Evaluating the effect of tuf and secA gene sequence length for discrimination of phytoplasmas

Figures & data

Table 1. Phytoplasma gene sequences used in this study

			Accession number
Phytoplasma Strains	16Sr Group	Abbreviation	16S rRNA gene	tuf gene	secA gene
Aster yellows witches’-broom phytoplasma AYWB	16SrI-A	AYWB	CP000061	CP000061	CP000061
Onion yellows phytoplasma OY-M DNA	16SrI-B	OY-M	NC_005303	NC005303	NC005303
Peanut witches’ broom	16SrII-A	PnWB	GI:471234556	GI:471234556	GI:471234556
Sweet potato little leaf	16SrII-A	SPLL	AJ289193	Draft Genome	Draft Genome
Witches’ broom disease of lime	16SrII-B	WBDL	EF186828	Draft Genome	Draft Genome
Candidatus Phytoplasma pini	16SrXXI-A	PinP	AJ310849		KF791912
Palm lethal yellowing phytoplasma	16SrIV		AF434989	EU413952	EU267187
Almond witches’ broom (Ca. Ph. Phoenicium)	16SrIX-B	AlmWB	JPSQ01000072	JPSQ01000008	JPSQ01000034
Candidatus Phytoplasma oryzae	16SrXI		AB052873		LTBM01000007
‘Echinacea purpurea’ witches’-broom phytoplasma	16SrII-A		JN885462	LKAC01000001	LKAC01000010
Candidatus Phytoplasma pruni	16SrIII-A		JQ044392	LHCF01000002	LHCF01000002
Candidatus Phytoplasma solani	16SrXII-A		JQ730741	FO393428	FO393428
Candidatus Phytoplasma mali	16SrX-A		NC-011047	NC-011047	NC-011047
Australian grapevine yellows (Ca. Ph. Australiense)	16SrXII-B	AGY	L76865	DQ094780
Yellows diseased strawberry (Ca. P. fragariae)	16SrXII-E		JX273493	KJ144900
Loofah witches’ broom	16SrVIII-A		AF086621	AF086617
Jujube witches’ broom	16SrV-B	JWB	AB052876	GU968760
Elm little leaf phytoplasma (Ca. P. ulmi)	16SrV-A	ULW	AY197655	KF440688
Lime witches’ broom	16SrII-B	WBDL	KX358574	KX358598	KX358586
Alfalfa witches’ broom	16SrII-D	AlWB	KX358564	KX358588	KX358576
Sesame phyllody	16SrII-D	SEWB	KX358563	KX358587	KX358575

Fig. 1 Phylogenetic tree of the 16S rRNA gene sequences from the 21 published phytoplasma strains using (a) Neighbour Joining method (NJ) and (b) Maximum Likelihood method (ML); the trees were rooted using Bacillus subtilis (AB042061)

Fig. 2 Phylogenetic trees of tuf gene sequences from the previously published 19 phytoplasma strains (Table 1) using the NJ method; (a) shows the tree based on the short DNA sequence (about 350 bp), (b) shows the tree based on the long DNA sequence (about 730 bp). The trees were rooted using Bacillus subtilis strain 168 (GCA:000789275)

Fig. 3 Phylogenetic trees of secA gene sequences from the previously published 16 phytoplasma strains (Table 1) using the NJ method; (a) shows the tree based on the short DNA sequence (about 530 bp), (b) shows the tree based on the long DNA sequence (about 1220 bp). The trees were rooted using Bacillus subtilis (D10279)

Fig. 4 Phylogenetic trees of tuf gene sequences from the previously published 19 phytoplasma strains (Table 1) using the ML method; (a) shows the tree based on the short DNA sequence (about 350 bp), (b) shows the tree based on the long DNA sequence (about 730 bp). The trees were rooted using Bacillus subtilis strain 168 (GCA:000789275)

Fig. 5 Phylogenetic trees of secA gene sequences from the previously published 16 phytoplasma strains (Table 1) using the ML method; (a) shows the tree based on the short DNA sequence (about 530 bp), (b) shows the tree based on the long DNA sequence (about 1220 bp). The trees were rooted using Bacillus subtilis (D10279)