Phytoplasma classification
Phytoplasmas are a large group of wall-less, non-helical bacteria, associated with plant diseases. They have been found in more than 1;000 plant species on all continents and some of their associated diseases are of major economic importance. In addition, several of them are regulated pests. As attempts to culture phytoplasmas in artificial growing media have failed so far, their study and taxonomic classification is difficult. Phytoplasmas are currently classified within the provisional genus ‘Candidatus Phytoplasma’ based primarily on 16S rRNA sequence analysis. Some less conserved genes have also been used to further differentiate closely related strains or variants within a given strain, which is of particular importance when differences are observed in pathogenicity or ecology in the field. The current ‘Candidatus Phytoplasma’ species classification is based on the 16S rRNA gene sequence, and a threshold of 97.5% similarity with any previously described species is used to propose any new species. During the last decade, the number of phytoplasma strains reported worldwide has increased exponentially. In order to classify phytoplasmas more rapidly, an alternative approach has been taken with the development of an online tool (iPhyClassifier). With this computerized system which simulates an RFLP analysis, researchers can affiliate a new sequence of a phytoplasma strain to a 16Sr group and subgroup. With this system, the phytoplasma classification has been largely expanded and updated, and more than 30 groups and 100 subgroups have been obtained. Updated classifications have been published in recent reviews (Marcone, 2014; Fránová et al., 2014). The table below shows the currently proposed ‘Candidatus Phytoplasma species’ but a fuller list of phytoplasma strains with their 16Sr group/subgroup can be found in Fránová et al. (2014).
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‘Candidatus Phytoplasma species’
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Associated diseases
|
16Sr group-subgroup
|
Genbank nb
|
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‘Ca. Phytoplasma allocasuarinae’
|
Allocasuarina yellows
|
XXXIII-A
|
AY135523
|
|
‘Ca. Phytoplasma americanum’
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Potato purple top wilt
|
XVIII-A
|
DQ174122
|
|
‘Ca. Phytoplasma asteris’
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Aster yellows
|
I-B
|
M30790
|
|
‘Ca. Phytoplasma aurantifolia’
|
Lime witches’ broom
|
II-B
|
U15442
|
|
‘Ca. Phytoplasma australasia’*
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Papaya dieback
|
II-D
|
Y10096
|
|
‘Ca. Phytoplasma australiense’
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Australian grapevine yellows
|
XII-B
|
L76865
|
|
‘Ca. Phytoplasma balanitae’
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Balanites witches’ broom
|
V-F
|
AB689678
|
|
‘Ca. Phytoplasma brasiliense’
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Hibiscus witches’ broom
|
XV-A
|
AF147708
|
|
‘Ca. Phytoplasma caricae’*
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Papaya bunchy top
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XVII-A
|
AY725234
|
|
‘Ca. Phytoplasma castaneae’
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Chestnut witches’ broom
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XIX-A
|
AB054986
|
|
‘Ca. Phytoplasma convolvuli’
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Bindweed yellows
|
XII-H
|
JN833705
|
|
‘Ca. Phytoplasma costaricanum’
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Soybean stunt
|
XXXI-A
|
HQ225630
|
|
‘Ca. Phytoplasma cynodontis’
|
Bermuda grass white leaf
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XIV-A
|
AJ550984
|
|
‘Ca. Phytoplasma fragariae’
