Table S1BCMV Specific Primer Set for Full Genome Sequencing of NL-1N Isolate

Table S1BCMV Specific Primer Set for Full Genome Sequencing of NL-1N Isolate

Table S1BCMV specific primer set for full genome sequencing of NL-1n isolate

S. No. / Gene / Primer No. / Primer / Sequence / Product Size
1. / P1 / P1-1 / F / AACTTCTTTCTCTCACTTTCAAGCA / 454
R / CTTCTTCATAAAAATGAGGGACTTC
P1-2 / F / ACCAAGGAAGTCCCTCATTTTTAT / 594
R / TCTTGTTAGTGATTCCACTTTCCTC
P1-3 / F / GAGGAAAGTGGAATCACTAACAAGA / 514
R / ATTGATGCTACAGTAATGGTGTTGA
2. / HC-Pro / HC-Pro-1 / F / CACTCAACAGCCCTTTATGATTATT / 562
R / TAGAGCCAAGTCTAACTCTTCCTGA
HC-Pro-2 / F / GCTCACTCACAACAATAAAAGTACA / 565
R / ACTCTTGAGCTCCGAATACATTG
HC-Pro-3 / F / GATCATTGATTGTTCCTCTGAGTTT / 657
R / CTGTCTCACATTTCATTCTGTATGG
3. / P3 / P3-1 / F / GATGAAGCACTATAGAGTTGGAGGA / 613
R / TCTTCCTTCTGTGACTCTCTTGATT
P3-2 / F / ATGTAAATCGTTTAAAGCAGGAGTG / 644
R / CACCATAGTGAGTAAAGCCATGAAT
4. / 6K1 / 6K1 / F / AGTGATGAGTTTTTGGAACACCTT / 309
R / GTCAAAATCGATTGTCAACTTCTTC
5. / CI / CI-1 / F / GCAAACTAAAGACTGTGTTCCAAAC / 628
R / AACTCCTTAAGAGCACAGTTGAATG
C1-2 / F / TTGATGAGTGTCATGTTATGGATTC / 703
R / GACAACATGTTTGTGGTAACTCCTT
6. / CI& 6K2 / CI & 6K2 / F / ACAGTGTACAGTGAAACAAGCAAAA / 959
R / TGGTATATGCTTCACCAAATGTATG
7. / NIa-VPg / NIa-VPg / F / GCCATATTAGCTGTATTCACCCTAC / 716
R / CAAACCAAACTAGAGATGCCATTAT
8. / NIa-Pro / NIa-Pro-1 / F / CCTGAAAGAGAAGATGAACTCAGAC / 620
R / TTATTCGAGTCATTTGAAGTCAAGC
NIa-Pro-2 / F / GGCGAGTTTGAGATAAAGAATACAA / 649
R / GACACTTACCCTTCACTACATGCTT
9. / NIb / NIb-1 / F / GGTTTTGGCAACCAGATAAGATAG / 704
R / GTCCATAGGAGCAGCTGTAAAAGT
NIb-2 / F / GATATGGACGACTTTGATAAGGAAA / 716
R / TAGTTCAATCCCAGCTCTCTAAATG
NIb-3 / F / CAGAGGGAATAACAGTGGACAAC / 719
R / CTTTGTTGCTCTTCTCCTTCTTGT
10. / CP / CP / F / TGGCTGCTTGAGAGAGATGA / 1200
3’-UTR / R / GTTGGGTAAACTGACCACAG
11. / 5’-UTR / 5’RACE / 1R / TGTGTATGCGCTCAGGCCCGCGCA
2R / TGGCCTCAACTGAACAGCCCCCTTAGGTTGCTG
3R / CAGCTGCACAATGAAATCTCCAAAC
12. / 3’-UTR / 3’RACE / 1F / TCGGCAACGAGAGACAAGGATGTGA
2F / GCAAAGCCAACACTCCGCCAAATCAT
3F / GACCACAGTTAGCATCTCGCGTCGCTGA

