Electronic supplementary material
Table S1.Specific primer pairss used in this study
Amplified region / Locating position / Specific primer pairs / TM(℃) / Product length
The two contigs / 31~393 / F: GCCACAAAATATACGAAGAGAGAG / 58.6 / 362
R: GAGATTGTCATCGGTTTGGAGC / 60.1
193~1537 / F: TTCTTCGCTCTATTTGTGCT / 53.7 / 1344
R: TGCTCTTGACTTCAGTTTCG / 55.8
1310~2842 / F: CGCTGGAGGTGAGAATGGAC / 61.9 / 1532
R: GCAATCAGTTGGCACAAGGT / 57.8
2050~3733 / F: ACCACCCGAAGCAAATCA / 55.0 / 1683
R: ACCACAACGACAGGGCGAAC / 61.9
3561~4020 / F: CAATCCCAATTTCTGTAGCA / 53.7 / 459
R: GGGTTCAGTATCCCAGTT / 55.0
4595~5987 / F: TGGCGGCGATCTCGATGGTA / 61.9 / 1392
R: CTGCGGGTTTCGTTGCTGTG / 61.9
4247~4973 / F: CAACATACGCTTCGTCAGTG / 54.7 / 726
R: CGGATAAGACCACGCCATTT / 56.5
Sequences between
the two contigs / 3768~4335 / F: AGACGACGAAATGGAGGC / 55.2 / 567
R: CTGGCAAGGTTGAGGAGTT / 56.1
Table S2.Pepper vein yellows virus isolates used in this study
Collection-Year / Host reported from / Isolate / Country reported / NCBI Accession Number / Reference2009 / hot pepper / Ma2 / Sudan（Africa） / KC692834
2009 / hot pepper / Ma4 / Sudan（Africa） / KC692833
2010 / hot pepper / VIF8 / Sudan（Africa） / KC685326 / CP,MP
2010 / hot pepper / S10 / Sudan（Africa） / KC685325 / CP,MP
2010 / hot pepper / S9 / Sudan（Africa） / KC685324 / CP,MP
2010 / hot pepper / S8 / Sudan（Africa） / KC685323 / CP,MP
2010 / hot pepper / S7 / Sudan（Africa） / KC685322 / CP,MP
2010 / hot pepper / S6 / Sudan（Africa） / KC685321 / CP,MP
2010 / hot pepper / S2 / Sudan（Africa） / KC685320 / CP,MP
2009 / hot pepper / Ma7 / Sudan（Africa） / KC685319 / CP,MP
2009 / hot pepper / Ma6 / Sudan（Africa） / KC685318 / CP,MP
2009 / hot pepper / Ma5 / Sudan（Africa） / KC685317 / CP,MP
2009 / hot pepper / Ma4 / Sudan（Africa） / KC685316 / CP,MP,RdRP
2009 / hot pepper / Ma3 / Sudan（Africa） / KC685315 / CP,MP
2009 / hot pepper / Ma2 / Sudan（Africa） / KC685314 / CP,MP,RdRP
2009 / hot pepper / Ma1 / Sudan（Africa） / KC685313 / CP,MP
2013 / Capsicum annuum / 8-13 / Spain (Europe) / KC839994
2013 / Capsicum annuum / 7-13 / Spain (Europe) / KC839993
2013 / Capsicum annuum / 2-13 / Spain (Europe) / KC839992
2013 / Capsicum annuum / 1-13 / Spain (Europe) / KC839991
2013 / Capsicum annuum / Almeria-1 / Spain (Europe) / KC769487
2009 / Capsicum sp. (chilli) / pTW3 / Taiwan (Asia) / JX427543 / CP,MP,RdRP
2009 / Capsicum sp. (chilli) / pTW1 / Taiwan (Asia) / JX427542 / CP,MP,RdRP
2009 / Capsicum sp. (chilli) / pTH4 / Thailand (Asia) / JX427541 / CP,MP,RdRP
