Molecular characterization of a naturally occurring intraspecific recombinant begomovirus with close relatives widespread in southern Arabia

Table 1 Comparison of nucleotide sequence percentage identity for Gez3.1 of Tomato leaf curl Sudan virus **(ToLCSDV-Sha[SD:Gez3.1:11]) and other five recognized strains* of the ToLCSDV using Species Demarcation Tool (SDT v1.0)**[19]

Virus	Full-length	ORF						IR	Rep binding iteron	Iteron-related domain
[GenBank accession]	Full-length	V1	V2	C2	C3	C1	C4	IR	Rep binding iteron	Iteron-related domain
ToLCSDV	94	99	99	98	98	89	89	71	GGTGTAGTGGGGT	FKIN
[AY044139]	94	99	99	98	98	89	89	71	GGTGTAGTGGGGT	FKIN
ToLCSDV	96	97	93	95	94	99	100	99	GGTGTATCGGTAC	FQIN
[AY044137]	96	97	93	95	94	99	100	99	GGTGTATCGGTAC	FQIN
ToLCSDV	92	97	93	87	88	89	87	86	TGTATATCGGTAC	FQIN
[JF919733]	92	97	93	87	88	89	87	86	TGTATATCGGTAC	FQIN
ToLCSDV	91	95	91	86	90	89	89	86	TGTATATCGGTAC	FQIN
[JF919731]	91	95	91	86	90	89	89	86	TGTATATCGGTAC	FQIN
ToLCSDV	92	97	93	86	87	90	87	81	GGTACATCGGTAC	FQIY
[JN591385]	92	97	93	86	87	90	87	81	GGTACATCGGTAC	FQIY
TYLCV	88	70	97	95	93	91	88	85	TGTATATCGGTAC	FQIN
[AY044138]	88	70	97	95	93	91	88	85	TGTATATCGGTAC	FQIN

*Different isolates of ToLCSDV from Gezira (AY044139), Shambat (AY044137), Yemen tomato (JF919731) and Yemen tobacco (JF919733) and Tomato yellow leaf curl virus from Gezira, Sudan (TYLCV). Comparisons are based on the complete genome sequence, and the nucleotide sequence of each individual open reading frame (ORF) (V1, V2, C1, C2, C3, C4) and the intergenic region (IR). The Rep-binding iteron and iteron-related domain for ToLCSDV-Sha[SD:Gez3.1:11] are identical to those for ToLCSDV-Sha[SD:Sha:96] strain (AY044137). Values in bold highlight the highest nucleotide sequence identities with ToLCSDV-Gez3.1 for each ORF or IR compared.

ISSN: 1743-422X