Table S2 Comparative putative cleavage sites of the viral proteases in the polyprotein of BCMV strains

Cleavage sites
P1 / HC-Pro / NIa-Pro (A-F &V)
Virus / A / B / C / D / V / E / F
P1/HC-Pro / HC-Pro/P3 / P3/6K1 / 6K1/CI / CI/6K2 / 6K2/VPg / VPg/NIa / NIa/NIb / NIb/CP
BCMV-NL-1n / IHHY/SQ / YRVG/GD / VSVQ/AK / VQIQ/SL / VRLQ/GK / VTTQ/GV / VAVE/SK / VATQ/SK / VHLQ/SG
BCMV-NL-1 / IHHY/SQ / YRVG/GD / VSVQ/AK / VQIQ/SL / VRLQ/GK / VTTQ/GV / VAVE/SK / VATQ/SK / VHLQ/SG
BCMV-NL-4 / IHHY/SQ / YRVG/GD / VSVQ/AK / VQVQ/SL / VRLQ/SK / VTTQ/GV / VTTE/SK / VATQ/SK / VHLQ/SG
BCMNV-5 / IEHY/TH / YRVG/GD / VDTQ/AK / VRPQ/SL / VRLQ/GK / VTTQ/GV / VELE/SK / VSVQ/SK / VSTQ/SS
BCMNV-8 / IEHY/TH / YRVG/GD / VDTQ/AK / VRPQ/SL / VRLQ/GK / VTTR/GV / VELE/SK / VSVQ/SK / VSTQ/SS
BCMNV-3 / IEHY/TH / YRVG/GD / VDTQ/AK / VRPQ/SL / VRLQ/GK / VTTQ/GV / VELE/SK / VSVQ/SK / VSTQ/SS

Table S3 Nucleotide sequences used for phylogenetic analysis of NL-1n isolate of BCMV

