Analysis of the global transcriptome of 'sijimi' longan (Dimocarpus longan Lour.) using Illumina paired-end sequencing

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

为优化基因注释并解答一系列生物学问题，我们从‘sijimi’龙眼的9种组织（根、茎、叶、花芽、花、幼果、果皮、果肉与种子）中获取了总计490,502,822条RNA测序（RNA-Seq）优质读段（clean reads），并将其用于龙眼基因组序列的比对与注释。来自9组RNA测序数据的唯一RNA序列中，约53.55%~79.40%可比对至该基因组。RNA测序数据验证了绝大多数已注释的内含子，鉴定出数千种全新的可变剪接mRNA异构体，同时扩展了基因、单核苷酸多态性（SNP）以及插入缺失（InDel）的注释范围，这表明相较于仅基于现有基因集的注释，存在更多的功能变异；此外还发现了一批潜在的全新龙眼特异性基因。对9个不同发育阶段的基因家族差异表达模式进行比较分析后发现，大部分显著差异表达基因主要富集于代谢通路、植物-病原体互作通路以及次生代谢产物生物合成通路，这与龙眼（D. longan）富含植物抗病基因、且尤其含有高水平多酚类化合物的物种特性完全一致。