Conventional and qPCR reveals the presence of ‘Candidatus Liberibacter solanacearum’ haplotypes A, and B in Physalis philadelphica plant, seed, and Βactericera cockerelli psyllids, with the assignment of a new haplotype H in Convolvulaceae

The husk tomato (Physalis philadelphica Lam.) is an important Solanaceae native to Mesoamerica that is grown for its green fruit used as an important ingredient in domestic and international cuisine. Nevertheless, husk tomato plants with symptoms resembling those caused by ‘Candidatus Liberibacter solanacearum’ (CLso) have been observed during the last decade in plantations located in the State of Mexico, Michoacan and Sinaloa in Mexico. These areas are located near other solanaceous crops where Bactericera cockerelli the well-known psyllid transmitter of CLso is frequently present. Thus, the goal of this study was to determine if CLso haplotypes are present in husk tomato varieties in commercial fields in Mexico. From 2015 to 2016, plants and fruit showing evident symptoms of CLso infection, as well as psyllids were collected in these states and assayed by PCR for CLso using primer sets OA2/OI2c and LpFrag 1-25F/427R. Phylogenetic reconstruction was performed with Bayesian analysis and maximum likelihood methods using amplicon sequences obtained in this work along with those deposited in the GenBank database corresponding to the CLso detected in Solanaceae, Apiaceae, and Convolvulaceae host families. In addition, all the sequences were subjected to haplotype determination through an analysis of DNA polymorphisms using the DnaSP software. Furthermore, quantitative PCR (qPCR) was performed using CLso-specific primers and probes. Phylogenetic reconstruction and qPCR confirmed the presence of CLso in plants, seeds and insect-vectors, and CLso sequences from plants and seeds completely matched haplotype B, whereas CLso haplotypes A and B were detected in B. cockerelli psyllids. Polymorphism analysis identified a novel Convolvulaceae-associated CLso haplotype, which was named haplotype H. The results of this study will enable the dissemination of infected seeds to new husk tomato production areas to be avoided.