S.No. / Accession No. / Virus / S. No. / Accession No. / Virus
1 / AY 112735 / BCMV-NL1 / 38 / AJ307057 / Leek yellow stripe virus (LYSV)
2 / KM023744 / BCMV-NL-1 / 39 / AJ564636 / Lily mottle virus (LMoV)
3 / EU761198 / BCMV-MS1 / 40 / AJ001691 / Maize dwarf mosaic virus (MDMV)
4 / DQ666332 / BCMV-NL4 / 41 / AJ510223 / Onion yellow dwarf virus (OYDV)
5 / NC_003397 / BCMV / 42 / BD171712 / Papaya leaf distortion mosaic virus (PLDMV)
6 / AY968604 / BCMV-Peanut stripe virus (PStV) / 43 / X67673 / Papaya ringspot virus (PRSV)
7 / U05771.1 / BCMV-Peanut stripe virus (PStV) / 44 / D10930 / Pea seed-borne mosaic virus (PSbMV)
8 / U34972.1 / BCMV-Peanut stripe virus ( PStV) / 45 / AF023848 / Peanutmottle virus (PeMoV)
9 / AJ 312437 / BCMV-cowpea isolate R (BCMV-CPR) / 46 / AY642590 / Pennisetum mosaic virus (PenMV)
10 / AJ 312438 / BCMV-cowpea isolate Y(BCMV-CPY) / 47 / M96425 / Pepper mottle virus (PepMoV)
11 / AY 575773 / BCMV-Blackeye cowpea mosaic virus(BlCMV) / 48 / AJ437280 / Peru tomato mosaic virus (PTMV)
12 / KJ645793 / BCMV-RU1M / 49 / D13751 / Plum pox virus (PPV)
13 / AY863025 / BCMV-RU1 / 50 / AJ296311 / Potato virus A (PVA)
14 / KF919297 / BCMV-RU1-OR-B / 51 / AJ243766 / Potato virus V (PVV)
15 / KF919298 / BCMV-RU1-OR-C / 52 / X12456 / Potato virus Y (PVY)
16 / KF919300 / BCMV-RU1-P / 53 / AJ865076 / Shallot yellow stripe virus (SYSV)
17 / GQ219793 / BCMV_RU1 / 54 / AJ310197 / Sorghum mosaic virus (SrMV)
18 / AY623626 / Agropyron mosaic virus (AgMV) / 55 / D00507 / Soybean mosaic virus (SMV)
19 / U19287 / Bean common mosaic necrosis virus (BCMNV) / 56 / D86371 / Sweet potato feathery mottle virus (SPFMV)
20 / HQ229993.1 / Bean common mosaic necrosis virus strain NL-5 (BCMNV-NL5) / 57 / AJ851866 / Thunberg fritillary mosaic virus (TFMV)
21 / HQ229994.1 / Bean common mosaic necrosis virus strain NL-8 (BCMNV-NL8) / 58 / M11458 / Tobacco etch virus (TEV)
22 / AY282577 / Bean common mosaic necrosis virus strain NL-3 (BCMNV-NL3) / 59 / X04083 / Tobacco vein mottling virus (TVMV)
23 / AY864314.2 / Bean common mosaic necrosis virus strain NL-3K (BCMNV-NL3K) / 60. / AF169561 / Turnip mosaic virus (TuMV)
24 / D83749 / Bean yellow mosaic virus (BYMV) / 61. / AY437609 / Watermelon mosaic virusFrench isolate (WMV-Fr)
25 / NC_005304 / Beet mosaic virus (BtMV) / 62. / AB218280 / Watermelon mosaic virus Pakistani isolate (WMV-Pk)
26 / NC_003501 / Brome streak mosaic virus (BrSMV) / 63. / AJ437279 / Wild potato mosaic virus (WPMV)
27 / AJ237843 / Chilli veinal mottle virus (ChiVMV) / 64. / AY656816 / Wisteria vein mosaic virus (WVMV)
28 / AB011819 / Clover yellow vein virus (ClYVV), / 65. / U42596 / Yam mosaic virus (YMV)
29 / AF499738 / Cocksfoot streak virus (CSV) / 66. / AF127929 / Zucchini yellow mosaic virus (ZYMV)
30 / AF348210 / Cowpea aphid-borne mosaic virus (CABMV)
31 / DQ299908 / Daphne virus Y (DVY)
32 / AJ298033 / Dasheen mosaic virus (DsMV)
33 / AB246773 / East Asian passiflora virus (EAPV)
34 / AY623627 / Hordeum mosaic virus (HoMV)
35 / AB027007 / Japanese yam mosaic virus (JYMV)
36 / Z26920 / Johnsongrass mosaic virus (JGMV)
37 / AB219545 / Konjak mosaic virus (KoMV)

Table S4 Pairwise similarity index of BCMV-NL-1n complete genome nucleotide sequence with other strains of BCMV determined by multiple alignment tool clustalW