2009 / Capsicum sp. (chilli) / pTH13 / Thailand (Asia) / JX427540 / CP,MP,RdRP
2009 / Capsicum sp. (chilli) / pTH1 / Thailand (Asia) / JX427539 / CP,MP,RdRP
2010 / Capsicum sp. (chilli) / pPH3 / Philippines (Asia) / JX427538 / CP,MP,RdRP
2009 / Capsicum sp. (chilli) / pPH2 / Philippines (Asia) / JX427537 / CP,MP,RdRP
2009 / Capsicum sp. (bell pepper) / pMA3 / Mali（Africa） / JX427536 / CP,MP,RdRP
2009 / Capsicum sp. (bell pepper) / pMA2 / Mali（Africa） / JX427535 / CP,MP,RdRP
2009 / Capsicum sp. (chilli) / pIN1 / India (Asia) / JX427534 / CP,MP,RdRP
2009 / Capsicum sp. (chilli) / pID12 / Indonesia (Asia) / JX427533 / CP,MP,RdRP
2009 / Capsicum sp. (chilli) / pID10 / Indonesia (Asia) / JX427532 / CP,MP,RdRP
2009 / Solanum nigrum L. (black nightshade) / nIN1 / India (Asia) / JX427531 / CP,MP,RdRP
2013 / Capsicum annuum / HN / China (Asia) / KP326573 / CP,MP,RdRP
2009 / Capsicum annuum L. Var. grossum Sendt / JP / Japan (Asia) / AB594828 / CP,MP,RdRP
2011 / Capsicum annuum / Turkey 1281 / Turkey (Europe) / HE978265
2011 / Capsicum annuum / Tunisia151 / Tunisia（Africa） / HE978264 / RdRP
2011 / Capsicum annuum / Tunisia62 / Tunisia（Africa） / HE978263
2011 / Capsicum annuum / Tunisia45 / Tunisia（Africa） / HE978262 / RdRP
2011 / Capsicum annuum / Tunisia7 / Tunisia（Africa） / HE978261 / RdRP
Table S3. Comparison of nucleotide and amino acid differences in the coat protein, movement protein and RNA- dependent RNA polymerase coding regions within subpopulations of pepper vein yellows virusa
Protein encoding region / Lineage / The number of sequences / Nucleotide / Amino acidDifferences / Standard error / Differences / Standard error
Coat protein / Africa / 14 / 0.03485 / 0.00731 / 0.00605 / 0.00422
Asia / 15 / 0.02330 / 0.00440 / 0.01622 / 0.00556
All / 29 / 0.03979 / 0.00651 / 0.01625 / 0.00543
Movement protein / Africa / 14 / 0.01358 / 0.00531 / 0.03997 / 0.01599
Asia / 15 / 0.02418 / 0.00721 / 0.03682 / 0.01571
All / 29 / 0.02104 / 0.00819 / 1.17397 / 1.87786
RNA- dependent RNA polymerase / Africa / 5 / 0.02285 / 0.00491 / 0.01622 / 0.00577
Asia / 15 / 0.05557 / 0.00654 / 0.00605 / 0.00445
All / 20 / 0.05734 / 0.00630 / 0.01625 / 0.00561
LOCUS KP326573 6244 bp RNA linear VRL 03-JUN-2015
DEFINITION Pepper vein yellows virus putative P0 protein gene, complete cds.
ACCESSION KP326573
VERSION KP326573.1 GI:824327268
KEYWORDS .
SOURCE Pepper vein yellows virus
ORGANISM Pepper vein yellows virus
Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
stage; Luteoviridae; Polerovirus.
REFERENCE 1 (bases 1 to 6244)
AUTHORS Liu,M.
