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ABSTRACT:
PROVIDER: PRJNA1222107 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Gray leaf spot (GLS) disease of maize can be caused by either of two sibling fungal species Cercospora zeina or Cercospora zeae-maydis. These species differ in geographical distribution, for example to date only C. zeina is associated with GLS in African countries, such as South Africa. Maize inbred line B73, which is susceptible to GLS, was planted in the field, and subjected to natural infection with C. zeina. Samples were collected from lower leaves with substantial GLS lesions and younger upper leaves of the same plants with very few immature GLS lesions. The first aim of the experiment was to determine which maize genes are induced in response to C. zeina infection. The second aim was to identify C. zeina genes expressed in planta during a compatible interaction. The third aim was to determine whether the C. zeina cercosporin biosynthetic (CTB) genes are expressed in planta. C. zeina fails to produce cercosporin in vitro in contrast to C. zeae-maydis. Cercosporin is a phytotoxin that is thought to play a role in pathogenicity of several Cercospora spp., however its role in the pathogenicity strategy of C. zeina is currently under investigation.
2017-06-14 | GSE94442 | GEO
Project description:Gray leaf spot (GLS) disease of maize is caused by the fungus Cercospora zeina in African countries, such as South Africa. The plant material was from maize inbred line B73-QTL, which was introgressed with a QTL region for resistance to GLS from the maize inbred line CML444 (Berger et al (2014) BMC Genetics 15 60 www.biomedcentral.com/1471-2156/15/60 ). This QTL was named 10G2_GLS and 10H_GLS from two field trials in KwaZulu-Natal province, South Africa in that study. B73-QTL plants were planted in the field, and subjected to natural infection with C. zeina. This was the same field trial as B73 plants that were sampled for RNAseq and the data reported in Swart et al (2017) Mol Plant Microbe Interact 30 710-724 (2017)(GSE94442). Samples were collected from lower leaves with moderate GLS lesions and younger upper leaves of the same B73-QTL plants with very few immature GLS lesions. The first aim of the experiment was to compare the maize transcriptomes during C.zeina challenge between B73 (from GSE94442 data) and B73-QTL plants (this study). The second aim was to identify novel transcripts expressed from the QTL region, which may underlie the quantitative disease resistance to GLS. The third aim was to identify C. zeina genes expressed in planta during infection.
2020-02-14 | GSE137198 | GEO
Project description:Purpose: The aim was to compare the transcriptome (using RNASeq) of a Cercospora zeina-resistant line (RIL387) and a Cercospora zeina susceptible line (RIL165), following inoculation by Cercospora zeina, in order to identify the defense responses associated with each line. Methods: Plants were grown in rows in three randomised blocks. Natural infection with Cercospora zeina was allowed to take place. Infected leves were harvested at the R5-early dent stage. Three leaves (one per plant) were harvested per block and pooled to make up one biological rep. One biological rep was harvested per block for each line. RNA was extracted and sequenced using Illumina. Sequencing reads were mapped to the B73 reference genome and were analysed using the Tuxedo suite of tools (Top hat, Cufflinks, Cuffmerge and Cuffdiff). Results: 5349 genes were differentially expressed between RIL165 and RIL387. In order to dissect responses specific to RIL165 and RIL387, 2394 genes with Log2FC ≤-1 were defined as having higher expression in RIL165 compared to RIL387 and 1393 genes with a Log2FC ≥1 as having increased expression in RIL387 compared to RIL165. Nine genes were validated using RT-qPCR. Four reference genes were included in the RT-qPCR analysis. Differentially expressed genes were further analysed for GO enrichment and pathway representation. Conclusions: Our RNA-Seq results show that a resistant and susceptible line repond differently to infection with Cercospora zeina, as differentially expressed genes were identified between the two lines.
2018-02-13 | GSE99005 | GEO
Project description:Gray leaf spot (GLS) disease of maize can be caused by either of two sibling fungal species Cercospora zeina or Cercospora zeae-maydis. These species differ in geographical distribution, for example to date only C. zeina is associated with GLS in Africa. C. zeae-maydis isolates produce the phytotoxin cercosporin in vitro, whereas C. zeina does not. C.zeina was grown in different in vitro conditions to determine if the cercosporin biosynthesis genes were expressed. Furthermore, the choice of a range of different in vitro conditions was aimed at capturing transcript sequences from a broad range of genes to aid in identification of gene models for annotation of the C.zeina genome sequence.
2017-06-14 | GSE90705 | GEO
Project description:Maize exhibits levels of structural variation (SV) of non-repeat sequences that are unprecedented among higher eukaryotes. This SV includes hundreds of copy number variants (CNVs) and thousands of presence/absence variants (PAVs). Many of the PAVs contain intact, expressed, single-copy genes that are present in one haplotype but absent from another. The goal of this project is to test the hypothesis that differences in gene copy number (both gains and losses) contribute to the extraordinary phenotypic diversity and plasticity of maize. Maize is a good model for these studies because it exhibits a rapid decay of linkage disequilibrium (LD) and because a draft genome sequence of the B73 inbred and mapping populations are available. As a first step, the Zeanome, a near-complete set of genes present in B73, other maize lines and the wild ancestor of maize (teosinte), is being defined using transcriptomic data.
2012-03-29 | E-MTAB-4311 | biostudies-arrayexpress
Project description:Maize exhibits levels of structural variation (SV) of non-repeat sequences that are unprecedented among higher eukaryotes. This SV includes hundreds of copy number variants (CNVs) and thousands of presence/absence variants (PAVs). Many of the PAVs contain intact, expressed, single-copy genes that are present in one haplotype but absent from another. The goal of this project is to test the hypothesis that differences in gene copy number (both gains and losses) contribute to the extraordinary phenotypic diversity and plasticity of maize. Maize is a good model for these studies because it exhibits a rapid decay of linkage disequilibrium (LD) and because a draft genome sequence of the B73 inbred and mapping populations are available. As a first step, the Zeanome, a near-complete set of genes present in B73, other maize lines and the wild ancestor of maize (teosinte), is being defined using transcriptomic data.
2012-03-29 | E-MTAB-4436 | biostudies-arrayexpress