Supplementary Table 1. Highest and lowest percent sequence identity values for sequence comparisons of the tomato yellow leaf curl virus isolates characterized here with the sequences of selected other begomoviruses.
Virus§# / Genome(percent nucleotide sequence identity / Gene
(percent amino acid sequence identity)$
CP / V2 / Rep / TrAP / REn / C4
TYLCV-OM (11) / 89.3-97.4 / 97.3-98.8 / 92.3-99.1 / 94.6-99.1 / 84.3-99.8 / 88.9-99.5 / 93.5-99.6
TYLCV-IR (1) / 88.8-91.6 / 97.3-98.1 / 96.6-97.4 / 93.2-94.1 / 80.7-84.4 / 86.6-90.3 / 85.7-87.8
TYLCV-IS (1) / 81.1-83.1 / 95.4-95.8 / 97.4-98.3 / 81.4-83.7 / 80.0-82.2 / 85.8-90.3 / 64.3-67.4
TYLCV-Mld (4) / 80.9-86.4 / 97.3-98.4 / 95.7-97.4 / 84.1-85.4 / 80.7-84.4 / 86.6-91.8 / 39.8-40.8
TYLCV-SD (1) / 84.3-85.7 / 96.1-96.9 / 94.8-95.7 / 85.4-86.0 / 81.5-83.0 / 85.8-87.3 / 43.9-46.9
TYLCSV (1) / 70.3-72.6 / 87.9-89.1 / 80.0-80.9 / 77.7-79.7 / 65.2-67.4 / 64.2-66.4 / 46.9-49.0
* Accession numbers of TYLCV-OM isolates compared with other begomoviruses are KF229723, KF229725, KF229724, KF229721, KF229722, KF229726, and HE819240.
$ In each case, the overall highest percentage sequence identity value is underlined and highlighted in grey.
# Values in parentheses are the number of begomovirus sequences used for comparison.
§TYLCV strains are given as Iran (IR), Israel (IS), Mild (Mld), Oman (OM) and Sudan (SD). A tomato yellow leaf curl Sardinia virus (TYLCSV) sequence is included for comparison.
Supplementary Table 2. Sequence comparisons of the chili leaf curl virus isolates characterized here with the sequences of other selected begomoviruses.
Virus(-strain#) / Highest and lowest percent sequence identity for comparisons of ChLCV-OM isolates characterised here with other selected begomoviruses$
Genome
(nucleotide sequence) / Gene comparisons (amino acid sequence)
CP / V2 / Rep / C2 / REn / C4
Tom-
26 / Tom-
27 / Tom-
33 / Tom-
26 / Tom-
27 / Tom-
33 / Tom-
26 / Tom-
27 / Tom-
33 / Tom-26 / Tom-27 / Tom-33 / Tom-26 / Tom-27 / Tom-33 / Tom-26 / Tom-27 / Tom-33 / Tom-26 / Tom-27 / Tom-33
ChLCV-PK
(6)* / 84.4-86.0 / 84.4-86.0 / 84.3-86.0 / 80.5-81.6 / 80.5-81.6 / 80.9-82.0 / 88.1-93.2 / 88.1-93.2 / 86.2-91.4 / 94.2-94.7 / 94.2-94.7 / 93.9-94.5 / 92.5-95.5 / 92.5-95.5 / 92.5-96.3 / 82.8-90.3 / 82.8-90.3 / 82.1-89.6 / 87.6-91.8 / 87.6-91.8 / 87.6-91.8
ChLCV-IN
(14)* / 80.0-81.7 / 80.0-81.7 / 79.9-81.7 / 78.9-82.0 / 78.9-82.0 / 79.3-82.4 / 88.1-92.6 / 88.1-92.6 / 86.2-92.2 / 88.4-91.4 / 88.4-91.4 / 88.4-91.4 / 83.6-94.8 / 83.6-94.8 / 83.6-95.5 / 82.8-85.8 / 82.8-85.8 / 82.8-85.8 / 78.6-84.7 / 78.6-84.7 / 78.6-84.7
ChLCV-Kha
(1)* / 84.7 / 84.7 / 84.5 / 80.5 / 80.5 / 80.9 / 85.6 / 85.6 / 84.5 / 94.5 / 94.5 / 94.2 / 90.3 / 90.3 / 91 / 84.3 / 84.3 / 84.3 / 91.8 / 91.8 / 91.8