TITLE Direct Submission
JOURNAL Submitted (31-DEC-2014) College of Plant protection, Hunan
Agricultural University, Renmin East Road 1, Changsha, Hunan
410128, P.R. ChinaCOMMENT ##Assembly-Data-START##
Sequencing Technology :: Sanger dideoxy sequencing
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..6244
/organism="Pepper vein yellows virus"
/mol_type="genomic RNA"
/isolate="HN"
/isolation_source="flowerbud"
/host="pepper"
/db_xref="taxon:909827"
/country="China"
/collection_date="07-Jul-2013"
CDS 52..801
/codon_start=1
/product="putative P0 protein"
/protein_id="AKI85236.1"
/db_xref="GI:824327269"
/translation="MNFELINGSHLKVSLTRKLSYRERILNLAVFLSQYLVTVQENAT
TSHFLRSICALLPFLLSSQCPFLSGNTPHRNGKREQKRVSKLALYCGVNITPCWNGEA
FSSTWLQTDNNLGAPRTHLKRCAGSALASYIQRFQTPLFQGSEEFSRFLCVWTHHCEN
VVERSFPKLSVDRGLIVELWHLGHCLLDLLSGDDIYHARRLSRIALRLHRIYGEGIAM
DVYRLAHLPRSVSFKSGEDYLHGSQIQKELQ"
ORIGIN
1 acaaaatata cgaagagaga gagcccttgc ttgtgatttc ttcaaagttt catgaacttt
61 gaattgatta acggaagcca tcttaaagtt tccctcactc gcaagctcag ttacagagaa
121 agaattttaa atttggcagt attcttgagc caatatctcg taaccgtaca agaaaatgca
181 accacaagtc attttcttcg ctctatttgt gctctcctcc ctttccttct cagcagccaa
241 tgtccctttt tatcagggaa tacaccgcac cggaacggca agcgggaaca gaagcgagtc
301 tctaagctcg ctctttactg tggagttaac atcactcctt gctggaatgg agaggccttt
361 tcctccactt ggctccaaac cgataataac ctcggagccc cacgaaccca ccttaagaga
421 tgcgctggat ctgctttggc aagttatatc cagagattcc agacgcctct cttccaaggc
481 tcagaagaat tttcaagatt cttgtgcgta tggactcacc actgcgaaaa cgtggttgaa
541 aggagctttc caaagctttc tgtggaccgt ggtctcattg tggagctttg gcatctgggt
601 cattgtctcc tggacctttt atctggtgac gacatttacc atgcccgtcg tttgtctcgc
661 attgctttac gcctgcacag aatttatggt gaaggcattg cgatggatgt ttaccggctg
721 gctcacttgc ctcgctctgt tagttttaaa agtggggaag actatcttca cggttcccaa
781 attcagaagg aactacagtg aagagaaaca agttaaggga tttatttctt tgaaaatccc
841 ccaaagcccc ccccgtggaa gcgtgctact cgtgcaacat gaagacaact ctcatgccgg
901 gtatgctagc tgtgtacggt tgtatgacgg cactttagcc ctcatgacct gtcaccacgt
961 gggcacaggg gttcccggag gaaaggtgac ctctacgaaa acacctaaca agataccact
1021 ccgcctattc acacctctga tctcttcaga aaaaggagat ttcatgttaa tgagcgggcc
1081 cccaaattgg gagagcctgt taggctgtaa aggagcccac ttcgtttccg catcacaact
1141 tgctaaatct aagatgcggt ttttcttcat tgagaagaac gagtggatgg ctgatcacgg
1201 tgagattgta ggtccacgtg atcactggtt tgctacaacg ctctgcaact cagagcctgg
1261 acactctggc accccgatct ttaatggcaa aaccatagtg ggtgtgcacg ctggaggtga
1321 gaatgaacag aacttcaatg tgatggcaac gatccctccc gtccccggtt tgacgacccc
1381 tcagtatgtc ttcgagacta ctgcccctca gggtcgagtc ttcactgatg aggacttaag
1441 cgagatgatg aagagcgtca cctcatatcc ccagttggaa aagttcaaaa gccatactgg
1501 gaagaactgg gcagatgatg aagacttcga agctgaagtc aagagcaaac ccaccccagc
1561 acccgtggct caagaagcta aacccaagag cggtgctgag gaagctccgc cggtgagtaa
