Phytoplasma classification
Phytoplasmas are a large group of bacteria lacking cell walls, associated with numerous plant diseases of economic importance. As attempts to routinely culture phytoplasmas in artificial growing media have failed, their study and classification is difficult. The current phytoplasma classification is largely based on the 16S rRNA gene sequence. The possible use of additional genes to better identify and classify phytoplasmas is being studied, as some closely related strains are currently difficult to separate using the 16S rRNA-encoding gene alone.
For the moment, phytoplasmas are classified either into ‘Candidatus Phytoplasma’ species based on percent sequence identity of a unique 16S rRNA gene (>1200 bp) with any previously described species (i.e. the threshold being less than 97.5% similarity), or into 33 ribosomal groups, each comprising a number of subgroups (obtained by RFLP and/or virtual RFLP analyses of the 16S ribosomal gene amplicon or sequence with a number of restriction enzymes).
The number of new ‘Candidatus Phytoplasma’ species and ribosomal groups and subgroups is constantly growing, and it has not yet been possible to attribute a ‘Candidatus Phytoplasma’ name to all studied phytoplasmas. In particular, for some diseases of quarantine importance, such as grapevine flavescence dorée (16SrV group, subgroups V-C and V-D) or some of the palm lethal yellowing diseases (16SrIV group), the grouping and subgrouping is still the accepted taxonomy (because no ‘Candidatus Phytoplasma’ species descriptions have been officially proposed).
The table below (from Bertaccini, 2019) shows the currently proposed ‘Candidatus Phytoplasma species’ and their 16Sr groups - subgroups. As explained above, many phytoplasmas have not been attributed a ‘Candidatus Phytoplasma’ species name but are classified only on the basis of their 16Sr group and subgroup only (these are not shown in the table).
16Sr group-subgroup | ‘Candidatus Phytoplasma species’ | Associated disease |
I-B | ‘Ca. Phytoplasma asteris’ | Aster yellows |
I-Y | ‘Ca. Phytoplasma lycopersici’ | Tomato 'brote grande' |
II-B | ‘Ca. Phytoplasma aurantifolia’ | Lime witches’ broom |
II-D | ‘Ca. Phytoplasma australasia’ | Papaya mosaic |
III-A | ‘Ca. Phytoplasma pruni’ | Peach X-disease |
V-A | ‘Ca. Phytoplasma ulmi’ | Elm yellows |
V-B | ‘Ca. Phytoplasma ziziphi’ | Jujube witches’ broom |
V-E | ‘Ca. Phytoplasma rubi’ | Rubus stunt |
V-F | ‘Ca. Phytoplasma balanitae’ | Balanites witches’ broom |
VI-A | ‘Ca. Phytoplasma trifolii’ | Clover proliferation |
VI-I | ‘Ca. Phytoplasma sudamericanum’ | Passionfruit witches’ broom |
VII-A | ‘Ca. Phytoplasma fraxini’ | Ash yellows |
VIII-A | ‘Ca. Phytoplasma luffae’ | Loofah witches' broom |
IX-B | ‘Ca. Phytoplasma phoenicium’ | Almond witches’ broom |
X-A | ‘Ca. Phytoplasma mali’ | Apple proliferation |
X-B | ‘Ca. Phytoplasma prunorum’ | European stone fruit yellows |
X-C | ‘Ca. Phytoplasma pyri’ | Pear decline |
X-D | ‘Ca. Phytoplasma spartii’ | Spartium witches’ broom |
XI-A | ‘Ca. Phytoplasma oryzae’ | Rice yellow dwarf |
XI-E | ‘Ca. Phytoplasma cirsii’ | Cirsium phytoplasma |
XII-A | ‘Ca. Phytoplasma solani’ | Stolbur |
XII-B | ‘Ca. Phytoplasma australiense’ | Australian grapevine yellows |
XII-D | ‘Ca. Phytoplasma japonicum’ | Japanese hydrangea phyllody |
XII-E | ‘Ca. Phytoplasma fragariae’ | Strawberry yellows |
XII-H | ‘Ca. Phytoplasma convolvuli’ | Bindweed yellows |
XIII-A | ‘Ca. Phytoplasma hispanicum’ | Mexican periwinkle virescence |
XIII-G | ‘Ca. Phytoplasma meliae’ | Chinaberry yellowing |
XIV-A | ‘Ca. Phytoplasma cynodontis’ | Bermuda grass white leaf |
XV-A | ‘Ca. Phytoplasma brasiliense’ | Hibiscus witches’ broom |
XVI-A | ‘Ca. Phytoplasma graminis’ | Sugarcane yellow leaf |
XVII-A | ‘Ca. Phytoplasma caricae’ | Papaya bunchy top |
XVIII-A | ‘Ca. Phytoplasma americanum’ | American potato purple top wilt |
XIX-A | ‘Ca. Phytoplasma castaneae’ | Chestnut witches’ broom |
XX-A | ‘Ca. Phytoplasma rhamni’ | Rhamnus witches’ broom |
XXI-A | ‘Ca. Phytoplasma pini’ | Pinus phytoplasma |
XXII-A | ‘Ca. Phytoplasma palmicola’ | Lethal yellowing |
XXIX-A | ‘Ca. Phytoplasma omanense’ | Cassia witches’ broom |
XXX-A | ‘Ca. Phytoplasma tamaricis’ | Salt cedar witches’ broom |
XXXI-A | ‘Ca. Phytoplasma costaricanum’ | Soybean stunt |
XXXII-A | ‘Ca. Phytoplasma malaysianum’ | Malaysian periwinkle virescence |
XXXIII-A | ‘Ca. Phytoplasma allocasuarinae’ | Allocasuarina phytoplasma |
XXXVI-A | ‘Ca. Phytoplasma wodyetiae’ | Foxtail palm phytoplasma |
- | ‘Ca. Phytoplasma noviguineense’ | Bogia coconut syndrome |
Sources
Bertaccini A (2019) The phytoplasma classification between ‘Candidatus species’ provisional status and ribosomal grouping system. Phytopathogenic Mollicutes 9(1), 1-2.
Bertaccini A, Lee IM (2018) Phytoplasmas: an update. In: Phytoplasmas: plant pathogenic bacteria – I. Springer, pp 1-29.
Perez-Lopez E, Olivier CY, Luna-Rodriguez, Dumonceaux TJ (2016) Phytoplasma classification and phylogeny based on in silico and in vitro RFLP analysis of cpn60 universal target sequences. International Journal of Systematic and Evolutionary Microbiology 66, 5600–5613.