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Genomics-enabled analysis of the emergent disease cotton bacterial blight

ABSTRACT: 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.

ORGANISM(S): Gossypium hirsutum

PROVIDER: GSE101778 | GEO | 2017/07/24

SECONDARY ACCESSION(S): PRJNA395458

REPOSITORIES: GEO

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Project description:Two winter wheat cultivars possessing a high tolerance to Al (Triticum aestivum L. cv. Atlas66 and the near isogenic line OK91G106, named Century-T in this work [59]) and two winter wheat cultivars with low tolerance to Al (T. aestivum L. cv. Bounty and the near isogenic line OK91G108, named Century-S in this work [59]) were grown as previously described, and treated under conditions where Al remains mostly under the Al3+ form [10]. To reduce pH variations and ensure that Al speciation was stable throughout the experiment, at least 100 ml of solution was used for each plant. The root growth inhibition (RGI) is expressed as 100 × [1- (root growth of Al-treated seedling divided by the root growth of control seedlings)]. Root tips (5-10 mm) were isolated after 24 hours of exposure to Al and frozen on dry ice. Total RNA was isolated from the root tips (5 mm long) of 50 plants collected from the various genotypes using the RNeasy Plant Mini Kit (Qiagen). The RNA quality was assessed on agarose gels and with the Bioanalyzer 2100 (Agilent). Microarray profiling was performed according to Affymetrix protocols at the Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre using the Affymetrix GeneChip Wheat Genome Array. Plants of the different lines were treated with Al concentrations resulting in 50% RGI: 50 ?M for the tolerant cultivars Atlas66 and Century-T and 5 ?M for the sensitive cultivars Bounty and Century-S. Three biological replicates were used and the results were analyzed using the Robust Multiarray Analysis (RMA version 0.2) freeware. Atlas66 and Bounty plants not exposed to Al were used as control for all the other conditions. Genes showing a differential expression greater than two-fold (RMA differential expression of log2 ? 1) between the Atlas66 and Bounty controls were excluded from the reference set as these may represent cultivar dependent differences in basal expression levels that could bias the analysis. Overall, this excluded 1.26% of the genes on the microarray (773 of 55,052) demonstrating that most genes are expressed at a similar level between the two cultivars. The microarray headings are the following : For each array headings: The first term represents the cultivar: A = Atlas66; B = Bounty, 106 = Century-T, 108 = Century-S. The second twerm represents the Al concentration: 0 = no aluminum 5 = 5 ?M aluminum and 50 = 50 ?M aluminum. The last term represents the sample replicate number S1, S2 or S3.

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Genomics-enabled analysis of the emergent disease cotton bacterial blight

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