Suppl. Fig 1. Multiple alignment of coat protein (CP) of 26 Garlic common latent virus(GarCLV) isolates from diverse geographical origin showing variability in amino acid sequences at the N-terminal of CP.
Suppl. Fig. 2. . Graphical representation of recombination event detected in CP of GarCLV-Anand isolate with maximum recombinant probability value (P value) of 3.018x10-02. Recombination breakpoints were estimated using the 3Seq and SiScan algorithms of RDP3. The breakpoint for the recombination events lies between nucleotide positions from 167 to 5 as shown in pink region.
Suppl Table 1. Sequence identity (%) of Garlic common latent virus (GarCLV) Indian isolates from garlic with other carlaviruses infecting diverse plant species.
S. no / Name of the virus / Acronym / Accession number in GenBank / Percent identity (Nt/AA) with Indian isolates of GarCLV1 / Narcissus symptomless virus / NSV / AM182569 / 49/40-42
2 / Sweet potato chlorotic fleck virus / SPCFV / AY461421 / 42-43/30-31
3 / Red clover vein mosaic virus / RCVMV / NC_012210 / 45-46/43-36
4 / Narcissus common latent virus / NCLV / AM158439 / 43/34-36
5 / Hop mosaic virus / HpMV / NC_010538 / 44/34-35
6 / Coleus vein necrosis virus / CVNV / NC_009764 / 61-62/57-60
7 / Cole latent virus / CoLV / AY340584 / 33-34/30-32
8 / Aconitum latent virus / AcLV / AB051848 / 42-43/33-34
9 / Blueberry scorch virus / BlScV / NC_003499 / 43-44/31
10 / Carnation latent virus / CLV / X52627 / 58-59/58-61
11 / Chrysanthemum virus B / CVB / NC_009087 / 40-41/30-31
12 / Cowpea mild mottle virus / CPMMV / AF024629 / 41-42/32-33
13 / Hop latent virus / HpLV / EF394784 / 43/32-33
14 / Lilly symptomless virus / LSV / HM222522 / 40/31-32
15 / Melon yellowing associated virus / MYaV / AY373028 / 40/27-28
16 / Passiflora latent virus / PLV / NC_008292 / 41/32-33
17 / Pea streak virus / PeSV / AF354652 / 44-45/34-35
18 / Potato latent virus / PotLV / EU433397 / 40-41/33-34
19 / Potato virus M / PVM / JN835299 / 42-43/34-36
20 / Potato virus P / PVP / NC_009759 / 44/32-33
21 / Potato virus S / PVS / HQ875141 / 43-44/33-34
22 / Shallot latent virus / SLV / JF320811 / 46/40-41
23 / American hop latent virus / AHLV / JQ245696 / 40-41/29
24 / Daphne virus S / DVS / AJ620300 / 43-44/34-35
25 / Butterbur mosaic virus / ButMV / AB517596 / 56/51
26 / Hellebores mosaic virus / HeMV / FJ196838 / 47/39
27 / Hellebores net necrosis virus / HeNNV / AB623047 / 49/45-46
28 / Hydrangea chlorotic mottle virus / HdCMV / EU754720 / 42-43/30
29 / Kalanchoe latent virus / KLV / AY238142 / 40/33
30 / Lingustrum necrotic ringspot virus / LNRSV / EU074853 / 40-41/31
31 / Mirabilis jalapa mottle virus / MjMV / JN039374 / 37-38/29-30
32 / Phlox virus B / PhlVB / EU162589 / 43-44/36
33 / Phlox virus S / PhlVS / EF492068 / 41-42/34-35
34 / Poplar mosaic virus / PopMV / AY505475 / 46-47/34
35 / Caper latent virus / CapLV / HQ588148 / 42-43/34
36 / Helenium virus S / HVS / D10454 / 42/34-35
37 / Nerine latent virus / NeLV / DQ098905 / 42/35
38 / Garlic common latent virus / GarCLV / DQ520092 / 96-97/96-99
Suppl. Table 2. Different conserved domains of coat protein of Garlic common latent virus
predicted using SMART (
Sl. No. / Name / Start / End1 / Pfam:Flexi_CP_N / 68 / 119
2 / Pfam:Flexi_CP / 128 / 267
3 / Coiled Coil / 6 / 75
4 / low complexity / 2 / 21
5 / THUMP / 37 / 114
6 / NADH_4Fe-4S / 59 / 85
7 / Ald_Xan_dh_C / 92 / 148
8 / PKS_TE / 99 / 260
9 / LINK / 107 / 160
10 / THEG / 134 / 153
11 / A_amylase_inhib / 151 / 206
12 / CBF / 232 / 291
13 / IENR2 / 260 / 276
Suppl. Table 3.Recombination events in coat protein gene of Carlavirusspecies infecting diverse plant species detected by RDP3.