BCMV-NL-1n(KF1140860) / BCMV-NL1(AY 112735) / BCMV-NL-1(KM023744) / BCMV-MS1(EU761198) / PStV(AY968604) / PStV(U05771.1) / PStV(U34972.1) / BCMV-CPY(AJ 312438) / BCMV-CPR(AJ 312437) / BlCMV(AY 575773) / BCMV-NL4(DQ666332) / BCMV(NC_003397) / BCMV-RU1(GQ219793) / BCMV-RU1-P(KF919300) / BCMV-RU1(AY863025) / BCMV-RU1-OR-C (F919298) / BCMV-RU1-OR-B(KF919297) / BCMV-RU1M(KJ645793) / BCMNV(U19287) / BCMNV-NL5(HQ229993.1) / BCMNV-NL8(HQ229994.1) / BCMNV-NL3(AY282577) / BCMNV-NL3K(AY864314.2)
BCMV-NL-1n(KF1140860) / - / 98 / 98 / 97 / 82 / 83 / 83 / 83 / 81 / 81 / 85 / 81 / 79 / 79 / 79 / 79 / 79 / 76 / 59 / 59 / 59 / 59 / 58
BCMV-NL1(AY 112735) / - / 99 / 97 / 82 / 83 / 83 / 83 / 81 / 81 / 86 / 81 / 79 / 79 / 79 / 79 / 79 / 76 / 59 / 59 / 59 / 58 / 59
BCMV-NL-1(KM023744) / - / 97 / 83 / 82 / 83 / 80 / 80 / 85 / 85 / 86 / 79 / 79 / 79 / 79 / 79 / 76 / 59 / 59 / 59 / 59 / 58
BCMV-MS1(EU761198) / - / 82 / 83 / 83 / 83 / 81 / 81 / 85 / 81 / 79 / 79 / 79 / 79 / 79 / 76 / 59 / 59 / 59 / 59 / 58
PStV(AY968604) / - / 92 / 92 / 80 / 79 / 79 / 80 / 79 / 78 / 78 / 78 / 78 / 77 / 75 / 60 / 60 / 60 / 60 / 59
PStV(U05771.1) / - / 100 / 81 / 79 / 80 / 81 / 79 / 77 / 77 / 78 / 78 / 77 / 75 / 60 / 60 / 60 / 60 / 59
PStV(U34972.1) / - / 81 / 79 / 80 / 81 / 79 / 78 / 78 / 78 / 78 / 76 / 75 / 60 / 60 / 60 / 60 / 59
BCMV-CPY(AJ 312438) / - / 89 / 87 / 84 / 89 / 82 / 82 / 82 / 82 / 81 / 78 / 59 / 59 / 59 / 59 / 59
BCMV-CPR(AJ 312437) / - / 93 / 81 / 100 / 85 / 84 / 84 / 84 / 84 / 81 / 59 / 59 / 59 / 59 / 60
BlCMV(AY 575773) / - / 81 / 93 / 84 / 84 / 84 / 84 / 83 / 81 / 59 / 59 / 59 / 59 / 60
BCMV-NL4(DQ666332) / - / 81 / 82 / 83 / 83 / 83 / 83 / 80 / 59 / 59 / 59 / 59 / 58
BCMV(NC_003397) / - / 85 / 84 / 84 / 84 / 84 / 81 / 59 / 59 / 59 / 59 / 60
BCMV-RU1(GQ219793) / - / 99 / 98 / 98 / 98 / 92 / 59 / 59 / 59 / 60 / 62
BCMV-RU1-P(KF919300) / - / 98 / 97 / 97 / 92 / 59 / 59 / 59 / 59 / 62
BCMV-RU1(AY863025) / - / 96 / 96 / 91 / 59 / 59 / 59 / 59 / 62
BCMV-RU1-OR-C( KF919298) / - / 99 / 92 / 59 / 59 / 59 / 59 / 57
BCMV-RU1-OR-B(KF919297) / - / 92 / 59 / 59 / 59 / 59 / 57
BCMV-RU1M(KJ645793) / - / 59 / 59 / 59 / 59 / 61
BCMNV(U19287) / - / 99 / 96 / 100 / 98
BCMNV-NL5(HQ229993.1) / - / 96 / 99 / 97
BCMNV-NL8(HQ229994.1) / - / 96 / 96
BCMNV-NL3(AY282577) / - / 98
BCMNV-NL3K(AY864314.2) / -

Table S5 Pairwise similarity index of BCMV-NL-1n complete genome deduced amino acid sequence of with other strains of BCMV determined by multiple alignment tool clustalW

