Transcriptomics

Dataset Information

26

Solanum chacoense Transcriptome or Gene expression


ABSTRACT: To provide a broad analysis of gene expression changes in developing embryos from a solanaceous species, we produced amplicon-derived microarrays with 7741 ESTs isolated from Solanum chacoense ovules bearing embryos from all developmental stages. Our aims were to: 1) identify genes expressed in a tissue-specific and temporal-specific manner; 2) define clusters of genes showing similar patterns of spatial and temporal expression; and 3) identify stage-specific or transition-specific candidate genes for further functional genomic analyses.We analyzed gene expression during S. chacoense embryogenesis in a series of experiments with probes derived from ovules isolated before and after fertilization (from 0 to 22 days after pollination), and from leaves, anthers, and styles. From the 6374 unigenes present in our array, 1024 genes were differentially expressed (≥ ±2 fold change, p value ≤ 0.01) in fertilized ovules and only limited expression overlap was observed between these genes and the genes expressed in the other tissues tested, with more than three quarters of the fertilization-regulated genes specifically or predominantly expressed in ovules. During embryogenesis three major expression profiles corresponding to early, middle and late stages of embryo development were identified. From the early and middle stages, a large number of genes corresponding to cell cycle, DNA processing, signal transduction, and transcriptional regulation were found. Defense and stress response-related genes were found in all stages of embryo development. Protein biosynthesis genes, genes coding for ribosomal proteins and other components of the translation machinery were highly expressed in embryos during the early stage. Genes for protein degradation were overrepresented later in the middle and late stages of embryo development. As expected, storage protein transcripts accumulated predominantly in the late stage of embryo development. Our analysis provides the first study in a solanaceous species of the transcriptional program that takes place during the early phases of plant reproductive development, including all embryogenesis steps during a comprehensive time-course. Our comparative expression profiling strategy between fertilized and unfertilized ovules identified a subset of genes specifically or predominantly expressed in ovules while a closer analysis between each consecutive time points allowed the identification of a subset of stage-specific and transition-specific genes. Overall design: We produced amplicon-derived microarrays with 7741 ESTs isolated from Solanum chacoense ovules bearing embryos from all developmental stages. To monitor the expression pattern from genes involved in fertilization and embryogenesis processes, flowers were hand-pollinated and ovules were isolated every two days during a 22 days period after pollination. Four independent biological replicates were produced from each time points. In addition, to isolate genes specifically or predominantly expressed in ovules, four biological replicates of leaf, anther, and style tissue mRNA preparations were individually hybridized against unfertilized ovule mRNAs and compared with the data obtained from unfertilized and fertilized ovules at various time points after pollination. To estimate reproducibility and to produce control data for statistical analysis, a large number of unfertilized ovules were isolated and separated between seven independent control groups. RNA from randomly selected pairs of control was hybridized on six microarrays. 6374 unigenes present in our array in duplicate.

INSTRUMENT(S): Microarray lab/BRI-NRC Solanum chacoense 7.7K V1.0 array

ORGANISM(S): Solanum chacoense  

SUBMITTER: Faiza Tebbji  

PROVIDER: GSE21552 | GEO | 2010-05-13

SECONDARY ACCESSION(S): PRJNA126221

REPOSITORIES: GEO

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