12752500 
Site Logo
ARS Home About Us Helptop nav spacerContact Us En Espanoltop nav spacer
Search
   return home
   

Welcome to the
Phytoplasma Resource Center

Hosted
By The
Molecular Plant Pathology Laboratory (MPPL)



II. 'Candidatus Phytoplasma' species*.

In the second system, phytoplasmas are classified into 'Candidatus Phytoplasma' species, based on the nucleotide sequence of the 16S rRNA gene. In this system, the nucleotide sequences of 16S rRNA genes from different phytoplasmas are aligned by a sequence alignment computer program, and the % identities among the sequences are calculated. If the 16S rRNA genes of two phytoplasmas share 97.5% or less nucleotide sequence identity, they are considered to represent two separate 'Candidatus Phytoplasma' species.

The Table below illustrates relationships between the two systems of phytoplasma classification. Each 16S rDNA RFLP group represents at least one distinct 'Candidatus Phytoplasma' species. The Table lists only phytoplasmas that have been formally named as 'Candidatus Phytoplasma' species, phytoplasmas for which 'Candidatus Phytoplasma' names have been suggested but not formally published in the literature, and phytoplasmas recognized as potential new 'Candidatus Phytoplasma' species but for which a 'Candidatus' name has not yet been suggested.

In a separate but related system, phytoplasmas are classified into groups and subgroups, based on the "fingerprint" (RFLP** pattern) of a segment of the gene that encodes 16S rRNA. (LINK TO GROUP section)

--R.E. Davis

-----------------------------------------------------------------------------------------

*Currently, there is no formal taxonomy of phytoplasmas. Phytoplasmas belong to class Mollicutes, which embraces bacteria that lack a cell wall. In class Mollicutes, formal recognition of species, and assignment of binomial Latin names to species, require description of properties of the species growing in pure culture. It is not possible to determine these properties for phytoplasmas, because they cannot be isolated in pure culture. The convention of 'Candidatus Phytoplasma' species has therefore been adopted as a means to refer to distinct phytoplasma lineages and putative species.

**RFLP, restriction fragment length polymorphism




Table 1. 16S rDNA RFLP group-subgroup classification and 'Candidatus Phytoplasma' species.