BCMV-NL-1n(KF1140860) / BCMV-NL1(AY 112735) / BCMV-NL-1(KM023744) / BCMV-MS1(EU761198) / PStV(AY968604) / PStV(U05771.1) / PStV(U34972.1) / BCMV-CPY(AJ 312438) / BCMV-CPR(AJ 312437) / BlCMV(AY 575773) / BCMV-NL4(DQ666332) / BCMV(NC_003397) / BCMV-RU1(GQ219793) / BCMV-RU1-P(KF919300) / BCMV-RU1(AY863025) / BCMV-RU1-OR-C (F919298) / BCMV-RU1-OR-B(KF919297) / BCMV-RU1M(KJ645793) / BCMNV(U19287) / BCMNV-NL5(HQ229993.1) / BCMNV-NL8(HQ229994.1) / BCMNV-NL3(AY282577) / BCMNV-NL3K(AY864314.2)
BCMV-NL-1n(KF1140860) / - / 99 / 99 / 98 / 90 / 89 / 90 / 90 / 87 / 87 / 92 / 87 / 87 / 87 / 85 / 87 / 86 / 82 / 68 / 68 / 68 / 69 / 67
BCMV-NL1(AY 112735) / - / 99 / 98 / 90 / 89 / 90 / 90 / 87 / 87 / 92 / 87 / 87 / 86 / 85 / 87 / 86 / 82 / 68 / 68 / 68 / 68 / 66
BCMV-NL-1(KM023744) / - / 98 / 90 / 90 / 90 / 90 / 87 / 88 / 92 / 87 / 87 / 87 / 86 / 87 / 87 / 82 / 68 / 68 / 68 / 69 / 66
BCMV-MS1(EU761198) / - / 90 / 89 / 90 / 90 / 87 / 87 / 92 / 87 / 87 / 87 / 86 / 87 / 86 / 82 / 68 / 68 / 68 / 69 / 66
PStV(AY968604) / - / 95 / 95 / 88 / 86 / 86 / 88 / 86 / 86 / 86 / 85 / 86 / 86 / 82 / 69 / 69 / 68 / 69 / 67
PStV(U05771.1) / - / 100 / 88 / 86 / 87 / 87 / 86 / 86 / 86 / 84 / 86 / 85 / 82 / 68 / 68 / 68 / 68 / 66
PStV(U34972.1) / - / 88 / 86 / 87 / 88 / 86 / 86 / 86 / 85 / 86 / 86 / 82 / 68 / 68 / 68 / 69 / 66
BCMV-CPY(AJ 312438) / - / 93 / 92 / 91 / 93 / 89 / 89 / 88 / 89 / 89 / 85 / 68 / 68 / 68 / 68 / 66
BCMV-CPR(AJ 312437) / - / 96 / 88 / 100 / 91 / 91 / 90 / 91 / 91 / 87 / 68 / 68 / 68 / 68 / 69
BlCMV(AY 575773) / - / 89 / 96 / 91 / 91 / 90 / 91 / 91 / 88 / 68 / 68 / 68 / 68 / 69
BCMV-NL4(DQ666332) / - / 88 / 89 / 89 / 88 / 89 / 89 / 85 / 68 / 68 / 68 / 68 / 66
BCMV(NC_003397) / - / 91 / 91 / 90 / 91 / 91 / 87 / 68 / 68 / 68 / 68 / 69
BCMV-RU1(GQ219793) / - / 99 / 98 / 98 / 98 / 92 / 68 / 68 / 68 / 68 / 70
BCMV-RU1-P(KF919300) / - / 98 / 98 / 98 / 92 / 68 / 67 / 68 / 68 / 70
BCMV-RU1(AY863025) / - / 96 / 96 / 91 / 67 / 67 / 67 / 68 / 69
BCMV-RU1-OR-C( KF919298) / - / 99 / 92 / 68 / 68 / 68 / 68 / 69
BCMV-RU1-OR-B(KF919297) / - / 92 / 68 / 68 / 68 / 68 / 69
BCMV-RU1M(KJ645793) / 68 / 68 / 68 / 68 / 69
BCMNV(U19287) / - / 99 / 97 / 100 / 99
BCMNV-NL5(HQ229993.1) / - / 97 / 99 / 99
BCMNV-NL8(HQ229994.1) / - / 97 / 97
BCMNV-NL3(AY282577) / - / 99
BCMNV-NL3K(AY864314.2) / -
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