Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
BMC Genomics. 2013 Aug 19;14:561. doi: 10.1186/1471-2164-14-561.
Longan is a tropical/subtropical fruit tree of great economic importance in Southeast Asia. Progress in understanding molecular mechanisms of longan embryogenesis, which is the primary influence on fruit quality and yield, is slowed by lack of transcriptomic and genomic information. Illumina second generation sequencing, which is suitable for generating enormous numbers of transcript sequences that can be used for functional genomic analysis of longan.
In this study, a longan embryogenic callus (EC) cDNA library was sequenced using an Illumina HiSeq 2000 system. A total of 64,876,258 clean reads comprising 5.84 Gb of nucleotides were assembled into 68,925 unigenes of 448-bp mean length, with unigenes ≥1000 bp accounting for 8.26% of the total. Using BLASTx, 40,634 unigenes were found to have significant similarity with accessions in Nr and Swiss- Prot databases. Of these, 38,845 unigenes were assigned to 43 GO sub-categories and 17,118 unigenes were classified into 25 COG sub-groups. In addition, 17,306 unigenes mapped to 199 KEGG pathways, with the categories of Metabolic pathways, Plant-pathogen interaction, Biosynthesis of secondary metabolites, and Genetic information processing being well represented. Analyses of unigenes ≥1000 bp revealed 328 embryogenesis-related unigenes as well as numerous unigenes expressed in EC associated with functions of reproductive growth, such as flowering, gametophytogenesis, and fertility, and vegetative growth, such as root and shoot growth. Furthermore, 23 unigenes related to embryogenesis and reproductive and vegetative growth were validated by quantitative real time PCR (qPCR) in samples from different stages of longan somatic embryogenesis (SE); their differentially expressions in the various embryogenic cultures indicated their possible roles in longan SE.
The quantity and variety of expressed EC genes identified in this study is sufficient to serve as a global transcriptome dataset for longan EC and to provide more molecular resources for longan functional genomics.
龙眼是东南亚一种具有重要经济价值的热带/亚热带果树。龙眼胚胎发生的分子机制的研究进展缓慢，而胚胎发生是影响果实品质和产量的主要因素。Illumina 第二代测序技术适用于生成大量的转录序列，可用于龙眼的功能基因组分析。
本研究采用 Illumina HiSeq 2000 系统对龙眼胚性愈伤组织（EC）cDNA 文库进行测序。共组装出 68925 条 unigenes，总长 448bp，平均长度为 448bp，其中长度≥1000bp 的 unigenes占总 unigenes的 8.26%。用 BLASTx 对 unigenes 进行同源性分析，共获得 40634 条与 Nr 和 Swiss-Prot 数据库中序列有显著相似性的 unigenes。其中 38845 条 unigenes被注释到 43 个 GO 功能分类，17118 条 unigenes被归类到 25 个 COG 功能分类。此外，17306 条 unigenes映射到 199 个 KEGG 通路，其中代谢途径、植物-病原体相互作用、次生代谢物的生物合成和遗传信息处理等类别得到了很好的代表。对长度≥1000bp 的 unigenes分析表明，有 328 条与胚胎发生相关的 unigenes，以及许多与生殖生长（如花、配子体发生和育性）和营养生长（如根和茎生长）相关的 EC 表达的 unigenes。此外，通过对不同阶段龙眼体细胞胚胎发生（SE）样本进行定量实时 PCR（qPCR）验证，共鉴定出 23 条与胚胎发生和生殖、营养生长相关的 unigenes；它们在不同胚胎发生培养物中的差异表达表明它们在龙眼 SE 中可能发挥作用。
本研究中鉴定的 EC 基因的数量和种类足以作为龙眼 EC 的全转录组数据集，并为龙眼功能基因组学提供更多的分子资源。
