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3' Tag RNA-seq analysis of wild type (S. pimpinellifolium accession LA1589) and SUN NIL during tomato fruit development.

ABSTRACT: 3' Tag RNA-seq analysis of wild type (S. pimpinellifolium accession LA1589) and SUN NIL during tomato fruit development.

PROVIDER: PRJNA559996 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9960070.fastq.gz	Fastqsanger.gz
	SRR9960080.fastq.gz	Fastqsanger.gz
	SRR9960090.fastq.gz	Fastqsanger.gz
	SRR9960100.fastq.gz	Fastqsanger.gz
	SRR9960110.fastq.gz	Fastqsanger.gz

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3' Tag RNA-seq analysis of wild type (S. pimpinellifolium accession LA1589) and SUN NIL during tomato fruit development.

Project description:This study is to decipher the effect of SUN overexpressed NIL on gene expression during fruit development in tomato. RNA libraries were sequenced through Illumina Nextseq500 at Georgia Genomics and Bioinformatics Core (GGBC) of University of Georgia for 75 bp single end sequencing. Clean reads were mapped to ITAG3.2. Processed data are normalized into TPM.

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Project description:Universally accepted landmark stages are necessary to highlight key events in tomato reproductive development. In this study, we provide a description of floral and fruit development in a red-fruited closely related wild relative of tomato, Solanum pimpinellifolium accession LA1589. We use established and propose new landmarks as the framework for the characterization of the tomato fruit shape gene SUN in fruit development. SUN controls fruit shape predominantly after fertilization and its effect reaches a maximum at 8 days post anthesis coinciding with fruit landmark 4 representing the globular embryo stage of seed development. We also analyzed gene expression profiles of floral buds 10 days before anthesis (floral landmark 7), anthesis-stage flowers (floral landmark 10 and fruit landmark 1), and 5 days post anthesis fruit (fruit landmark 3). The expression profiles of the NILs that differ at sun showed that 34 genes were differentially expressed and most of them at a less than 2-fold difference. However, many genes were differentially expressed between the developmental times points, including many genes involved in phytohormone biosynthesis or signaling as well as organ identity and patterning of tomato fruit. Three biological replicates were conducted with three sets of LA1589 sun NILs that differ at sun growing during different time periods resulting in 3 time points x 2 genotypes x 3 replicates = 18 array hybridizations.

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