Transcriptome Sequencing to Detect Genes Involved in Nucellar Embryony Mechanism in Citrus

Many citrus cultivar produce apomictic seeds by a mechanism termed nucellar embryony in which the adventive embryos develop from nucellus tissue surrounding the embryo sac and have the same genetic constitution as the female plant. The aim of the present study is to determine differentially expressed genes involved in nucellar embryony mechanism. In this study we used ‘Orlando Tangelo’ producing almost 100% apomictic seeds and ‘Clementine Mandarin’ known as monoembryonic for high-throughput sequencing. Firstly it is determined that the stage of nucellar embryo initial cells when began to develop in ‘Orlando Tangelo’ by histological analysis. Nucellar embryo initial cells were observed in third day after anthesis. Ovarium samples were collected from Orlando and Clementine before anthesis and third day after anthesis for transcriptome sequencing. Primary sequencing were produced by Illumina HiSeqTM 2000, called as raw reads, was subjected to quality control (QC). After QC, raw reads were filtered into clean reads aligned to the reference sequences. Full genome of Citrus clementina was used as a reference genome. We performed downstream analysis including gene expression, deep analysis based on gene expression, deep analysis based on DEGs, including Gene Ontology (GO) enrichment analysis. We identified 2359 differentially expressed genes (DEGs) (1996 up-regulated, 363 down-regulated), 2123 (1372 up-regulated, 751 down-regulated), genes from the samples at Orlando balloon stage - Orlando third day and Clementine third day - Orlando third day, respectively. This dataset provides valuable information regarding citrus transcriptome changes for nucellar embryony mechanism and may help guide future identification and functional analysis of genes that are important for polyembrony.