Location: Horticultural Crops Research
Project Number: 2072-22000-043-35-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 15, 2018
End Date: Sep 30, 2020
1. Collect Globodera spp. populations from South America. 2. Molecularly characterize and generate global phylogenies of Globodera spp.
Globodera spp. populations will be collected in collaboration with collaborators in Chile, Peru, and Bolivia. These contacts have already been made with collaborations in place with Servicio Agricola y Ganadero, Chile (Pancheco and Acevedo) and CABI, Bolivia (Franco). Sampling will focus on the Andes region which is assumed to be the place of origin of Globodera spp. Compared to other globally important pathogens (i.e., Phytophthora) there are only a handful of South American Globodera populations that have been included in population genetics studies; this study will significantly add to the number of populations which can be included in phylogenetic analyses to encompass Globodera diversity worldwide. Preliminary results from samples collected in Chile indicate that populations will likely be a mix of species, therefore, all analyses will be conducted on single cysts. Whole genome shotgun sequencing from cyst extracted genomic DNA will be conducted on the Illumina HiSeq 3000 platform. Genomes will be assembled using a combination of de novo assembly methods and reference guided methods utilizing closely related Globodera genomes; there are genomes available for G. rostochiensis, G. pallida, and G. ellingtonae. Single-copy orthologous protein sequences will be mined from assembled genomes using hidden Markov models (HMM) and aligned to one another. The resulting multi-gene alignment will be used to generate a phylogenomic tree to visualize the revolutionary relationships of new populations and known Globodera species.