ChLCV- Gun
(2)* / 84.2-84.7 / 84.2-84.7 / 84.1-84.7 / 81.6 / 81.6 / 82.0 / 90.8-91.7 / 90.8-91.7 / 88.8-91.4 / 94.5-94.7 / 94.5-94.7 / 94.2-94.5 / 94.0 / 94.0 / 94.8 / 88.1 / 88.1 / 87.3 / 92.8-94.8 / 92.8-94.8 / 92.8-94.8
ChLCV- OM
(19)* / 91.8-
93.3 / 91.8-
93.3 / 92.1-
93.7 / 77.9-
82.4 / 77.9-
82.4 / 78.3-
82.8 / 97.5-
100 / 97.5-
100 / 96.6-
98.3 / 97.0-
100 / 97.0-
100 / 96.7-
99.7 / 91.0-
99.3 / 91.0-
99.3 / 91.8-
100 / 94.8-
100 / 94.8-
100 / 94.8-
99.3 / 99.0-
100 / 99.0-
100 / 99.0-
100
PepLCLV
(3)* / 75.7-76.5 / 75.7-76.5 / 75.9-76.7 / 81.2-81.6 / 81.2-81.6 / 81.6-82.0 / 91.7-92.4 / 91.7-92.4 / 90.5-91.4 / 73.4-75.4 / 73.4-75.4 / 73.4-75.4 / 94.8 / 94.8 / 95.5 / 84.3 / 84.3 / 83.6 / 38.8-40 / 38.8-40 / 38.8-40
PepLCBDV
(3) / 74.9-75.1 / 74.9-75.1 / 74.5-75.0 / 81.7 / 81.7 / 82.1 / 86.6-90.8 / 86.6-90.8 / 85.3-89.7 / 77.1 / 77.1 / 77.1 / 91.9-93.3 / 91.9-93.3 / 91.9-94.1 / 80.7-85.8 / 80.7-85.8 / 80-85.1 / 37.2-38.4 / 37.2-38. / 37.2-38.
# Chili leaf curl virus (ChLCV) strains are given as Guntur (Gun), India (IN), Khanewal (Kha), Oman (OM) and Pakistan (PK).
$ In each case, the overall highest percentage sequence identity value is underlined and highlighted in grey.
Supplementary Table 3. Pairwise comparisons of the genes and gene products of ToLCABV with the sequences of other selected begomoviruses
Begomovirus* / Highest and lowest percent nucleotide sequence and amino acid sequence identities for pairwise comparisons of the genesequences of the ToLCABV isolates with other selected begomoviruses§
CP / V2 / Rep / TrAP / REn / C4
Tom-28 / Tom-42 / Tom-43 / Tom-44 / Tom-28 / Tom-42 / Tom-43 / Tom-44 / Tom-28 / Tom-42 / Tom-43 / Tom-44 / Tom-28 / Tom-42 / Tom-43 / Tom-44 / Tom-28 / Tom-42 / Tom-43 / Tom-44 / Tom-28 / Tom-42 / Tom-43 / Tom-44
PepLCBDV (7) / 74.6-78.7 (81.3-82.9) / 74.7-77.8 (80.2-81.7) / 75.2-78.1 (81.3-82.9) / 74.8-77.6 (80.5-82.1) / 88.8-91.1 (85.3-89.7) / 89.1-91.8 (86.6-90.8) / 88.8-91.5 (85.7-89.9) / 89.1-91.8 (86.6-90.8) / 86.0-89.8 (85.1-87.6) / 87.5-91.4 (90.6-93.6) / 87.4-91.3 (90.6-93.6) / 87.1-91.2 (89.8-92.8) / 90.1-95.6 (87.4-94.8) / 90.9-95.3 (86.7-93.3) / 90.4-95.3 (85.2-92.6) / 87.9-92.3 (80-88.8) / 83.2-90.9 (77.8-88.1) / 82.7-90.9 (77.8-87.4) / 82.7-90.9 (77.8-88.1) / 80-87.4 (71.9-80.7) / 93.0-94.6 (88.4-90.7) / 92.6-94.2 (87.2-89.5) / 92.6-94.2 (87.2-89.5) / 91.9-93.4 (86-88.4)
PepLCLV
(8) / 74.6-77.8 (79.0-82.1) / 74.3-76.8 (77.8-80.9) / 74.8-77.0 (79.0-82.1) / 74.3-76.5 (78.2-81.3) / 89.7-92.0 (87.9-91.4) / 89.9-92.3 (87.7-91.8) / 89.6-92.1 (86.9-91) / 89.9-92.3 (87.7-91.8) / 86.8-90.2 (83.7-88.1) / 88.6-92.1 (89.5-94.2) / 88.5-92 (89.5-94.2) / 88.3-91.7 (88.7-93.4) / 94.1-94.8 (93.3-94.8) / 93.8-94.8 (91.9-93.3) / 93.8-94.8 (91.1-92.6) / 90.9-91.6 (85.2-87.4) / 86.9-88.6 (83-88.1) / 86.2-88.4 (82.2-87.4) / 86.7-88.9 (83-88.1) / 83.2-85.7 (75.6-80.7) / 90.7-97.7 (84.9-94.2) / 90.3-97.3 (83.7-93.0) / 90.3-97.3 (83.7-93.0) / 89.5-96.5 (82.6-91.9)
