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Table S1. Primers used in this study Virus or Forward Primer (5'-3') Reverse Primer (5'-3') Size Gene ID (bp) For detection of apple viruses and viroids ASGV GGAATTTCACACGACTCCTAACCC CCCGCTGTTGGATTTGATACACCTC 500a TCC 794b ACLSV GAGARTTTCAGTTTGCTMGA AGTCTACAGGCTATTTATTATAAGT ASPV ATGTCTGGAACCTCATGCTGC TTGGGATCAACTTTACTAAAAAGC AA ATAA ASSVd CTCGTCGTCGACGAAGG CAGCACCACAGGAACCTCACGG 278d ADFVd GAGGAAAACTCCGTGTGGTTC AAGTCCACTCCCTGCCAGACC 274e Actin AACTGGGATGACATGGAGAAGAT CCCTCCAATCCAGACACTGTAC 797 370c For expression analysis by quantitative real-time PCR MDP00005 CGGGTCTGCTTCTTTGCTCA AGGACTGTTTGGCGACATTGG ACCGAAGGGTAAGGGAGATG TGGAGGCTTGTGTGGTGGTT 180 01598 MDP00003 03449 MDP00005 85239 MDP00001 181 A CAAGCAGCAGAAATAGCAACY AATGAGCAGCGAGCGTAGA 222 G TTTCATCACCGCCATCCGT AGAGGCATTGTGAGAGCATTCT CAAGGGCACGAAAGTGGATT TCCCAGTCATACACACCAAGA ATTTCTGGTCGGGTCTGTCG CGTTATCCTTCCACTGCCRAG GCATCCAATCCCTCATCAACG CCAGTCAGCCACACCAAAGA CTTAGGGTTTGTCTCCTTCATC GACCTTTCCATCCTGTGGCTA 199 29445 MDP00002 97 27287 MDP00002 176 79459 MDP00008 196 59492 MDP00004 78473 MDP00004 152 AC ATTTCGGGATTGGGCACA GCGATGTATTGGTGATGAGTAT ACAACCGAAATGGAAACCGA GGAACTCACTCCGAATAGTCCT 256 41013 MDP00006 91215 MDP00005 91 G ATTGGGTCTCTCTGCCAGGT AGGGTGTCCTAAAGTTYCRCCA CCTAAAGAGATTCCGCTCCCT GTCAGCCATAGACCTCCAGT TTCGTGAACCTGTTTCTGG GCAACAACAATCCAAGGG CTATGTTCCCTGGTATTGCAGA GCCACAACCTTGTTTTTCATGC 131 97996 MDP00004 176 64827 MDP00003 250 27226 actin2 CC a James D. 1999. A simple and reliable protocol for the detection of apple stem grooving virus by RT-PCR and in a multiplex PCR assay. Journal of Virological Methods 83, 1–9. b Yaegashi H, Isogai M, Tajima H, Sano T, Yoshikawa N. 2007. Combinations of two amino acids (Ala40 and Phe75 or Ser40 and Tyr75) in the coat protein of apple chlorotic leaf spot virus are 1 82 crucial for infectivity. Journal of General Virology 88, 2611–2618. c Menzel W, Jelkmann W, Maiss E. 2002. Detection of four apple viruses by multiplex RT-PCR assays with coamplification of plant mRNA as internal control. Journal of Virological Methods 99, 81–92. d Zhao Y, Niu J. 2008. Apricot is a new host of Apple scar skin viroid. Australasian Plant Disease Notes 3, 98–100. e Li R, Mock R, Huang Q, Abad J, Hartung J, Kinard G. 2008. A reliable and inexpensive method of nucleic acid extraction for the PCR-based detection of diverse plant pathogens. Journal of Virological Methods 154, 48–55 2 3
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