GENOME-BASED STRATEGIES FOR DETECTION AND IDENTIFICATION OF PLANT PATHOGENIC PHYTOPLASMAS AND SPIROPLASMAS
Title: Onion is a host for two phytoplasma lineages, subgroups 16SrI-A and 16SrI-L, in Lithuania: a HinfI site revealed a SNP marking divergent branches of evolution
Submitted to: Journal of Plant Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 25, 2010
Publication Date: September 1, 2010
Citation: Jomantiene, R., Davis, R.E., Lee, I., Zhao, Y., Bottner-Parker, K.D., Valiunas, D., Petkauskaite, R. 2010. Onion is a host for two phytoplasma lineages, subgroups 16SrI-A and 16SrI-L, in Lithuania: a HinfI site revealed a SNP marking divergent branches of evolution. Journal of Plant Pathology. 92:461-470.
Interpretive Summary: Phytoplasmas are very small bacteria that cause damaging diseases in agriculturally important crops and in plants growing in natural areas. There is need to determine whether phytoplasmas are involved in newly recognized diseases of plants, including diseases of vegetables, and to identify phytoplasmas associated with emerging diseases, so that appropriate disease control measures may be devised based on knowledge of the disease-causing agents. The present work focused on a disease of onion (Alliun cepa) in Europe; the cause of the disease was unknown. Using molecular methods for detection and identification, we found that phytoplasmas apparently cause the disease, which we have named onion proliferation (OnP) disease. We discovered that two different phytoplasmas were associated with the disease. While studying how to identify one of the phytoplasmas, we discovered that differences n a single base (single nucleotide polymorphism, SNP, in building block of DNA) was a powerful molecular marker of phytoplasma evolution. Our results provide molecular markers useful for following the spread of the onion disease phytoplasmas to new geographic regions. This report will be of interest to diagnostics laboratories, research scientists, international quarantine agencies including APHIS, and scientists researching the evolution of bacteria, including phytoplasmas. By revealing a new vegetable disease and its apparent cause, the work immediately impacts food security and efforts to attain sustainable agriculture systems.
Onions (Allium cepa.L) being grown for seed production in the Kaunas region of Lithuania exhibited symptoms including mild yellowing of leaves and stems, stunting of plants, phyllody, and proliferation of flowers. RFLP and sequence analysis of PCR-amplified 16S rRNA, ribosomal protein, and secY genes revealed the presence of phytoplasmas that belonged to subgroups 16SrI-A (rpI-A) and 16SrI-L (rpI-B, secY-IB). The results indicated that strains in subgroup16SrI-A (rpI-A) have potential to damage onions in Europe, as well as in North America, and for the first time demonstrated onion as a host for subgroup 16SrI-L. Subgroup 16SrI-L was distinguished based on a composite HinfI RFLP pattern of 16S rDNA that revealed the presence of two sequence heterogeneous rRNA operons in this subgroup, illustrating the significance of composite RFLP patterns for phytoplasma identification and classification. A single nucleotide polymorphism (SNP) in the first base of one HinfI recognition site (GAnTC) marked the divergence of major phylogenetic branches, supporting the concept that SNPs provide powerful molecular markers of phytoplasma evolution.