PaLCV
(14) / 74.2-77.0 (80.5-81.3) / 74.3-78 (79.4-80.2) / 74.8-78.3 (80.5-81.3) / 74.4-77.8 (79.8-80.5) / 86.5-88.5 (81.9-86.2) / 85.2-88.8 (82.4-87.4) / 85-88.5 (81.5-86.6) / 85.2-88.8 (82.4-87.4) / 88.2-90.6 (80.2-85.6) / 90.2-92.1 (78.5-92.3) / 90.0-92.0 (78.5-92.3) / 89.9-91.8 (77.9-91.4) / 85.2-88.1 (81.5-87.4) / 85.7-88.6 (81.5-86.7) / 85.2-88.1 (80-85.2) / 82.0-84.7 (74.1-79.3) / 81-86.2 (76.2-82.2) / 80.4-85.9 (74.6-81.5) / 80.4-85.9 (74.6-81.5) / 79.3-82.2 (70.4-74.8) / 94.6-97.3 (89.5-93.5) / 94.2-96.9 (88.4-91.9) / 94.2-96.9 (88.4-91.9) / 93.4-96.2 (87.2-90.7)
ChLCV-OM (19) / 77.4-79.5 (80.2-82.5) / 75.5-77.7 (77.1-81.3) / 76-78.2 (78.3-82.5) / 75.5-77.7 (77.5-81.7) / 96.8-99.1 (96.6-98.3) / 97.5-99.7 (96.7-99.2) / 97.3-99.5 (95.9-98.4) / 97.5-99.7 (96.7-99.2) / 77.3-78.1 (73.8-76.8) / 78.5-79.7 (77.3-80.4) / 78.5-79.7 (77.3-80.4) / 78.2-79.5 (76.5-79.6) / 96.3-99.5 (91.1-99.3) / 96.3-99.5 (89.6-97.8) / 96-99.3 (88.9-97.0) / 92.8-96.0 (83.7-91.1) / 97.5-99.8 (94.1-98.5) / 97.0-99.3 (93.3-97.8) / 97.3-99.5 (93.3-98.5) / 93.8-96.0 (87.4-91.1) / 60.1-60.5 (36.0) / 60.5-60.9 (36.0-37.2) / 60.5-60.9 (36.0-37.2) / 59.7-60.1 (36.0-37.2)
ToLCOMV (2) / 89.5-92.0 (92.2-92.6) / 90.1 (91.1-91.5) / 90.2-90.3 (91.5-91.9) / 90.1-90.2 (91.5-91.9) / 71.6-72.1 (73.3-74.1) / 70.4-71.2 (71.8-72.6) / 70.1-70.9 (70.9-71.8) / 70.4-71.2 (71.8-72.6) / 83.6-86 (81.7-83.7) / 84.9-87.1 (87.0-89.6) / 84.6-86.9 (87.0-89.6) / 84.5-86.8 (86.2-88.7) / 71.4 (63.7-64.4) / 71.1 (63.0-63.7) / 70.4 (61.5-62.2) / 66.7 (57.8-58.5) / 73.3-75.1 (69.6) / 73.1-74.8 (68.9) / 73.1-74.8 (68.9) / 69.4-71.1 (62.2) / 99.6-100 (98.8) / 99.2-99.6 (97.7) / 99.2-99.6 (97.7) / 98.4-98.8 (96.5)
TYLCV-OM (7) / 89.8-91.9 (91.9-93.0) / 89.8-91.0 (90.7-91.9) / 89.9-91.1 (91.1-92.2) / 89.8-91.1 (91.1-92.2) / 71.6-73.9 (73.3-75.0) / 70.4-72.9 (71.8-73.5) / 70.1-72.6 (70.9-72.6) / 70.4-72.9 (71.8-73.5) / 63.5-65.5 (61.7-68.2) / 64.5-66.2 (63.8-70.4) / 64.3-65.9 (63.8-70.4) / 64.2-65.8 (63.0-69.0) / 70.9-71.6 (63.0-64.4) / 70.6-71.1 (62.2-63.7) / 69.9-70.4 (60.7-62.2) / 65.9-66.7 (57.0-57.8) / 73.3-75.3 (68.1-71.1) / 73.1-75.1 (67.4-70.4) / 73.1-75.1 (67.4-70.4) / 69.4-71.4 (60.7-63.7) / 53.9-60.1 (30.2-37.2) / 54.3-60.5 (31.4-38.4) / 54.3-60.5 (31.4-38.4) / 53.5-59.7 (31.4-38.4)
*Figures in brackets indicate the number of isolates available in the databases and used in the sequence comparisons.
§Figures in brackets are percent amino acid sequence identity. In each case, the overall highest identity is highlighted by a grey background and underlining.