..................................................
Table 1
|
List of the oligonucleotide primers used in this study for amplification of cassava mosaic geminiviruses from Tanzania (anfl = near-full length, ps = partial sequence)
|
Primer name
|
Nucleotide sequence (5'→3')
|
Begomovirus isolate
|
DNA component
|
|
UGT-F
|
TCGTCTAGAACAATACTGATCGGTCTCC
|
EACMV-KE-[TZT]
|
DNA-A fla
|
UGT-R
|
CGGTCTAGAAGGTGATAGCCGAACCGGGA
|
EACMV-KE-[TZT]
|
DNA-A fl
|
3T-F
|
ACGTCTAGAACAATACTGATCGGTCTC
|
EACMV-TZ-[YV]
|
DNA-A fl
|
3T-R
|
GTGCTCTAGAAGGTGATAGCCGAACCGGGA
|
EACMV-TZ-[YV]
|
DNA-A fl
|
TZ1B-F
|
GCGCGGAATCACTTGTGAAGCAGTCGT
|
EACMCV-[TZ1]
|
DNA-B fl
|
TZ1B-R
|
GCCGGGATTCGGTGAGTGGTTTACATCAC
|
EACMCV-[TZ1]
|
DNA-B fl
|
EAB555/F
|
TACATCGGCCTTTGAGTCGCATGG
|
CMGs
|
BC1/CR
|
EAB555/R
|
CTTATTAACGCCTATATAAACACC
|
CMGs
|
BC1/CR
|
UNI/F
|
KSGGGTCGACGTCATCAATGACGTTRTAC
|
CMGs
|
DNA-A nfl
|
UNI/R
|
AARGAATTCATKGGGGCCCARARRGACTGGC
|
CMGs
|
DNA-A nfl
|
AT-F
|
GTGACGAAGATTGCATTCT
|
ACMV-[TZ]
|
DNA-A ps
|
AT-R
|
AATAGTATTGTCATAGAAG
|
ACMV-[TZ]
|
DNA-A ps
|
ATZ1-F
|
TAAGAAGATGGTGGGAATCC
|
EACMCV-[TZ1]
|
DNA-A ps
|
ATZ-R
|
CGATCAGTATTGTTCTGGAAC
|
EACMCV-[TZ1]
|
DNA-A ps
|
TZ7-F
|
TGGTGGGAATCCCACCTT
|
EACMCV-[TZ7]
|
DNA-A ps
|
TZ7-R
|
GTATTGTTATGGAAGGTGATA
|
EACMCV-[TZ7]
|
DNA-A ps
|
TZM-F
|
TATATGATGATGTTGGTC
|
EACMV-UG2Svr-[TZ10]
|
DNA-A ps
|
TZ10-R
|
TAGAAGGTGATAGCCGTA
|
EACMV-UG2Svr-[TZ10]
|
DNA-A ps
|
TZM-F
|
TATATGATGATGTTGGTC
|
EACMV-KE-[TZM]
|
DNA-A ps
|
TZM-R
|
TAGAAGGTGATAGCCGAAC
|
EACMV-KE-TZM]
|
DNA-A ps
|
|
..................................................
Table 2
|
Nucleotide sequence identities (percentages) of the DNA-A full-length of cassava mosaic geminiviruses from Tanzania and other geminiviruses from Africa and the Indian sub-continent. Values above 89% are in bold and names of isolates from Tanzania are in bold.
|
Virus Isolate
|
ACMV-[TZ]
|
EACMCV-[TZ1]
|
EACMCV-[TZ7]
|
EACMV-[KE/TZT]
|
EACMV-[KE/TZM]
|
EACMV-[TZ/YV]
|
EACMV-UG2 [TZ10]
|
|
ACMV-[CM]
|
95
|
68
|
68
|
70
|
70
|
69
|
73
|
ACMV-[CM/DO2]
|
95
|
68
|
68
|
70
|
70
|
69
|
73
|
ACMV-[IC]
|
96
|
68
|
68
|
70
|
71
|
70
|
73
|
ACMV-[KE]
|
96
|
68
|
68
|
70
|
70
|
70
|
73
|
ACMV-[NG]
|
95
|
68
|
68
|
70
|
70
|
70
|
73
|
ACMV-[NG/Ogo]
|
96
|
68
|
68
|
70
|
70
|
70
|
73
|
ACMV-UGMld
|
97
|
68
|
68
|
70
|
71
|
70
|
73
|
ACMV-UGSVr
|
96
|
68
|
68
|
70
|
71
|
70
|
74
|
ACMV-[TZ]
|
-
|
68
|
68
|
70
|
70
|
70
|
73
|
|
EACMCV-[CM]
|
67
|
90
|
89
|
87
|
87
|
85
|
84
|
EACMCV-[CI]
|
67
|
90
|
90
|
88
|
87
|
86
|
85
|
EACMCV-[TZ1]
|
68
|
-
|
96
|
88
|
88
|
87
|
85
|
EACMCV-[TZ7]
|
68
|
96
|
-
|
88
|
88
|
87
|
85
|
|
EACMMV-[K]
|
71
|
81
|
81
|
87
|
88
|
86
|
87
|
EACMMV-[MH]
|
71
|
81
|
81
|
87
|
88
|
86
|
88
|
|
EACMV-[KE/K2B]
|
70
|
88
|
88
|
97
|
96
|
94
|
92
|
EACMV-[TZ]
|
69
|
88
|
88
|
94
|
94
|
95
|
91
|
EACMV-[KE/TZT]
|
70
|
88
|
88
|
-
|
95
|
93
|
92
|
EACMV-[KE/TZM]
|
70
|
88
|
88
|
96
|
-
|
94
|
92
|
EACMV-[TZ/YV]
|
70
|
87
|
87
|
94
|
93
|
-
|
90
|
EACMV-UG2
|
73
|
85
|
85
|
92
|
92
|
92
|
98
|
EACMV-UG2Mld
|
73
|
86
|
86
|
93
|
92
|
92
|
99
|
EACMV-UG2Svr
|
73
|
86
|
86
|
93
|
92
|
92
|
99
|
EACMV-UG2 [TZ10]
|
73
|
85
|
85
|
92
|
92
|
91
|
-
|
|
EACMZV-[ZB]
|
72
|
80
|
80
|
86
|
86
|
86
|
83
|
EACMZV-[KE/Kil]
|
72
|
79
|
79
|
86
|
86
|
85
|
83
|
|
SACMV-[ZA]
|
74
|
73
|
73
|
80
|
80
|
79
|
80
|
SACMV-[ZW]
|
74
|
73
|
73
|
80
|
80
|
80
|
80
|
SACMV-[M12]
|
74
|
73
|
73
|
80
|
80
|
80
|
80
|
|
SLCMV-[Col]
|
73
|
67
|
67
|
67
|
67
|
67
|
67
|
|
TGMV-[Com]
|
58
|
59
|
59
|
59
|
59
|
59
|
59
|
|
..................................................
