Understanding a Plant Pathogen Through Genomics: the Interactions of Biogeography, Invasion, and Recombination in the Infection of Plants by Xylella fastidiosa Leonard Nunney, Professor of Biology, University of California, Riverside, CA 92521, 306 SPIETH HALLCorrespondencia: leonard.nunney@ucr.edu My research is in population genetics and evolutionary genomics, with an emphasis on the application of evolutionary theory to practical problems. Current areas of research are: the evolutionary genomics of the plant pathogenic bacterium Xylella fastidiosa; the evolution of cancer suppression; and conservation genetics. The goal of the Xylella project is to understand host adaptation in order to control this bacterium that causes serious disease in a wide range of agricultural crops. Xylella fastidiosa is a xylem-limited bacterium that causes leaf scorch and dwarfing diseases in a wide range of plant hosts (Hopkins & Purcell 2002), including more than 40 species of landscape trees (Sherald 2007). X. fastidiosa is transmitted between plant hosts by xylem-feeding insects, typically leafhoppers (Redak et al 2004). It is restricted to the Americas, and, based on DNA hybridization and sequence data, has been divided into four subspecies, fastidiosa, multiplex, sandyi, and pauca (Schaad et al 2004; Schuenzel et al 2005), with subsp. pauca unique to South America where it causes citrus variegated chlorosis (CVC) and coffee leaf scorch. The other subspecies are all found in North America. To document genetic variation within and between subspecies in more detail we typed X. fastidiosa isolates using multilocus sequence typing (MLST). MLST is based on sequencing regions of (usually) seven housekeeping genes (Maiden et al 1998). Applied to X. fastidiosa it has confirmed the subspecific distinctions, and provided insight into their biogeography, host plant specialization, and the role of homologous recombination. MLST of isolates has shown that there is very little overlap among the subspecies in the host plants that they naturally infect (see Nunney et al. 2013). Subsp. fastidiosa causes Pierce's disease (PD) of grapevine, although it also causes disease in elderberry, alfalfa, and almond. Subsp. multiplex is also found on almond, but otherwise infects hosts not infected by subsp. fastidiosa, including plum, peach, apricot, pecan, oak and sycamore. In contrast to the broad range of subsp. multiplex, subsp. sandyi was first discovered in the 1980s in southern California and it is almost entirely limited to oleander. MLST data allow us to categorize isolates using a very simple system, and this remains useful even when we have whole genome data. X. fastidiosa subsp. pauca was the first plant bacterial pathogen to be fully sequenced by a Brazilian group (Simpson et al. 2000). We now have many more genome sequences; however, MLST allows a massive amount of sequence data to be summarized at a level that is useful for understanding important biological questions (Nunney et al 2012a). Using MLST sequence we examined the phylogenetic relationships among the subspecies and their genetic diversity. Based on the rate of synonymous substitutions, a rough estimate of the age of the subspecies is a few tens of thousands of years (Figure 1), with the South American subsp. pauca being the most divergent. XL Congreso Nacional y XV Congreso Internacional de la Sociedad Mexicana de Fitopatología Revista Mexicana de Fitopatología, Vol. 31 (Suplemento). 2013 S16 fastidiosa sandyi Unknown multiplex N. America pauca S. America Central America 26K yrs 13K yrs 25K yrs 24K yrs 60Kyrs 20K yrs Figure 1. The relationships of the X. fastidiosa subspecies, showing their approximate times of divergence and the probable geographical region where they originated (redrawn from Nunney et al. 2012b). Also shown in Figure 1 are the geographical regions in which we believe these subspecies originated. Based on the genetic data, we concluded that subsp. fastidiosa was native to Central America but that a single strain was introduced into the US just prior to the first recorded outbreak of PD in the late 1800s (Nunney et al. 2010). Subsp. sandyi is almost certainly a form recently introduced into the US, but its native range is unknown. One possibility is that this subspecies is native to southern Mexico. An unexpected feature of the MLST data was the finding of extensive evidence of intersubspecific recombination. We have found intersubspecific genetic introgression in subsp. fastidiosa (Yuan et al. 2010) and in subsp. multiplex in the US (Nunney et al. 2013), and in subsp. pauca from Brazil (Nunney et al. 2012b). We have proposed that intersubspecific recombination can facilitate changes in host range. In particular, the data from subsp. pauca found in Brazil is consistent with the hypothesis that the recent invasion of citrus and coffee (crops cultivated in Brazil for several hundred years) became possible only after the introduction of new genetic variation via intersubspecific recombination. Bibliographic References Hopkins DL, Purcell AH. 2002. Xylella fastidiosa: cause