Sl no / Recombinanta / Break point / Donar (Major x Minor) / Detection by methodb,c / P valued1 / DVS / 525-876 / HpLV x PhlVB / M, S,L,&3S / 2.496X10-02
2 / PhlVB / 895-413 / CPMMV (U)x CoLV / C&L / 2.315X10-08
3 / CVB / 923-449 / CPMMV (U)x CoLV / C&L / 2.315X10-08
4 / PhlVS / 307-740 / NeLV x CapLV (U) / M,C,S&L / 1.908X10-02
5 / NeLV / 254-868 / HVS (U) x CoLV / S &L / 1.486X10-02
6 / CPMMV / 341-847 / HVS (U) x CoLV / S &L / 1.486X10-02
7 / PVM / 132-71 / HeMV x NCLaV / C,S,L&3S / 2.009X10-02
8 / HpLV / 13-174 / PVM (U) x AcLV / C,S & L / 3.053X10-03
9 / HPMV / 478-622 / CNV x SPCFV (U) / C&L / 1.441X10-05
10 / HdCMV / 514-U / CNV x SPCFV (U) / C&L / 1.441X10-05
11 / PVP / 697-206 / LNRSV x CPMMV (U) / M, S&L / 6.809X10-10
12 / PVP / 559-691 / CVNV x SPCFV (U) / C&L / 1.441X10-05
13 / KLV / 849-80 / CPMMV x SLV / M &L / 1.248X10-06
14 / KLV / 485-625 / CVNC x SPCFV (U) / C &L / 1.441X10-05
15 / KLV / 0-759 / LNRV x CPMMV (U) / M,S&L / 6.809X10-10
16 / MjMV / 98-1023 / LNRSV x CPMMV (U) / M,S&L / 6.809X10-10
17 / PLV / 721-857 / SLV x BlSCV / M& C / 1.656X10-01
18 / PLV / 491-631 / CVNV x SPCFV (U) / C&L / 1.441X10-05
19 / PVS / 521-655 / CVNV x SPCFV (U) / C&L / 1.441X10-05
20 / PVS / 47-828 / LNRSV x CPMMV (U) / M,S&L / 6.809X10-10
21 / LNRSV / U-872 / SLV x BlSCV / M&C / 1.656X10-01
22 / LNRSV / 527-671 / CVNV x SPCFV (U) / C&L / 1.441X10-05
23 / AHLV / 155-U / HeNNV x HPMV / C&L / 2.963X1002
24 / AHLV / 587-722 / CVNV x SPCFV (U) / C&L / 1.441X10-05
25 / PotLV / 539-686 / CVNV x SPCFV (U) / C&L / 1.441X10-05
26 / PotLV / 858-104 / CPMMV x SLV / M&L / 1.248X10-06
27 / CVNV / 601-817 / GarCLV-RAU x NSV / M,C,S&L / 3.460X10-02
28 / ButMV / 636-846 / GarCLV-K2 x PopMV / C&L / 1.629X10-02
29 / RCVMV / 559-582 / PVS (U) x PhlVS / R&G / 3.236X10-03
30 / HeNNV / 472-587 / SLV x ButMV / M&C / 1.089X10-02
a: Complete name of the viruses were given in the fig.1
b: B-Boot Scan, M-Maxchi, C-Chimera, S-Siscan, L-lard and 3s-3SEQ algorithms implemented in RDP3
c:Maximum P value obtained in the particular method in RDP3 was marked by bold letter
d: P value evidence of detected recombination
U: Undetermined