Fig. 1

Identification of de novo viral genome assembly and SNVs for ASGV from RNA-Seq data. a Genome structure of ASGV isolate Fuji. The conserved domains were identified by the SMART program (http://smart.embl-heidelberg.de/). Abbreviations: MT (Methyltransferase), Hel (Helicase), RNA-dependent RNA polymerase (RdRP), Movement protein (MP), and Coat protein (CP). b Alignment of raw data against genome of ASGV isolate Fuji by BWA was visualized by Tablet program. c Positions of identified SNVs in ASGV-infected apple transcriptome were visualized by Tablet program. d Identified sequence reads from ASGV-free apple sample, which were associated with ASGV by BWA alignment. e BLAST results showing sequence reads from ASGV-free apple sample matched to ASGV genome. f Alignment of raw data using ASGV-infected sRNA data from cultivar GD against reference ASGV genome by BWA was visualized by Tablet program. g Positions of identified SNVs in ASGV-infected apple sRNA transcriptome were visualized by Tablet program. h Alignment of raw data from pear sample against genome ASGV isolate Cuiguan by BWA was visualized by Tablet program. i Positions of identified SNVs of ASGV in pear mRNA transcriptome were visualized by Tablet program