Xanthomonas citri pv. malvacearum Raw sequence reads. Xanthomonas citri pv. malvacearum

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 a vengeance. The Xcm pathovar can be further divided into at least 19 races according to virulence phenotypes on a panel of historical cotton cultivars. Historically, the most common race observed in the U.S. has been race 18, which was first isolated in 1973. This race is highly virulent, causing disease on all cultivars in the panel except for 101-102.B. Thirteen Xcm strains were sequenced using Illumina technology to determine the phylogenetic relationship between recent isolates of Xcm and historical isolates. Isolates designated as race 1, race 2, race 3, race 12 and race 18 have been maintained at Mississippi State University with these designations. Additional isolates were obtained from the Collection Française de Bactéries associées aux Plantes (CFBP) culture collection. Together, these isolates include nine strains from the US, three from Africa, and one from South America and span collection dates ranging from 1958 through 2014. 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.

棉花细菌性枯斑病（Cotton bacterial blight, CBB）由地毯草黄单胞菌锦葵致病变种（Xanthomonas citri pv. malvacearum, Xcm）引发，曾在20世纪早期严重制约棉花产量，但通过经典抗病基因已实现长达50余年的有效防控。2011年，该病原菌再度强势复发。依据供试历史棉花品种集合的致病型表型，Xcm致病变种可被划分为至少19个生理小种。历史上，美国境内检出的最常见生理小种为18号小种，该小种于1973年首次被分离获得。该小种致病力极强，可侵染供试集合中的全部棉花品种，仅101-102.B除外。本研究采用Illumina测序技术对13株Xcm菌株进行全基因组测序，以解析新近分离菌株与历史分离菌株之间的系统发育关系。编号为1号、2号、3号、12号及18号小种的分离菌株由密西西比州立大学保藏并沿用上述编号。其余分离菌株取自法国植物相关细菌菌种保藏中心（Collection Française de Bactéries associées aux Plantes, CFBP）。综上，本次研究涵盖的分离菌株共计13株：其中9株分离自美国、3株来自非洲、1株源自南美，采集时间跨度为1958年至2014年。本研究通过对不同病原菌分离菌株与棉花品种开展联合分析，旨在深入解析Xcm的致病机制，并筛选出具有应用潜力的抗病防控策略。