EPPO Global Database

EPPO Reporting Service no. 06 - 2015 Num. article: 2015/118

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).

Candidatus Phytoplasma species’
Associated diseases
16Sr group-subgroup
Genbank nb
Ca. Phytoplasma allocasuarinae’
Allocasuarina yellows
XXXIII-A
AY135523
‘Ca. Phytoplasma americanum’
Potato purple top wilt
XVIII-A
DQ174122
Ca. Phytoplasma asteris’
Aster yellows
I-B
M30790
Ca. Phytoplasma aurantifolia’
Lime witches’ broom
II-B
U15442
Ca. Phytoplasma australasia’*
Papaya dieback
II-D
Y10096
Ca. Phytoplasma australiense’
Australian grapevine yellows
XII-B
L76865
Ca. Phytoplasma balanitae’
Balanites witches’ broom
V-F
AB689678
Ca. Phytoplasma brasiliense’
Hibiscus witches’ broom
XV-A
AF147708
Ca. Phytoplasma caricae’*
Papaya bunchy top
XVII-A
AY725234
Ca. Phytoplasma castaneae’
Chestnut witches’ broom
XIX-A
AB054986
Ca. Phytoplasma convolvuli’
Bindweed yellows
XII-H
JN833705
Ca. Phytoplasma costaricanum’
Soybean stunt
XXXI-A
HQ225630
Ca. Phytoplasma cynodontis’
Bermuda grass white leaf
XIV-A
AJ550984
Ca. Phytoplasma fragariae’
Strawberry yellows
XII-E
DQ086423
Ca. Phytoplasma fraxini’
Ash yellows
VII-A
AF092209
Ca. Phytoplasma graminis’
Sugarcane yellow leaf
XVI-A
AY725228
Ca. Phytoplasma japonicum’
Japanese hydrangea phyllody
XII-D
AB010425
Ca. Phytoplasma lycopersici’
‘Brote grande’
I-Y
EF199549
Ca. Phytoplasma malaysianum’
Periwinkle virescence and phyllody
XXXII-A
EU371934
Ca. Phytoplasma mali’
Apple proliferation
X-A
AJ542541
Ca. Phytoplasma omanense’
Cassia witches’ broom
XXIX-A
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’
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.
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.