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United States Department of Agriculture

Agricultural Research Service

Research Project: GENOME SEQUENCE-BASED STRATEGIES FOR DETECTION & IDENTIFICATION OF PLANT PATHOGENIC PHYTOPLASMAS & SPIROPLASMAS, & VASCULAR WALLED BACTERIA

Location: Molecular Plant Pathology

Title: ‘Candidatus Phytoplasma palmicola’, a novel taxon associated with a lethal yellowing-type disease (LYD) of coconut (Cocos nucifera L.) in Mozambique

Authors
item Harrison, Nigel -
item Davis, Robert
item Oropeza, Carlos -
item Eden-Green, Simon -
item Dollet, Michel -
item Dickinson, Matthew -
item Konan, Jean -

Submitted to: International Journal of Systematic and Evolutionary Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 27, 2014
Publication Date: June 1, 2014
Citation: Harrison, N., Davis, R.E., Oropeza, C., Eden-Green, S., Dollet, M., Dickinson, M., Konan, J.L. 2014. ‘Candidatus Phytoplasma palmicola’, a novel taxon associated with a lethal yellowing-type disease (LYD) of coconut (Cocos nucifera L.) in Mozambique. International Journal of Systematic and Evolutionary Microbiology. 64:1890-1899.

Interpretive Summary: Coconut (Cocos nucifera L.) is a member of the palm family and sole recognized species in the genus Cocos. Although coconut originated in the Indo-Pacific region, either around Melanesia, Malesia or land masses bordering the Indian Ocean, this tree has been known for three millennia in Asia Minor, at least two millennia in East Africa, and about five centuries in West Africa and the Americas. Pan-tropical in present day distribution, coconut is often cultivated in environments where few alternative crops can thrive, providing a sustainable source of food and shelter, as well as an important source of rural income to small farmers. Unfortunately, lethal diseases caused by phytoplasmas pose serious threats to sustainability of coconut cultivation worldwide. Phytoplasmas are very small bacteria that are spread from plant-to-plant by insects that feed in the veins of plants including coconut, but unlike many bacteria, phytoplasmas cannot be isolated in laboratory culture. Therefore, molecular methods, primarily DNA-based technologies, are employed to detect, identify, and classify phytoplasmas. There is need to obtain precise molecular markers for identification and classification of the coconut-infecting phytoplasmas to aid the design of appropriate disease control measures and to enable quarantine measures that effectively prevent spread of the disease. Using molecular methods to study specific genes, we found that a phytoplasma causing a lethal coconut disease in western Africa and Mozambique represents a previously undescribed species level lineage, for which in this manuscript we propose the designation, ‘Candidatus Phytoplasma palmicola’. Our results provide molecular markers by which the this phytoplasma may be detected and identified, benefitting measures to control the disease, as well as aiding implementation of quarantine measures to prevent its spread. Such measures will aid the cause of food security and sustainable production of a valued source of raw materials for varied economical uses. This report will be of interest to diagnostics laboratories, research scientists, farmers, quarantine agencies internationally, and international agencies engaged in outreach to underserved populations on several continents.

Technical Abstract: In this study, the taxonomic position and group classification of the phytoplasma associated with a lethal yellowing-type disease (LYD) of coconut (Cocos nucifera L.) in Mozambique were addressed. Pairwise sequence similarity values based on alignment of near full-length 16SrRNA genes (1530 bp) revealed that the Mozambique coconut phytoplasma (LYDM) shared 100% identity with a comparable sequence derived from a phytoplasma strain (LDN), responsible for Awka wilt disease of coconut in Nigeria, and shared 99-99.6% identity with 16S rRNA sequences from strains associated with Cape St. Paul wilt (CSPW) disease of coconut in Ghana and Côte d'Ivoire. Similarity scores further determined the 16S rRNA gene of LYDM phytoplasma to share <97.5% sequence identity with all prior descriptions of ‘Ca. Phytoplasma’ species. Presence of unique regions in the 16S rRNA distinguished LYDM phytoplasma from all currently described ‘Candidatus Phytoplasma’ species, justifying its recognition as reference strain of a novel taxon, ‘Candidatus Phytoplasma palmicola’. Restriction fragment length polymorphism (RFLP) profiles of the F2n/R2 portion (1251 bp) of the 16S rRNA gene and pattern similarity coefficients delineated coconut LYDM phytoplasma strains as new members of group 16SrXXII, subgroup A (16SrXXII-A). Also, Similarity coefficients of 0.97 obtained for comparisons between each latter subgroup 16SrXXII-A strain and CSPW phytoplasmas from Ghana and Côte d'Ivoire matched the threshold value for recognition of new subgroups. On this basis, CSPW phytoplasma strains were designated as members of a new subgroup, 16SrXXII-B.

Last Modified: 10/30/2014
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