Multigene characterization of a ‘Candidatus Phytoplasma australasia’ strain associated with Roystonea regia in Oman

Figures & data

Fig. 1 Symptoms of leaf yellowing (a, b), reduction in internodes (c), leaf stunting (d), and dryness and collapse of older fronds (e) in Roystonea regia.

Table 1. The 16S rDNA sequences of different phytoplasma strains obtained from the National Centre for Biotechnology Information (NCBI) GenBank database for phylogenetic analysis

Accession Numbers	16S rDNA groups	Acronym	Phytoplasma strains
NC_007716	I-A	AYWB	Aster yellows witches’ broom (AYWB)
AF222066	I	CPPb	Clover phyllody P. (strain CPh rrnB)
L33760	I-A	BB	Tomato big bud
M30790	I-B	MAY	Aster yellows (MAY) ‘Ca. P. asteris’
NC_005303	I-B	OY-M	Onion yellows mild strain (OY-M)
AF222065	I-C	CPh	Clover phyllody (CPh)
Y10097	II	PYC	Mollicutes sp.(Papaya yellow crinkle)
GI:471234556	II-A	PnWB	Peanut witches’ broom
EF186828	II-B	LWB	‘Ca. Phytoplasma aurantifolia’ strain LWB
U15442	II-B	WBDL	Lime witches’ broom ‘Ca. P. aurantifolia’
X83432	II-C	FBP	Faba bean phyllody
AB257291	II-D	ScaWB	Scaevola WB
AJ289193	II-A	SPLL	Sweet potato little leaf strain V4
Y10096	II-D	PpM	Papaya mosaic ‘Ca. P. australasia’
Y16393	II-E	PEY	Pichris echioides phyllody
EF186827	II-F	CoP	cotton phyllody
AF056095	III	SCYP-IA	Sugarcane yellows IA, Africa
AF175304	III	CloY	Clover yellows edge
AF495657	III	ChiY	Chinaberry yellows
JQ044392	III-A	PX11CT1	Peach X-disease ‘Ca. P. pruni’
AF173558	III-B	CYE	Clover yellow edge
GU004371	III-C	PB	Pecan bunch
AF190226	III-G	WWB	Walnut WB (rrnA)
AF302841	III-Q	BRWB7	Black raspberry witches’ broom
FJ914654	I-S	COAH10	Mexican potato purple top phytoplasma strain COAH10
AF434989	IV	TexPp	Texas Phoenix palm phytoplasma
AF248957	IX-A	PPWB	Pigeon pea witches’ broom
AF515636	IX-B	AlWB	Almond witches’ broom ‘Ca. P. phoenicium’
AF515637	IX-D	AlWB	Almond witches’ broom
AY197655	V-A	EY	Elm yellows ‘Ca. P. ulmi’
AB052876	V-B	JWB-G1	Jujube witches’ broom ‘Ca. P. ziziphi’
AY390261	VI-A	CP	Clover proliferation ‘Ca. P. trifolii’
AF190224	VI-B	MC	Strawberry multiplier disease
AF409069	VI-C	EY-IL1	Illinois elm yellows
AF092209	VII-A	AshY	Ash yellows ‘Ca. P. fraxini’
AY034608	VII-B	ErWB	Erigeron witches’ broom
AY147038	VII-C	ArAWB	Argentinian alfalfa witches’ broom
AF086621	VIII-A	LufWB	Loofah witches’ broom
AJ542541	X-A	AP	Apple proliferation ‘Ca. P. mali’
AJ542544	X-B	ESFY	European stone fruit yellows ‘Ca. P. prunorum’
AB052873	XI-A	RYD	Rice yellow dwarf ‘Ca. P. oryzae’
L76865	XII-B	AUSGY	Australian grapevine yellows ‘Ca. P. australiense’
AJ243045	XII-C	StrawLY	Strawberry lethal yellows
AF248960	XIII-A	MPV	Mexican periwinkle virescence
AJ550984	XIV-A	BGWL	Bermudagrass white leaf ‘Ca. P. cynodontis’
AB054986	XIX-A		Chestnut witches’ broom ‘Ca. P. castaneae’
AF147708	XV-A	HibWB	Hibiscus witches’ broom ‘Ca. P. brasiliense’
HQ258882	XV-B	GWB	Guazuma witches’ broom
AY725228	XVI-A		Sugarcane yellow leaf syndrome ‘Ca. P. graminis’
AY725234	XVII-A		Papaya bunchy top ‘Ca. P. caricae’
DQ174122	XVIII-A		American potato purple top wilt ‘Ca. P. americanum’
X76431	XX-A		Rhamnus witches’ broom ‘Ca. P. rhamni’
AJ310849	XXI-A	PinP	Pinus phytoplasma ‘Ca. P. pini’
KF751387	XXII-A	LYDM	Lethal yellow disease Mozambique ‘Ca. P. palmicola’
AY083605	XXIII-A		Buckland valley grapevine yellows
AF509322	XXIV-A		Sorghum bunchy shoot
EF666051	XXIX-A	CaWB	Cassia witches’ broom (CaWB) ‘Ca. P. omanense’
AF521672	XXV-A		Weeping tea witches broom
AJ539179	XXVI-A		Sugarcane phytoplasma strain D3T1
AJ539180	XXVII-A		Sugarcane phytoplasma strain D3T2
AY744945	XXVIII-A		Derbid phytoplasma
FJ432664	XXX-A		Salt cedar witches’ broom ‘Ca. P. tamaricis’
HQ225630	XXXI-A	SoyST1c1	Soybean stunt isolate SoyST1c1 ‘Ca. P. costaricanum’
EU371934	XXXII-A	MaPV	Malaysian p. virescence (MaPV) ‘Ca. P. malaysianum’