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Strawberry yellows
|
XII-E
|
DQ086423
|
|
‘Ca. Phytoplasma fraxini’
|
Ash yellows
|
VII-A
|
AF092209
|
|
‘Ca. Phytoplasma graminis’
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Sugarcane yellow leaf
|
XVI-A
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AY725228
|
|
‘Ca. Phytoplasma japonicum’
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Japanese hydrangea phyllody
|
XII-D
|
AB010425
|
|
‘Ca. Phytoplasma lycopersici’
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‘Brote grande’
|
I-Y
|
EF199549
|
|
‘Ca. Phytoplasma malaysianum’
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Periwinkle virescence and phyllody
|
XXXII-A
|
EU371934
|
|
‘Ca. Phytoplasma mali’
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Apple proliferation
|
X-A
|
AJ542541
|
|
‘Ca. Phytoplasma omanense’
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Cassia witches’ broom
|
XXIX-A
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EF666051
|
|
‘Ca. Phytoplasma oryzae’
|
Rice yellow dwarf
|
XI-A
|
AB052873
|
|
‘Ca. Phytoplasma palmicola’*
|
Coconut lethal yellowing (Mozambique)
|
XXII-A
|
KF751387
|
|
‘Ca. Phytoplasma phoenicium’
|
Almond witches’ broom
|
IX-B
|
AF515636
|
|
‘Ca. Phytoplasma pini’
|
Pine shoot proliferation
|
XXI-A
|
AJ310849
|
|
‘Ca. Phytoplasma pruni’
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Peach X-disease
|
III-A
|
JQ044392/JQ044393
|
|
‘Ca. Phytoplasma prunorum’
|
European stone fruit yellows
|
X-B
|
AJ542544
|
|
‘Ca. Phytoplasma pyri’
|
Pear decline
|
X-C
|
AJ542543
|
|
‘Ca. Phytoplasma rhamni’
|
Buckthorn witches’ broom
|
XX-A
|
AJ583009
|
|
‘Ca. Phytoplasma rubi’
|
Rubus stunt
|
V-E
|
AY197648
|
|
‘Ca. Phytoplasma solani’
|
Stolbur
|
XII-A
|
AF248959
|
|
‘Ca. Phytoplasma spartii’
|
Spartium witches’ broom
|
X-D
|
X92869
|
|
‘Ca. Phytoplasma sudamericanum’
|
Passionfruit witches’ broom
|
VI-I
|
GU292081
|
|
‘Ca. Phytoplasma tamaricis’
|
Salt cedar witches’ broom
|
XXX-A
|
FJ432664
|
|
‘Ca. Phytoplasma trifolii’
|
Clover proliferation
|
VI-A
|
AY390261
|
|
‘Ca. Phytoplasma ulmi’
|
Elm yellows
|
V-A
|
AY197655
|
|
‘Ca. Phytoplasma ziziphi’
|
Jujube witches’ broom
|
V-B
|
AB052876
|
* Included in the review from Marcone (2014) and in LPSN website, but not in Fránová et al. (2014).
The following names have been proposed in the literature but without being accompanied by a valid description.
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Names
|
Associated diseases
|
16Sr group-subgroup
|
|
[Ca. Phytoplasma cocosnigeriae]
|
Nigerian awka disease
|
XXII-A
|
|
[Ca. Phytoplasma cocostanzaniae]
|
Coconut lethal yellowing (Tanzania)
|
IV-C
|
|
[Ca. Phytoplasma luffae]
|
Loofah witches' broom
|
VIII-A
|
|
[Ca. Phytoplasma palmae]
|
Palm lethal yellowing
|
IV-A
|
|
[Ca. Phytoplasma vitis]
|
Grapevine flavescence dorée
|
V-C
|
Useful websites on phytoplasmas
- International Phytoplasmologist Working Group. http://www.ipwgnet.org/
- LPSN – bacterio.net. List of prokaryotic names with standing in nomenclature. Some names included in the category Candidatus (Taxonomic category not covered by the Rules of the Bacteriological Code) http://www.bacterio.net/-candidatus.html
- Phytoplasma resources Center and iPhyClassifier. http://plantpathology.ba.ars.usda.gov/pclass/pclass_phytoplasmaclassification_system2.html
http://plantpathology.ba.ars.usda.gov/cgi-bin/resource/iphyclassifier.cgi
Sources
Fránová J, Bertaccini A, Duduk B (2014) Molecular tools in COST FA0807 Action. In: Bertaccini A (ed.) Phytoplasmas and phytoplasma disease management: how to reduce their economic impact, 179-184.
Available online: http://www.cost.eu/download/FAP_FA0807
Marcone C (2014) Molecular biology and pathogenicity of phytoplasmas. Annals of Applied Biology 165(2), 199-221.