Dnaman version 6 program

Contigs and gaps were confirmed and filled by RT-PCR using specific primer pairs 1, 2, 3, 4, 1-2, 2-3, and 3-4 F/R (Table S1) designed according to the consensus sequences of the assembled viral contigs with more than 70-nt overlapping. The sugarcane yellow leaf virus (ScYLV, AF157029.1) genome sequence was used for the alignment and positioning of the contigs. The terminal sequences of the viral genome were obtained using 5′ and 3′ rapid amplification of cDNA ends (RACE) kits according to the manufacture (Invitrogen). The PCR products were collected using Wizard SV Gel and PCR Clean-Up System (Promega). The purified PCR products were then cloned into the pEASY-T5 vector (TransGen Biotech, China) and used to transformed Trans-T1 competent cells (TransGen Biotech) following the manufacturers' instructions. The clones harboring the transformed vector were identified by PCR and Sanger sequencing (Sangon Biotech (Shanghai) Co., China). The results of sequencing were assembled using DNAMAN (version 6) program (Lynnon Biosoft, San Ramon, CA, USA) with more than 70-nt overlapping regions to form the full-length viral genome.

To clone the TaRar1 gene, a pair of primers (forward and reverse) was designed using Primer 5.0 software. The primers were designed based on the cDNA sequence from our laboratory database, which was obtained from the interaction between the Suwon11 cultivar and CYR23 (avirulent) or CYR31 (virulent) (Table 1). The primers were used to amplify the open reading frame (ORF) of TaRar1. The template was a mixture of the first strand cDNA samples extracted from leaves of Suwon11 at 12, 24, 48, and 72 h post inoculated with CYR23 (an incompatible combination). The PCR products were cloned into the pGEM-T Easy Vector System (Promega, Madison, WI, USA) or the pMD18-T Simple Vector (TaKaRa Biotechnology)¹ and sequenced using an ABI PRISM 3130XL Genetic Analyzer (Applied BioSystems). The amino acid sequence of TaRar1 was analyzed to determine the alignment of the deduced protein sequences using the DNAMAN (version 6) program (Lynnon Biosoft, Quebec, Canada).