle associated virus (AGCaV) isolates Aurora-1 and CYD. Rectangles indicate the commonly deleted amino acid sites in ASPV isolates LYC and FJ-12, and two AGCaV isolates Aurora-1 and CYD. Dots indicate identical amino acid residues among all isolates. Consensus sequence was shown in the bottom lane.