ABSTRACT: To improve the gene annotation and address a series of biological questions, we generated 490,502,822 clean reads of RNA-Seq data from nine tissue types of 'sijimi' longan, including root, stem, leaf, flower_bud, flower, young fruit, pericarp, pulp, and seed, and used them for mapping, and annotation of the longan genome sequence. About 53.55 ~79.40 % of the unique RNA sequences from nine RNA-seq data could be mapped to the genome. RNA-Seq data confirmed a majority of annotated introns, identified thousands of novel alternatively spliced mRNA isoforms, extend gene, SNP and indel, indicative of more functional variation than represented by the gene set alone, and a collection of potentially new and longan-specific gene. A comparative analysis of differential expression in the gene family at the nine different developmental stages showed that most of significant differentially expressed genes were mainly involved in the metabolic pathway, plant- pathogen interaction, and biosynthesis of secondary metabolities, which was fully consistent with the standpoint of D. longan specise containing a lot of plant pahtogen resistant genes, and in particular containing high levels of polyphenolic compounds
