Contigexpress

PCR products were sequenced using BigDye technology and processed by Sanger sequencing by the Australian Genome Research Facility (AGRF). The resulting chromatograms were analysed using Contig Express (Vector NTI, Informax, Gaithersburg, MD, USA).
Viral RNA was extracted from samples using the Macherey Nagel Nucleospin RNA Virus isolation kit, following the manufacturer’s protocol. First strand cDNA was transcribed using Superscript III (Invitrogen, Carlsbad, CA, USA) according to the manufactures instructions and amplified using Phusion (Finnzymes, Thermo Fischer Scientific, Queensland, Australia) and sequenced by AGRF. The resulting chromatograms were analysed using Contig Express (Vector NTI, Informax, Gaithersburg, MD, USA).

To obtain the full-length cDNA of the rbcL and rbcS genes, DOP-PCR (degenerated oligonucleotideo-primed-PCR), 3′-RACE (rapid-amplification of cDNA ends) and 5′ TAIL-PCR (Thermal asymmetric interlaced polymerase chain reaction) were performed by using the double-stranded cDNA of SR and DR as a template, respectively. All primers, conditions and cycle settings for PCR were provided in Supplementary Tables S3, S4. The resulting PCR products were ligated into vector TA, cloned, and sequenced. Every sequence was confirmed by examining both strands; in addition, at least two bacterial clones obtained by TA cloning were examined. By assembling the sequences of 3′, 5′ and the core partial sequences on Contig Express (Vector NTI Advance11.5.1), the full-length cDNA sequence of rbcL and rbcS gene was deduced. The nucleotide sequence data for rbcL and rbcS, from SR and DR, have been deposited in the GenBank nucleotide sequence databases under accession no. KF697233, KF697234, KF697235, and KF697236, respectively. Finally, the sequence alignments between SR and DR were determined using AlignX (Vector NTI Advance11.5.1) (see Supplementary Figure S2).