Genomics-enabled analysis of the emergent disease cotton bacterial blight

Cotton bacterial blight (CBB), an important disease of (Gossypium hirsutum) in the early 20th century, had been controlled by resistant germplasm for over half a century. Recently, CBB re-emerged as an agronomic problem in the United States. Analysis of cotton variety planting statistics indicates a steady increase in the percentage of susceptible cotton varieties grown each year since 2009. Phylogenetic analysis revealed that strains from the current outbreak cluster with race 18 Xanthomonas citri pv. malvacearum (Xcm) strains. Illumina based draft genomes were generated for thirteen Xcm isolates. These genomes, along with 4 previously published Xcm genomes, encode 24 conserved and nine variable type three effectors. Strains in the race 18 clade contain 3 to 5 more effectors than other Xcm strains. SMRT sequencing of two geographically and temporally diverse strains of Xcm yielded circular chromosomes and accompanying plasmids. These genomes encode eight and thirteen distinct transcription activator-like effector genes. RNA-sequencing revealed 52 genes induced within two cotton cultivars by both tested Xcm strains. This gene list includes a homeologous pair of genes, with homology to the known susceptibility gene, MLO. In contrast, the two strains of Xcm induce different class III SWEET sugar transporters. Subsequent genome wide analysis revealed patterns in the overall expression of homeologous gene pairs in cotton after inoculation by Xcm. These data reveal host-pathogen specificity at the genetic level and strategies for future development of resistant cultivars. Overall design: The cotton varieties Acala Maxxa and DES56 were syringe inoculated with two strains of Xcm (MS14003 and AR81009) and a mock treatment. Tissue was collected in three biological replicates 24 and 48 hours after inoculation.

棉花细菌性枯病（Cotton bacterial blight, CBB）是20世纪早期陆地棉（Gossypium hirsutum）的重要病害，半个多世纪以来一直通过抗病种质资源实现有效防控。近年来，CBB再度在美国成为农业生产难题。对棉花品种种植统计数据的分析显示，自2009年起，每年种植的感病棉花品种占比呈持续稳步上升趋势。系统发育分析表明，当前爆发的病菌菌株聚类于18号柑橘黄单胞菌锦葵致病变种（Xanthomonas citri pv. malvacearum, Xcm）的类群中。本研究对13株Xcm分离株进行了基于Illumina平台的草图基因组测序；连同此前已发表的4株Xcm基因组，共鉴定出24个保守型与9个可变型Ⅲ型效应因子。18号小种进化支的菌株较其他Xcm菌株多携带3至5个效应因子。对两株地理来源与采集时间均存在差异的Xcm菌株进行SMRT测序，获得了包含环状染色体及伴随质粒的完整基因组；这两个基因组分别编码8个与13个不同的转录激活类效应因子。RNA测序分析显示，在两个供试棉花品种中，共有52个基因可被两种测试Xcm菌株诱导表达；其中包括一对部分同源基因对，其序列与已知感病基因MLO具有同源性。与之相对，两种Xcm菌株分别诱导了不同的Ⅲ类SWEET糖转运蛋白基因。后续的全基因组分析揭示了棉花被Xcm接种后，部分同源基因对的整体表达模式特征。上述数据从遗传层面揭示了寄主-病原物的特异性互作关系，也为未来抗病品种的培育提供了可行策略。整体实验设计：选用Acala Maxxa与DES56两个棉花品种，分别采用两株Xcm菌株（MS14003与AR81009）以及空白对照处理进行注射器接种。分别在接种后24小时与48小时采集植物组织样本，设置3次生物学重复。