1621 atcccggcag tggtatccac gtcttcccga gtcgggaaac gagaaaggca gagctgtctg
1681 ccaaaccaac agcaaccctg cccctgcaca agagaagggc aaggagaagg aggtagaggc
1741 cgaaaaggcc cccgcatcgc ccaccccctc aaagcttcca gaatcagccg acggcggcga
1801 aaaatattta gagaagcttt tagagaagct agtggagagg atcgaccttt ccactataga
1861 aaagaaagtg gtggaagtgg tggctcagaa agccatgaag aagccccagg gaagccagcg
1921 gcgcagacga ccgcggagaa cttccaacga tacttcgaag gaagctacaa atgggaggta
1981 ccagcctcct cacaagagat cccagggttc caacaatgcg gaagcctccc ccagtactac
2041 cacccaaaac aaatcaaagg tagtgactgg ggctcccagc tcatccaaga gcacccagag
2101 ctgggagaga aagtctccgg cttcggctgg ccagcagtag gcccccaagc cgaggtgacc
2161 tctctcactt tacaagcaga gaggtggctg caacgcgcgc agtcagctaa aaccccgtcg
2221 tctgaggacc gggagcgcgt cattaacaaa actgtggagg cctattccaa tgttaaaacc
2281 tttggcccca cagctactag agggaacaag ctcgagtggc ggcaatttct agaagatttt
2341 aagtcagccg tcttctcttt ggagcttgat gcaggtatag gcgtaccata catcgcctat
2401 ggaaggccca ctcacaaagg ttgggtggaa gacccgaaac tcctgccagt gctcgcccga
2461 ctcactttca accgtttaca gaagatgttg gaagtcgagt cttctgatat gagcgctgaa
2521 gagcttgttc aagctggtct ctgtgatcct ataaggactt ttgtgaagag agaaccgcac
2581 aagcaatcta aactcgatga aggacgctac cgcctcatca tgagtgtttc cctagtagat
2641 caattggtag cccgggttct gttccaaaac cagaacaagc gagaaatcgc actttggagg
2701 gctaatccct caaaacccgg ttttggcttg tcaactgacg agcaagtgct ggagttcgta
2761 caagctctgg ccgcacaagt gggagcccct gtggaggaag tgattacctc atgggataaa
2821 taccttgtgc cgactgactg ctccggtttt gactggagcg ttgcggaatg gatgctctat
2881 gacgatatgg tcatccgcaa caaactcaca ctagacttaa atcctacaac ggagaagctg
2941 cgctttgcgt ggctgaagtg cattagcaac agtgtcttgt gtttgagtga tggcactctc
3001 cttgcccaac gggtccccgg tgttcaaaag tctggtagct acaatacaag tagctctaat
3061 tcaaggattc gggtcatggc cgcatatcat tgtggagccg actgggccat tgcaatggga
3121 gacgatgctc ttgagtcagt caacaccaac ctagaggtgt ataaagatct aggtttcaaa
3181 gtcgaggttt caggacaact ggaattctgc tctcacatct ttagagcgcc tgacctcgcc
3241 cttcccgtga atgagcgtaa aatgctgtac aagctcatct tcggatataa tccgggaagt
3301 gggaatctgg aggtgatctc caattacatt gccgcctgtg tatcagtttt gaatgaactg
3361 cggcatgacc cagattctgt tgctctcctt cactcgtggc tagtctctcc agtgctgcca
3421 caaaataatt gaagagagag catataacta gccaagcata catcagttgc aagcgttgga
3481 aagttttagt ctgattacca acagcctgac acaatagatt ataaattttt agcaggattt
3541 gcgtttggat ttttatccgc aatcccaatt tctgtagcag gcatatacct agtctacctt
3601 aagatctcag cccacgttcg cgcaatcgtt aatgaatacg ggaggagtta ggagaaacaa
3661 caatggaaat ggtggatcac gtaacacccg ccgtcgtaga cgcccacgac aggttcgccc
3721 tgtcgttgtg gtcgcacccc ctgggcgcac acggcgagga aatcgaagac gacgaaatgg
3781 aggcaggaac cgaagaagcc gagatagagt tggaggaagg tcgagcaaca gcgaaacttt
3841 catcttcaac aaggactcaa tcaaggatag ttcctcagga tctgtcacct tcgggccgtc
3901 tctatcagag agcgtcgcgc tttcaggtgg agttctcaaa gcctaccatg aatataagat
3961 cacaatggtc aacatacgct tcgtcagtga atcctcttcc acagcggagg gctccatcgc