______________________________________________________________________________________________________________________

Phytoplasma/disease
common name1
16S rDNA
group-subgroup2
GenBank
no.3
Named 'Candidatus
Phytoplasma' species
Informally proposed
'Candidatus Phytoplasma' species4
_________________________________________________________________________________________________
Aster yellows (AY) 16SrI M30790 'Candidatus Phytoplasma asteris'
WB disease of lime 16SrII-B U15442 'Ca. Phytoplasma aurantifolia'
Papaya yellow crinkle 16SrII-D Y10097 'Ca. Phytoplasma australasiae'
Western X-disease 16SrIII-A L04682 'Ca. Phytoplasma pruni'
Palm lethal yellowing 16SrIV-A U18747 'Ca. Phytoplasma palmae'
Elm yellows 16SrV-A AY197655 'Ca. Phytoplasma ulmi'
Jujube WB 16SrV-BAB052876 'Ca. Phytoplasma ziziphi'
Flavescence dorée 16SrV-C AF176319 'Ca. Phytoplasma vitis'
Clover proliferation 16SrVI-A AY390261 'Ca. Phytoplasma trifolii'
Ash yellows 16SrVII-A AF092209 'Ca. Phytoplasma fraxini'
Loofah WB 16SrVIII-A AF086621 'Ca. Phytoplasma luffae'
Almond lethal disease 16SrIX-D AF515636 'Ca. Phytoplasma phoenicium'
Apple proliferation 16SrX-A AJ542541 'Ca. Phytoplasma mali'
Pear decline 16SrX-C AJ542543 'Ca. Phytoplasma pyri'
Spartium WB 16SrX-D X92869 'Ca. Phytoplasma spartii'
European stone fruit Y 16SrX-F AJ542544 'Ca. Phytoplasma prunorum'
Rice yellow dwarf 16SrXI-A AB052873 'Ca. Phytoplasma oryzae'
Stolbur phytoplasma 16SrXII-A AF248959 'Ca. Phytoplasma solani'
Australian GY 16SrXII-B Y10097 'Ca. Phytoplasma australiense'
Hydrangea phyllody 16SrXII-D AB010425 'Ca. Phytoplasma japonicum'
Strawberry yellows 16SrXII-E DQ086423 'Ca. Phytoplasma fragariae'
Mexican periwinkle Vir 16SrXIII-A AF248960 No 'Candidatus' name proposed5
Bermuda grass WL 16SrXIV AJ550984 'Ca. Phytoplasma cynodontis'
Hibiscus WB 16SrXV AF147708 'Ca. Phytoplasma brasiliense'
Sugarcane yellow leaf 16SrXVI AY725228 'Ca. Phytoplasma graminis'
Papaya bunchy top 16SrXVII AY725234 'Ca. Phytoplasma caricae'
Potato purple top wilt 16SrXVIII DQ174122 'Ca. Phytoplasma americanum'
Chestnut WB 16SrXIX AB054986 'Ca. Phytoplasma castaneae'
Buckthorn WB 16SrXX X76431 'Ca. Phytoplasma rhamni'
Pine shoot proliferation 16Sr XXI AJ632155 'Ca. Phytoplasma pini'
Nigerian Awka disease 16Sr XXII-A Y14175 'Ca. Phytoplasma cocosnigeriae'
Buckland Valley GY 16SrXXIII-A AY083605 No 'Candidatus' name proposed5
Sorghum bunchy shoot 16SrXXIV-A AF509322 No 'Candidatus' name proposed5
Weeping tea WB 16SrXXV-A AF521672 No 'Candidatus' name proposed5
Sugarcane yellows
phytoplasma D3T1
16SrXXVI-A AJ539179 No 'Candidatus' name proposed5
Sugarcane yellows
phytoplasma D3T2
16SrXXVII-A AJ539180 No 'Candidatus' name proposed5
Derbid phytoplasma 16SrXXVIII-A AY744945 No 'Candidatus' name proposed5
Cassia italica WB 16SrXXIX EF666051 'Ca. Phytoplasma omanense'
Salt cedar WB 16SrXXX FJ432664 'Ca. Phytoplasma tamaricis'
Allocasuarina yellows Undetermined AY135523 'Ca. Phytoplasma allocasuarinae'
Parsley leaf of tomato " EF199549 'Ca. Phytoplasma lycopersici'
Tanzanian lethal disease " X80117 'Ca. Phytoplasma cocostanzaniae'
Chinaberry yellows " AF495882 No 'Candidatus' name proposed5

______________________________________________________________________________________________________________________

1Abbreviations are as follows: AY, aster yellows; WB, witches'-broom; Y, yellows; GY, grapevine yellows; Vir, virescence; WL, white leaf.

2Group and subgroup are determined on the basis of RFLP patterns of 1.2 kbp segments of 16S rDNA that are delimited by the annealing sites of PCR primers R16F2n and R16R2. 'Candidatus Phytoplasma' species are distinguished on the basis of 16S rDNA nucleotide sequence homology/identity.

3GenBank accession number of 16S rRNA gene sequence documenting description of the 'Candidatus Phytoplasma' species or strain.

4Potentially distinct 'Candidatus Phytoplasma' species names noted by the IRPCM Phytoplasma/Spiroplasma Working Team - Phytoplasma Taxonomy Working Group (2004. International Journal of Systematic and Evolutionary Microbiology 54:1243-1255.). These names have not been formally published.

5Recognized in Wei et al. 2007 (International Journal of Systematic and Evolutionary Microbiology 57:1855-1867.) as potential representatives of new 'Candidatus Phytoplasma' species.

Dr. Robert E. Davis, Research Leader
United States Department of Agriculture Building 004, BARC-West
10300 Baltimore Ave. Beltsville, MD. 20705


[New window link]

-->

webmaster Jonathan Shao, jonathan.shao@.ars.usda.gov

   
 

Databases

 Phytoplasma Classification Database
 
 
ARS Home | USDA.gov | Site Map | Policies and Links 
FOIA | Accessibility Statement | Privacy Policy | Nondiscrimination Statement | Information Quality | FirstGov | White House