Table 2. Representative phytoplasma 16S rRNA, tuf, secA, and imp gene sequences from the National Centre for Biotechnology Information (NCBI) GenBank database used in phylogenetic analysis

Phytoplasma strain	16Sr Group	Abbreviation	Accession number
			16S rRNA gene	tuf gene	imp gene
Chrysanthemum yellows	I-A	CHRYM	AY265214	JQ824240	GU214179
New Jersey aster yellows	I-A	NJ-AY	HM590622	JQ824265	AB469011
Maryland aster yellows	I-B	AY-1	AF322644	JQ824205	AB469008
Aster yellows AY-J 24126	I-B	AY-J	HM590616	JQ824215	AB469007
Atypical aster yellows	I-B	VUT		JQ824285
Clover phyllody	I-C	KVE	AY265217	JQ824248
Carrot yellows	I-C	CA	HM448473	JQ824226
Apricot chlorotic leaf roll	I-F	A-AY		JQ824251
Peanut witches’ broom	II-A	PnWB	GI:471234556	GI:471234556	GI:471234556
Witches’ broom disease of lime	II-B	WBDL	EF186828	JQ824276	JQ745272
Faba bean phyllody	II-C	FBP		JQ824262
Primula blue yellow	II-C	PrBY	JQ868438	JQ824229	JQ745278
Tomato big bud	II-D	TBB-KG	AF494527	JQ824250	JQ745285
Sweet potato little leaf	II-A	SPLL	AJ289193	Draft Genome	Draft Genome
Pichris echoides phyllody	II-E	PEP	Y16393	JQ824244
Peach X disease	III-A	CX	HQ589202	JQ824211	GU247985
X disease	III-A	BF	HQ589203	JQ824233
Green valley X disease	III-A	GVX		JQ824252
Plum leptonecrosis	III-B	LNI	JQ868444	JQ824230	KJ462027
Goldenrod yellows	III-D	GRI	GU004372	JQ824232	KJ462028
Spirea stunt	III-E	SPI	HQ589206	JQ824281	KJ462029
Vaccinium witches’ broom	III-F	VAC	HQ589201	JQ824260	KJ462030
Milkweed yellows	III-F	MW1	HQ589200	JQ824206	KJ402031
Poinsettia branching factor	III-H	JRI		JQ824267
Elm yellows	V-A	EY1	AY197655	JQ824225	KJ462034
Elm witches’ broom	V-A	ULW		JQ824259
Jujube witches’ broom	V-B	JWB	AY197661	JQ824203	KJ462036
Rubus stunt	V-E	RuS	AY197648	JQ824210	KJ462043
Potato witches’ broom	VI-A	PWB		JQ824282
Clover proliferation	VI-A	CP1	AY390261	JQ824231	KJ462045
Brinjal little leaf	VI-A	BLL		JQ824268
Catharanthus phyllody	VI-C	CPS		JQ824293
Apple proliferation	X-A	AT	CU469464	JQ824224	KJ462047
Apple proliferation	X-A	AP15		JQ824216
Plum leptonecrosis	X-B	LNp	JQ868450	JQ824235	KJ462048
Napier grass stunt	XI	NGS-BS	JQ868440	JQ824249	KJ462053
From unknown insect	XII-A	BA	JQ868436	JQ824228	KJ462058
Australian grapevine yellows	XII-B	AGY	NC_010544	JQ824254	KJ462054
Coconut lethal yellowing	IV-A			JQ824292
Ash yellows	VII-A	ASHY 4		JQ824219