4021 ttacgagctg gacccccact gcaagcttac tagtctccaa tccaccctgc gtaagttccc
4081 cgtcaccaaa ggcgggcaag cgacttttcg ggcttcgcag attaacgggg tagagtggca
4141 tgatacatcc gaagatcaat ttaggctgct ctacaaaggc aatgggacga agaacgttgc
4201 cgccggtttc ttccagatcc ggttcaccgt gcaattgcac aacccgaaat aggtagaagg
4261 tagtaccccc cccccccccc ccccttcagg tcccgaaccg ccaccacccg cgccaactcc
4321 tcaaccttgc cagaaaagca ggttttgggg ttatgaaggt aatccgcaga acaagattct
4381 gacggcagag aatgatagaa atatcgactc tcgaccgttg aaatttgtct cgatgtacaa
4441 gtgggaagat gagaaatggg acaaagtcaa cctccaagct ggttattctc gaaatgatcg
4501 gcggtgtatg gaaacgtacc tcactattcc agcagacaaa ggaaaattcc atgtctatct
4561 tgaagctgat ggtgaatttg tcgtcaagca tattggcggc gatttggatg gtagttggct
4621 tggcaacatt gcctatgatg tctctcaacg cggttggaca gtggggaatt acaaaggttg
4681 caagattaaa aattttcaaa ccaacacaac ttttgtagcg gggcacccgg atgcaaagat
4741 gaatggtaaa actttcgaca atgcccgggc agtagaagtt gattggttcg cttcctttga
4801 acttgaatgt gatgatgaag aaggaagctg gatgatttat ccccccccga tccagaaaga
4861 tgcctcttat aattacaccg tgtcctacgg aaattatacg gagaagtatt gtgagtgggg
4921 agccatttct gtttctattg atgaagataa tgaggggtat gcagcaagaa gaataccgcg
4981 caagggggaa atggcgtggt cagatccgga aaaagattac tccaaaaaca aaccccagaa
5041 ggaaaactgg aatactgaac ccctggaccc aggtgaaata cagcgagaaa gacaactcgt
5101 taaaactccg tctccggatg tctctgattc tggttcagag ttcaggacag atcctgtgcc
5161 tcaggatctg atcgataaag tgaataaggg agaagcattg gatcctatgc aacaacttga
5221 gtatgataaa tataggttcc gagataacat tatcgagctc ggcgggtcag aagatcaatc
5281 ttccgagtac ccaaagcttc cccccctcat cccacataag ccgcttcacc caggcaggac
5341 tgtaaagccc ttcaagccta gtgctgatct tttagaagcc tgggacaagg accacttcga
5401 ccccggttat acgaaggaag aagtggcagc ggctacaata atctctcacg gttctataac
5461 agatgggaga aatgctttgg aagaaaggga taacaagatc cagcgagctc gaatctcctg
5521 gtctgaggat aagaaaccga ttagtccgtc catagcaagg ttgagagaaa aagccgctga
5581 aaagcgagct ttaactggcg ggtctttgag acctaagtct gaaaccgcct cctctatagg
5641 gggtggatct attgttggtg gttctttgaa gccgaaggtt tccgtggaag agagcattgt
5701 ctctcaactt tcaactgctc aaagaatgga gtacgaacaa ctcaaggcga agaaccaagc
5761 ggctgccact gagtatttgt ggtctgttca agttccgcca tcaaaaccac ccggcccgtc
5821 cagttttaca aggcgatcct agctctagga ccttaaattc tgtgagcata atttgtagtc
5881 taagctctat gactataaaa taacgagcac actgaactcc aagcctgtta gagtataacc
5941 caggtcgtct tagctgtatg acgttaaaat aacgagcata ctgaactcca agcctgttag
6001 agtataaccc aggcagtcta agctctatga ctttaaaata acgagcgtac tgaactccaa
6061 gcctgttaga gtataaccca ggtcgtcatt agctgtagac gtaaaatcag cggtccagtg
6121 ttgaaggctg taaagcactg agtaacttac agcaacgaaa cccgcagaca gatctgtgtg
6181 gaagtaggca tcataattct tagggtaggg gggtgtatag ataccccccc ctggtctatg
6241 atgt
92% sequence identity with the Japanese PeVYV genome sequence at the nucleotide levels
92% sequence identity with the Japanese PeVYV genome sequence at the amino acid levels