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hugh.harries · hugh.harries@gmail.com | Group Owner  - Edit Membership Start a Group | My Groups
CICLY · Lethal Yellowing Disease of Coconut Palm

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Re: C I C L Y Differentiation and classification of phytoplasmas.   Message List  
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Hello Hugh,
Unfortunately, not very much.  The rp gene cluster S19-L22-S3, or portions therof, has beeen the subject of considerable investigation because RFLP or sequence analysis of the amplified genes has a seemingly greater resolving power for strain identification than do similar analyses of the 16S rRNA gene. 
This statement certainly holds true for aster yellows (RFLP group 16SrI) phytoplasmas (i.e. 'Candidatus Phytoplasma asteris' and related strains) and seemingly for group 16SrV strains too.  Precise identification of strains is very helpful of course for accurately determining plant and insect hosts for understanding disease epidemiology.
I have had an opportunity to evaluate the S19-L22-S3 rp gene cluster for resolving coconut lethal yellowing (CLY) and related 16SrIV group strains and found that this marker delineates the strains I have at my disposal into 2 subgroups (lineages) only.  A very different outcome from work with groups 16SrI or 16SrV.
One often overlooked or never stated advantage to working with some of these alternative genetic markers is that primers used for their apmflification are often quite robust and more exacting than the phytoplasma 'universal' rRNA gene primers which while detecting all phytoplasmas occasionally detect bacteria other than phytoplasmas too.
We are wrapping up a study in which we have developed PCR assays targeting several other LY gene markers in addition to the rp genes, with mixed results.  However, two of these assays clearly distinguish the strain associated with CLY in Jamaica, from strains associated with CLY in Florida, Mexico, Belize and Honduras. I choose my words carefully here because there are numerous LY group 16SrIV strains that have been recently described in Jamaica. These newly detected strains have been found in an assortment of understory dicot plant species and insects (Cedusa sp.) and characterized on the basis of their 16S rRNA gene sequence.  So far none of these strains have been shown to occur (infect) in LY-affected coconut.
On a related note, we have been investigating a new phytoplasma disease of palms in west-central Florida affecting mostly Phoenix sp. Known hosts so far include P. dactylifera, P. canariensis and P. syslvestris as well as Queen palm (Syagrus romanzoffiana).  The 16S rRNA gene sequence of the associated strain is identical to that of another LY group strain we had previously characterized from declining P. canariensis in coastal southern Texas (Corpus Christi). 
We expended much energy speculating upon vectors and developing scenarios that might account for spread of the Texas disease (strain) into Florida.  Since this initial finding, we have compared these two strains (Texas vs. Florida) using another gene marker which clearly shows they are not identical. Based on this new information, it now seems unlikely that the new disease arrived in Florida from Texas. So there is value to looking at other genetic markers for finer distinction of strains.  Unfortunately, this is an example of how additional information can ruin a good story without providing any alternative insight into the source of the disease.
Best regards, Nigel
----- Original Message -----
Sent: Thursday, September 06, 2007 7:01 AM
Subject: C I C L Y Differentiation and classification of phytoplasmas.


Can you say what this might mean specifically to LY?


Ribosomal protein gene-based phylogeny for finer differentiation and classification of phytoplasmas.
M Martini, IM Lee, KD Bottner, Y Zhao, S Botti, A Bertaccini, NA Harrison, L Carraro, C Marcone, AJ Khan, and R Osler
Int J Syst Evol Microbiol, September 1, 2007; 57(Pt 9): 2037-51.            

Extensive phylogenetic analyses were performed based on sequences of the 16S rRNA gene and two ribosomal protein (rp) genes, rplV (rpl22) and rpsC (rps3), from 46 phytoplasma strains representing 12 phytoplasma 16Sr groups, 16 other mollicutes and 28 Gram-positive walled bacteria. The phylogenetic tree inferred from rp genes had a similar overall topology to that inferred from the 16S rRNA gene. However, the rp gene-based tree gave a more defined phylogenetic interrelationship among mollicutes and Gram-positive walled bacteria. Both phylogenies indicated that mollicutes formed a monophyletic group. Phytoplasmas clustered with Acholeplasma species and formed one clade paraphyletic with a clade consisting of the remaining mollicutes. The closest relatives of mollicutes were low-G+C-content Gram-positive bacteria. Comparative phylogenetic analyses using the 16S rRNA gene and rp genes were performed to evaluate their efficacy in resolving distinct phytoplasma strains. A phylogenetic tree was constructed based on analysis of rp gene sequences from 87 phytoplasma strains belonging to 12 16Sr phytoplasma groups. The phylogenetic relationships among phytoplasmas were generally in agreement with those obtained on the basis of the 16S rRNA gene in the present and previous works. However, the rp gene-based phylogeny allowed for finer resolution of distinct lineages within the phytoplasma 16Sr groups. RFLP analysis of rp gene sequences permitted finer differentiation of phytoplasma strains in a given 16Sr group. In this study, we also designed several semi-universal and 16Sr group-specific rp gene-based primers that allow for the amplification of 11 16Sr group phytoplasmas."

Source: http://highwire.stanford.edu/cgi/medline/pmid;17766869

Thu Sep 6, 2007 6:03 pm

"Nigel A. Harrison" <naha@ufl.edu>
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Hello Hugh, Unfortunately, not very much. The rp gene cluster S19-L22-S3, or portions therof, has beeen the subject of considerable investigation because RFLP...
Nigel A. Harrison
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Sep 6, 2007
8:34 pm

Nigel Thanks for you prompt and detailed answer. If only some others could do likewise . . . I have taken a couple of your points to start other lines of...
Hugh Harries
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Sep 8, 2007
3:12 pm

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