Supplementary Table 1Percentage nucleotide and amino acid sequence identity between ToLCJoV-[IN:Kal:Tom:08]and other selected begomoviruses

Begomoviruses / Abbreviation / Accession No. / DNAa / IR / AV1b / AV2b / AC1b / AC2b / AC3b / AC4b
Tomato leaf curl Joydebpur virus / ToLCJoV-[IN:Kal:Chi:06] / EF194765 / 93.6 / 76.1 / 99.2 / 96.6 / 91.6 / 97.7 / 99.2 / 78.7
Tomato leaf curl Joydebpur virus / ToLCJoV-[IN:Chi:06] / DQ673859 / 93.6 / 91.6 / 98.4 / 95.8 / 93.3 / 93.2 / 91.0 / 89.8
Tomato leaf curl Joydebpur virus / ToLCJoV-[BD:Joy:Tom:05] / AJ875159 / 91.4 / 83.4 / 98.8 / 94.2 / 91.1 / 92.5 / 88.8 / 73.7
Tomato leaf curl Joydebpur virus / ToLCJoV-[IN:Amad1:Ken:07] / EU431116 / 91.4 / 81.7 / 99.2 / 92.5 / 90.3 / 91.7 / 88.0 / 74.7
Tomato leaf curl Joydebpur virus / ToLCJoV-[IN:Amad2:Ken:07] / FJ345401 / 91.4 / 81.7 / 99.2 / 92.5 / 90.3 / 91.7 / 88.0 / 74.7
Tomato leaf curl Joydebpur virus / ToLCJoV-[IN:Pon:Ken:07] / FJ345402 / 91.2 / 82.1 / 98.4 / 90.9 / 90.0 / 91.7 / 88.0 / 73.7
Pepper leaf curl Bangladesh virus / PepLCBV-[BD:Chi:99] / AF314531 / 85.5 / 70.8 / 99.6 / 94.2 / 79.7 / 92.5 / 88.0 / 34.3
Tomato leaf curl Bangalore virus / ToLCBaV-[IN:Bang:Tom:07] / GU474418 / 78.7 / 57.4 / 90.6 / 68.5 / 83.3 / 83.5 / 78.3 / 72.7
Tomato leaf curl Gujarat virus / ToLCGuV-[IN:Pune:Tom:08] / HM625838 / 80.8 / 66.6 / 80.4 / 80.1 / 85.3 / 88.8 / 76.1 / 73.7
Tomato leaf curl Karnataka virus / ToLCKaV-[IN:BangII:95] / U38239 / 83.2 / 64.6 / 96.8 / 88.4 / 84.7 / 88.8 / 80.5 / 69.6
Tomato leaf curl Karnataka virus / ToLCKaV-[IN:Del:Tom:09] / HM803118 / 83.4 / 65.0 / 97.6 / 88.4 / 84.2 / 88.0 / 79.8 / 72.7
Tomato leaf curl Rajasthan virus / ToLCRaV-[[IN:Raj:05] / DQ339117 / 76.0 / 63.6 / 97.6 / 86.7 / 75.9 / 56.7 / 64.7 / 34.3
Tomato leaf curl Ranchi virus / ToLCRnV-[IN:Ran:Tom:07] / GQ994095 / 84.0 / 68.3 / 97.6 / 87.6 / 84.7 / 77.6 / 73.8 / 70.7
Tomato leaf curl Patna virus / ToLCPaV-[IN:Pat:Tom:08] / NC_012492 / 75.2 / 62.8 / 82.1 / 72.9 / 78.6 / 65.1 / 65.6 / 48.0
Tomato leaf curl Pune virus / ToLCPuV-[IN:Pun:05] / AY754814 / 80.5 / 58.6 / 91.7 / 70.2 / 86.7 / 82.0 / 76.1 / 72.7
Tomato leaf curl New Delhi virus / ToLCNDV-[IN:Del:Luf:10] / HM989845 / 72.4 / 51.4 / 93.7 / 63.6 / 76.7 / 53.9 / 65.4 / 34.3
Tomato leaf curl Palampur virus / ToLCPalV-[IN:Var:08] / FJ931537 / 71.0 / 50.0 / 89.8 / 66.1 / 73.0 / 55.3 / 64.7 / 32.3
Tomato leaf curl Bangladesh virus / ToLCBV-[BD:Tom:03] / AF188481 / 87.8 / 81.2 / 98.4 / 90.9 / 90.0 / 83.5 / 76.8 / 75.7
Tomato leaf curl Karnataka virus / ToLCKaV-[IN:Punj:Ment:07] / FJ514798 / 84.2 / 63.0 / 96.8 / 85.9 / 84.4 / 88.0 / 77.6 / 71.7
Tomato leaf curl Kerala virus / ToLCKeV-[IN:Tom:08] / EU910140 / 81.9 / 63.1 / 96.0 / 86.7 / 84.2 / 87.3 / 79.8 / 48.4
Tomato leaf curl Bangalore virus / ToLCBaV-[IN:Har:Cot:03] / AY456684 / 81.8 / 68.2 / 91.0 / 70.2 / 88.0 / 83.5 / 80.5 / 77.7
Pepper leaf curl Pakistan virus / PepLCPKV-[PK:Chi:05] / DQ116878 / 84.5 / 58.4 / 96.8 / 85.9 / 89.1 / 91.0 / 83.5 / 73.7
Tomato leaf curl Pakistan virus / ToLCPKV-[PK:Naw:Gly:08] / AM948961 / 84.5 / 75.4 / 98.4 / 89.2 / 86.4 / 87.3 / 79.8 / 50.5
Tobacco curly shoot virus / TbCSV-[CN:Pep:09] / GU001879 / 84.2 / 70.2 / 98.0 / 87.6 / 85.0 / 77.6 / 74.6 / 72.7
Papaya leaf curl virus / PaLCuV-[PK:Kun:Rhy:08] / FM955601 / 81.7 / 65.7 / 98.0 / 87.6 / 79.5 / 87.3 / 79.8 / 24.2
Papaya leaf curl virus / PaLCuV-[IN:Pa:97] / Y15934 / 79.7 / 64.4 / 96.8 / 85.1 / 74.7 / 79.8 / 75.3 / 34.3

a Nucleotide sequence identity.

