0Xanthomonas perforans is the predominant pathogen responsible for bacterial leaf spot of tomato 1 1 and X. euvesicatoria of pepper in the southeast United States. Previous studies have indicated 1 2 significant changes in the X. perforans population collected from Florida tomato fields over the 1 3 span of two decades including a shift in race, diversification into three genetic groups, and host 1 4 range expansion to pepper. Recombination originating from X. euvesicatoria was identified as 1 5 the primary factor driving the diversification of X. perforans in Florida. The aim of this study 1 6 was to genetically characterize X. perforans strains that were isolated from tomato and pepper 1 7 plants grown in Alabama and compare them to the previously published genomes available from 1 8GenBank. Surprisingly, a maximum likelihood phylogeny coupled with a Bayesian analysis of 1 9 population structure revealed the presence of two novel genetic groups in Alabama, which each 2 0 harbored a different transcription activation-like effector (TALE). While one TALE, avrHah1, 2 1 2 was associated with adaptation of X. perforans to pepper, the other was identified as a new class 2 2 within the avrBs3 family, designated here as pthXp1. Examination of patterns of homologous 2 3 recombination between X. perforans and other closely related Xanthomonas spp. indicated that 2 4 the lineages identified here emerged in part through recent recombination events originating 2 5 from xanthomonads associated with diverse hosts of isolation. Our results also suggest that the 2 6 evolution of pathogenicity to pepper has likely emerged independently within X. perforans and 2 7 in one lineage, was associated with the recombination-mediated remodeling of the Xps type II 2 8 secretion and TonB transduction systems. 2 9 Importance 3 0The emergence of novel pathogen lineages has important implications in the sustainability of 3 1 genetic resistance as a disease management tool in agricultural ecosystems. In this study, we 3 2 identified two novel lineages of X. perforans in Alabama. While one lineage was isolated from 3 3 symptomatic pepper plants, confirming the host range expansion of X. perforans, the other 3 4 lineage was isolated from tomato and acquired a novel transcription activation-like effector, 3 5 pthXp1. Unlike AvrBs4, PthXp1overcomes Bs4-mediated resistance in tomato, indicating the 3 6 evolution of this novel lineage towards fitness on this host. Our findings also show that different 3 7 phylogenetic groups of the pathogen have experienced independent recombination events 3 8 originating from multiple Xanthomonas species. This suggests a continuous gene flux between 3 9 related xanthomonads associated with diverse plant hosts which results in the emergence of 4 0 novel pathogen lineages and associated phenotypes, including host range expansion.4 1