Dataset for transcriptome response of mature tomato seed tissues to light and heat during fruit ripening
To investigate how light and temperature have an impact on the molecular mechanisms governing tomato seed vigour at harvest, RNA sequencing was performed on Solanum lycopersicum cv. Moneymaker seed tissues (i.e. embryo and endosperm) that were dissected from fruits submitted to standard or high temperature and/or standard or dim light. Differentially expressed genes between standard light and temperature condition and other environmental conditions were assessed and Gene Set Enrichment Analysis (GSEA) on GO terms were performed.
Steps to reproduce
Tomato fruits at breaker stage (i.e 63 DAF) were collected from mother plants grown in greenhouse and transfered to growth chambers for 7 days under 4 different environments: standard temperature (ST, 23°C day/20°C night) + high light (HL, 16h photoperiod 300 µE m-2 s-1), ST + dim light (DL, 16h photoperiod 25 µE m-2 s-1), high temperature (HT, 32°C day/26°C night) + HL or HT + DL. Three or four replicates of 10 fresh tomato seeds were harvested at mature stage for each maturation environment. Total RNA was extracted using the NucleoSpin® RNA Plant and Fungi kit (Macherey-Nagel, Germany), according to the manufacturer instructions (protocol 5.1, sample type “alfalfa seed” for embryo (Em) and “potato tuber” for endosperm (End) ) without the 56°C incubation step. Samples were sent to Beijing Genomics Institute (https://www.bgi.com) for library preparation and sequencing on BGISEQ-500 platform, generating an average 20M reads of 50bp per sample. High-quality reads were mapped onto the reference tomato transcriptome build SL4.0 and transcript abundances were quantified with Salmon algorithm (version 0.14.1). Differential expressions of transcripts were calculated using DESeq2. Gene Set Enrichment Analysis (GSEA) on GO Terms were performed with hypergeometric test using clusterProfiler package (v3.10.1) in R.