Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Maize tumors caused by Ustilago maydis require organ-specific genes in host and pathogen

ABSTRACT: Two-organism transcriptome profiling of infected seedling, adult leaf, and tassel demonstrated that both the host and pathogen exhibit organ-specific expression programs. Phenotypic screening of U. maydis mutants deleted for suites of secreted protein genes and maize growth mutants demonstrated organ-restricted tumorigenesis. Two-dye, competitive hybridizations were performed on Agilent oligo arrays. Keywords: maize, pathogen, fungus, Ustilago, organ-specificity Comparisons were done 1) between mock and infected samples at 1dpi and 3dpi for seedlings and at 3dpi and 9dpi for adult leave and tassels, 2) between the three 3dpi infected samples, 3) between timepoints of infected samples.

ORGANISM(S): Zea mays

SUBMITTER: John Fernandes

PROVIDER: E-GEOD-20130 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Maize tumors caused by Ustilago maydis require organ-specific genes in host and pathogen.

Skibbe David S DS Doehlemann Gunther G Fernandes John J Walbot Virginia V

Science (New York, N.Y.) 20100401 5974

Infection of maize by corn smut (Ustilago maydis) provides an agronomically important model of biotrophic host-pathogen interactions. After penetration of the maize epidermis, fungal colonization of host tissue induces tumor formation on all aerial maize organs. We hypothesized that transformation of different primordia into plant tumors would require organ-specific gene expression by both host and pathogen and documented these differences by transcriptome profiling. Phenotypic screening of U. m ...[more]

PMID: 20360107

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Project description:Small RNAs (sRNAs) are hypothesized to contribute to hybrid vigor because they maintain genome integrity, contribute to genetic diversity, and control gene expression. We used Illumina sequencing to assess how sRNA populations vary between two maize inbred lines (B73, Mo17) and their hybrid. We sampled sRNAs from the seedling shoot apex and the developing ear, two rapidly growing tissues that program the greater growth of maize hybrids. We found that parental differences in siRNAs primarily originate from repeat regions. Although the maize genome contains greater number and complexity of repeats compared to Arabidopsis or rice, we confirmed that like these simpler plant genomes, 24-nt siRNAs whose abundance differs between maize parents also show a trend of downregulation following hybridization. Surprisingly, hybrid vigor is fully maintained when 24-nt siRNAs are globally reduced by mutation of the RNA-dependent RNA polymerase2 (RDR2) encoded by modifier of paramutation1 (mop1). We also discovered that 21-22nt siRNAs derived from a number of distinct retrotransposon families differentially accumulate between B73 and Mo17 as well as their hybrid. Thus, maize possesses a novel source of genetic variation for regulating both transposons and genes at a genomic scale, which may contribute to its high degree of observed heterosis. sRNA libraries were derived from RNA isolated from the seedling shoot apex and developing ear tissues from B73, Mo17, B73xMo17 and Mo17xB73. The shoot apex was chosen because it is enriched for meristematic tissue where cell proliferation occurs, rates of organ initiation are determined, and organ size is specified. The developing ear was examined because it is enriched in meristematic tissue and is undergoing rapid growth, and also because the mature ear shows the highest degree of heterosis. Total RNA was isolated and separated on a 15% TBE-Urea polyacrylamide gel. Using a 10-bp ladder, the sRNA fraction representing 10-40-bp was excised. sRNA libraries were prepared according to Lu et al. (2007) or manufacturer's instructitions (Illumina). A combination of Perl scripts and FASTX toolkit scripts were used to remove adapters, collapse identical sequences and count reads per sequence. Supplementary processed data text files contain the distinct sRNA sequences for all of the genotypes analyzed in that experiment. Abundance (reads per million) was calculated for each distinct sequence by dividing the number of reads of distinct sRNA in a library by the total number of sRNA reads for that library and multiplying this by 1 million. Genome builds: B73 genome, maizesequence.org release 4a.53 (October, 2009); Mo17 whole genome shotgun clones.

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Dataset Information

Maize tumors caused by Ustilago maydis require organ-specific genes in host and pathogen

Publications

Maize tumors caused by Ustilago maydis require organ-specific genes in host and pathogen.

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