Table 3
|
CP gene nucleotide sequence identity (%) of cassava mosaic geminiviruses from Tanzania and other published CMG CP sequences. Values above 89% are in bold and names of isolates from Tanzania are in blue.
|
Virus Isolate
|
ACMV-[TZ]
|
EACMCV-[TZ1]
|
EACMCV-[TZ7]
|
EACMV-[KE/TZT]
|
EACM-[KE/TZM]
|
EACMV-[TZ/YV]
|
EACMV-UG2 [TZ10]
|
|
ACMV-[CM]
|
97
|
77
|
77
|
78
|
79
|
77
|
90
|
ACMV-[CI]
|
96
|
77
|
78
|
78
|
79
|
77
|
90
|
ACMV-[KE]
|
97
|
76
|
76
|
77
|
78
|
76
|
90
|
ACMV-[NG]
|
96
|
77
|
77
|
78
|
78
|
77
|
90
|
ACMV-UGMld
|
97
|
76
|
77
|
78
|
78
|
76
|
90
|
ACMV-[TZ]
|
-
|
77
|
77
|
78
|
78
|
77
|
89
|
|
EACMCV-[CM]
|
77
|
94
|
94
|
95
|
96
|
93
|
84
|
EACMCV-[TZ1]
|
77
|
-
|
97
|
95
|
96
|
94
|
84
|
EACMCV-[TZ7]
|
77
|
97
|
-
|
95
|
97
|
95
|
84
|
|
EACMMV-[K]
|
77
|
80
|
80
|
80
|
80
|
80
|
79
|
EACMMV-[MH]
|
77
|
79
|
80
|
80
|
80
|
80
|
79
|
|
EACMV-[KE/K2B]
|
77
|
95
|
96
|
96
|
97
|
96
|
84
|
EACMV-TZ
|
77
|
95
|
95
|
96
|
97
|
96
|
85
|
EACMV-[KE/TZT]
|
78
|
95
|
95
|
-
|
97
|
95
|
85
|
EACMV-[KE/TZM]
|
78
|
96
|
97
|
97
|
-
|
97
|
84
|
EACMV-[TZ/YV]
|
77
|
94
|
95
|
95
|
96
|
-
|
84
|
EACMV-UG2
|
90
|
84
|
84
|
85
|
85
|
84
|
99
|
EACMV-UG2Mld
|
89
|
84
|
84
|
85
|
85
|
84
|
98
|
EACMV-UG2Svr
|
90
|
84
|
84
|
85
|
85
|
84
|
99
|
EACMV-UG2 [TZ10]
|
89
|
84
|
84
|
85
|
84
|
84
|
-
|
|
EACMZV-[ZB]
|
78
|
96
|
96
|
97
|
97
|
96
|
85
|
|
SACMV-[ZA]
|
77
|
78
|
79
|
80
|
79
|
79
|
73
|
|
ICMV-[Tri]
|
74
|
73
|
73
|
74
|
74
|
73
|
64
|
|
TGMV-[Com]
|
63
|
65
|
65
|
64
|
64
|
65
|
78
|
|
..................................................
Table 4
|
Percent similarity (in the upper triangle) in the nucleotide sequence of the common region of East and West African isolates of EACMCV. Values of 89% and above are in bold.
|
Virus isolate
|
EACMCV-[TZ1] CRA
|
EACMCV-[TZ7] CRA
|
EACMCV-[TZ1] CRB
|
EACMCV-[CM] CRA
|
EACMCV-[CM] CRB
|
EACMCV-[CI] CRA
|
EACMCV-[IC] CRB
|
|
EACMCV-[TZ1] CRA
|
***
|
80
|
80
|
89
|
76
|
82
|
76
|
EACMCV-[TZ7] CRA
|
|
***
|
86
|
88
|
74
|
82
|
73
|
EACMCV-[TZ1] CRB
|
|
|
***
|
91
|
80
|
82
|
78
|
EACMCV-[CM] CRA
|
|
|
|
***
|
86
|
91
|
83
|
EACMCV-[CM] CRB
|
|
|
|
|
***
|
78
|
97
|
EACMCV-[CI] CRA
|
|
|
|
|
|
***
|
77
|
EACMCV-[CI] CRB
|
|
|
|
|
|
|
***
|
|
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