Dataset Information

EST sequencing and microarray analysis of the floral transcriptome of Eustoma grandiflorum

ABSTRACT: Genome-wide DNA sequence resources are expected to enhance our understanding of the molecular basis of plant development and lead to improvements in desirable traits in horticultural crops. In this study, we sequenced 643,366 ESTs from Eustoma grandiflorum flowers using a normalised cDNA library constructed for several different flower development stages, times of day, and pollinated stamens. The sequences were assembled into 63,401 contigs and 242,212 singletons. BlastX searches for all of the contigs in the GenBank database matched 65% of the contigs to registered sequences, while 35% presented no hits. GO mapping assigned 48% of the 63,401 contigs to GO terms. Microarray analysis showed that subsets of genes were up- or downregulated as the flower developed. The downregulated genes were enriched for GO terms related to 1) oligopeptide transport, 2) response to jasmonic acid stimulus, and 3) cell wall modification, whereas the upregulated genes were enriched for GO terms involved in 1) secondary metabolism, such as the flavonoid biosynthetic process and the terpenoid biosynthetic process, and 2) epidermal cell modification.

ORGANISM(S): Eustoma grandiflorum

PROVIDER: GSE34332 | GEO | 2012/09/01

SECONDARY ACCESSION(S): PRJNA151455

REPOSITORIES: GEO

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Project description:Background: Tomato (Solanum lycopersicum) self-compatibility (SC) is defined as self-pollen tubes that can penetrate their own stigma, elongate in the style and fertilize their own ovules. Self-incompatibility (SI) is defined as self-pollen tubes that are prevented from developing in the style. To determine the influence of gene expression on style self-pollination, a transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles was performed using RNA-sequencing (RNA-seq) data. Results: Transcriptome profiles of 24-h unpollination (UP) and self-pollination (P) styles from SC and SI tomato species were generated using high-throughput next generation sequencing. From the comparison of SC self-pollinated and unpollinated styles, 1341 differentially expressed genes (DEGs) were identified, of which 753 were downregulated and 588 were upregulated. From the comparison of SI self-pollinated and unpollinated styles, 804 DEGs were identified, of which 215 were downregulated and 589 were upregulated. Nine gene ontology (GO) terms were enriched significantly in SC and 78 GO terms were enriched significantly in SI. A total of 105 enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified in SC and 80 enriched KEGG pathways were identified in SI, among which “Cysteine and methionine metabolism pathway” and “Plant hormone signal transduction pathway” were significantly enriched in SI. Conclusions: This study is the first global transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles. Advanced bioinformatic analysis of DEGs uncovered the pathways of “Cysteine and methionine metabolism” and “Plant hormone signal transduction”, which are likely to play important roles in the control of pollen tubes growth in SI species. 24-h unpollination (UP) and self-pollination (P) styles mRNA profiles from SC and SI tomato species were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 platform.

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EST sequencing and microarray analysis of the floral transcriptome of Eustoma grandiflorum

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