TY - JOUR T1 - Genomics-enabled analysis of the emergent disease cotton bacterial blight JF - bioRxiv DO - 10.1101/127670 SP - 127670 AU - Anne Z. Phillips AU - Jeffrey C. Berry AU - Mark C. Wilson AU - Anupama Vijayaraghavan AU - Jillian Burke AU - J. Imani Bunn AU - Tom W. Allen AU - Terry Wheeler AU - Rebecca Bart Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/04/15/127670.abstract N2 - Cotton bacterial blight (CBB), an important disease of (Gossypium hirsutum) in the early 20th century, had been controlled by resistance genes for over half a century. Recently, CBB re-emerged as an agronomic problem in the United States. Here, a comparative genomics analysis of host and pathogen was conducted. Phylogenetic analysis revealed that strains from the current outbreak cluster with race 18 Xanthomonas citri pv. malvacearum (Xcm) strains. Type three effector repertoires of 16 Xcm isolates reveal 24 conserved effectors as well as nine variable effectors. In addition, virulent race 18 strains contain 3 to 5 more effectors than non-race 18 strains. Genome assemblies for two geographically and temporally divergent strains of Xcm, yielded circular chromosomes and accompanying plasmids. These genomes encode eight and thirteen distinct transcription activator-like effector genes. RNA-sequencing revealed that both strains induced 52 conserved gene targets in diverse cotton cultivars, including a homeologous pair of genes, with homology to the known susceptibility gene, MLO. In contrast, the two strains of Xcm induced different SWEET sugar transporters and in one case, only one homeolog was significantly induced. Subsequent genome wide analysis revealed the overall expression patterns of the homeologous gene pairs in cotton after inoculation by Xcm. These data reveal host-pathogen specificity in the Xcm-G. hirsutum pathosystem, give explanations for the CBB reemergence, and strategies for future development of resistant cultivars.Author Summary Cotton bacterial blight (CBB), caused by Xanthomonas citri pv. malvacearum (Xcm), significantly limited cotton yields in the early 20th century but has been controlled by classical resistance genes for more than 50 years. In 2011, the pathogen re-emerged with vengeance. In this study, we compare diverse pathogen isolates and cotton varieties to further understand the virulence mechanisms employed by Xcm and to identify promising resistance strategies. We generate fully contiguous genome assemblies for two diverse Xcm strains and identify pathogen proteins used to modulate host transcription and promote susceptibility. RNA-Sequencing of infected cotton reveals novel putative gene targets for the development of durable Xcm resistance. Together, the data presented reveal the underlying cause of CBB re-emergence in the U.S. and highlight several promising routes towards the development of durable resistance including classical resistance genes and potential manipulation of susceptibility targets. ER -