b Amino acid sequence identity.

The highest identities in each column are highlighted in bold.

Supplementary Table 2 Comparison of amino acid sequence identity between unknown ORF of ToLCJoV-[IN:Kal:Tom:08]

Begomoviruses / Abbreviation / Accession No. / Start-Stop / MW / AA / Unknown ORF
Tomato leaf curl Joydebpur virus / ToLCJoV-[IN:Kal:Tom:08] / JN176565 / 970-296 / 25.0 KDa / 224 / --
Tomato leaf curl Joydebpur virus / ToLCJoV-[IN:Kal:Chi:06] / EF194765 / 967-287 / 25.3 KDa / 226 / 96.0
Tomato leaf curl Joydebpur virus / ToLCJoV-[IN:Chi:06] / DQ673859 / 1144-296 / 31.6 KDa / 282 / 66.3
Tomato leaf curl Joydebpur virus / ToLCJoV-[BD:Joy:Tom:05] / AJ875159 / 1139-291 / 30.7 KDa / 282 / 72.6
Tomato leaf curl Joydebpur virus / ToLCJoV-[IN:Amad1:Ken:07] / EU431116 / 971-297 / 25.0 KDa / 224 / 92.8
Tomato leaf curl Joydebpur virus / ToLCJoV-[IN:Amad2:Ken:07] / FJ345401 / 971-297 / 25.0 KDa / 224 / 92.8
Tomato leaf curl Joydebpur virus / ToLCJoV-[IN:Pon:Ken:07] / FJ345402 / 971-297 / 25.0 KDa / 224 / 91.5

The highest identities in column are highlighted in bold.

Supplementary Table 3Percentage nucleotide and amino acid sequence identity between ToLCJoB and other selected begomoviruses

Betasatellites / Abbreviation / Accession No. / DNA-βa / βC1b
Tomato leaf curl Joydebpur betasatellite / ToLCJoB-[IN:Ama1:Ken:07] / EU431115 / 96.7 / 90.4
Tomato leaf curl Joydebpur betasatellite / ToLCJoB-[IN:Ama2:Ken:07] / EU880232 / 96.7 / 90.4
Tomato leaf curl Joydebpur betasatellite / ToLCJoB-[IN:Pond:Ken:07] / EU880233 / 96.4 / 90.4
Tomato leaf curl Joydebpur betasatellite / ToLCJoB-[BD:Joy:Tom:05] / AJ966244 / 93.2 / 85.7
Tomato leaf curl Joydebpur betasatellite / ToLCJoB-[IN:Kal:Chi:06] / EF190216 / 91.9 / 82.5
Tomato leaf curl Joydebpur betasatellite / ToLCJoB-[IN:Kal:Chi:06] / NC_010236 / 91.9 / 82.5
Tomato leaf curl betasatellite / ToLCB-[IN:Bih6:10] / GU732206 / 76.0 / 67.4
Tomato leaf curl Patna betasatellite / ToLCPaB-[IN:PUSA2:10] / HQ180394 / 75.3 / 71.4
Tomato leaf curl betasatellite / ToLCB-[IN:Bih3:10] / GU732205 / 75.4 / 65.8
Tomato leaf curl Bangladesh betasatellite / ToLCBB-[IN:Bih09:10] / HQ257376 / 65.6 / 38.2
Tomato leaf curl betasatellite-Panipath / ToLCB-Pani[IN:Pani:Pap:08] / HM143902 / 67.0 / 56.3
Tomato leaf curl Bangladesh betasatellite / ToLCBB-[IN:PUSA3:10] / HQ180395 / 67.2 / 55.5
Tomato leaf curl betasatellite-DU / ToLCB-DU[IN:Del:Pap:09] / HM143910 / 66.9 / 52.3
Tomato leaf curl Patna betasatellite / ToLCPaB-[IN:Pat:Tom:08] / EU862324 / 75.9 / 65.0
Tomato leaf curl Bangladesh betasatellite / ToLCBB-[IN:Bih9:10] / GU732208 / 65.7 / 38.2
Tomato leaf curl Bangalore betasatellite / ToLCBaB-[IN:Hess:Tom:08] / GU984046 / 56.5 / 57.9
Tomato leaf curl Pune betasatellite / ToLCPuB-[IN:Pune:04] / AY754815 / 57.1 / 57.9
Tomato leaf curl Karnataka betasatellite / ToLCKaB-[IN:Janti:04] / AY754813 / 61.0 / 58.7
Tomato leaf curl Maharastra betasatellite / ToLCMaB-[IN:Pune:04] / AY838894 / 57.2 / 57.1

a Nucleotide sequence identity.

b Protein sequence identity.

The highest identities in each column are highlighted in bold.