Bermudagrass white leaf ‘Ca. P. cynodontis’	XIV-A		AJ550984	JQ824264	KJ462061
Stolbur ‘Ca. P. solani’	XII-A	STOL11		JQ797670
Suriname virescence -	XV-A	SUV		JQ824234
Rhamnus cathartica stunt –	XX	RhCa		JQ824207
Cotton phyllody –	II-F	CoP		JQ824204
‘Flavescence dorée’- FD-C Serbia 86/09	V-C	FD-C		JQ824291
”Flavescence dorée” – FD-D Veneto 107/06	V-D	FD-D		JQ824294
Naxos yellows -NAXOS	IX-C	NAXOS		JQ824245
Pear decline – PD	X-C	PD		JQ824247
Paulownia witches’ broom	I-D			KP662171
Yellows diseased strawberry ‘Ca. P. fragariae’	XII-E			KJ144900
Loofah witches’ broom	VIII-A			AF086617

*The GenBank accession strains of 16S rRNA gene which used in combined phylogenetic tree only.

Fig. 2 Phylogenetic tree based on the 16S ribosomal RNA gene sequences of Roystonea regia phytoplasmas (black circles) with 41 phytoplasma strains from different groups and subgroups. The tree was rooted using Bacillus subtilis (AB04261). The phylogenetic tree was constructed by the Maximum Likelihood method and units are the number of base substitutions per site. Bootstrap values are expressed as percentage of 1,000 replicates

Fig. 3 Phylogenetic tree based on tuf gene sequences of Roystonea regia phytoplasmas (black circles) with 41 phytoplasma strains from different groups and subgroups. The tree was rooted using Bacillus subtilis (GCA000789275). The phylogenetic tree was constructed by the Maximum Likelihood method and units are the number of base substitutions per site. Bootstrap values are expressed as percentage of 1,000 replicates

Fig. 4 Phylogenetic tree based on imp gene sequences of Roystonea regia phytoplasmas (black circles) with 17 phytoplasma strains from different groups and subgroups. The phylogenetic tree was constructed by the Maximum Likelihood method and units are the number of base substitutions per site. Bootstrap values are expressed as percentage of 1,000 replicates

Fig. 5 Phylogenetic tree based on the combined 16S ribosomal RNA, tuf and imp gene sequences of Roystonea regia phytoplasmas (black circles) with 41 phytoplasma strains from different groups and subgroups. The tree was rooted using Bacillus subtilis (GCA000789275). The phylogenetic tree was constructed by the Maximum Likelihood method and units are the number of base substitutions per site. Bootstrap values are expressed as percentage of 1,000 replicates