AZ1.0

Background The Azadirachta indica (neem) tree is a source of a wide number of natural products, including the potent biopesticide azadirachtin. In spite of its widespread applications in agriculture and medicine, the molecular aspects of the biosynthesis of neem terpenoids remain largely unexplored. The current report describes the draft genome and four transcriptomes of A. indica and attempts to contextualise the sequence information in terms of its molecular phylogeny, transcript expression and terpenoid biosynthesis pathways. A. indica is the first member of the family Meliaceae to be sequenced using next generation sequencing approach. Results The genome and transcriptomes of A. indica were sequenced using multiple sequencing platforms and libraries. The A. indica genome is AT-rich, bears few repetitive DNA elements and comprises about 20,000 genes. The molecular phylogenetic analyses grouped A. indica together with Citrus sinensis from the Rutaceae family validating its conventional taxonomic classification. Comparative transcript expression analysis showed either exclusive or enhanced expression of known genes involved in neem terpenoid biosynthesis pathways compared to other sequenced angiosperms. Genome and transcriptome analyses in A. indica led to the identification of repeat elements, nucleotide composition and expression profiles of genes in various organs. Conclusions This study on A. indica genome and transcriptomes will provide a model for characterization of metabolic pathways involved in synthesis of bioactive compounds, comparative evolutionary studies among various Meliaceae family members and help annotate their genomes. A better understanding of molecular pathways involved in the azadirachtin synthesis in A. indica will pave ways for bulk production of environment friendly biopesticides.背景 印楝树（Azadirachta indica）是多种天然产物的来源，其中包括高效生物农药印楝素（azadirachtin）。尽管其在农业与医药领域应用广泛，但印楝萜类化合物生物合成的分子机制仍未得到充分解析。本研究报道了印楝的草图基因组（draft genome）与4组转录组（transcriptomes），并尝试从分子系统发育（molecular phylogeny）、转录本表达以及萜类化合物生物合成通路（terpenoid biosynthesis pathways）等维度对序列信息进行注释与解读。印楝是首个通过下一代测序（next generation sequencing）技术完成测序的楝科（Meliaceae）植物。 结果 本研究通过多种测序平台与文库对印楝的基因组及转录组进行了测序。印楝基因组属于AT富集型，仅含少量重复DNA序列元件，共编码约20000个基因。分子系统发育分析将印楝与芸香科（Rutaceae）的甜橙（Citrus sinensis）归为一类，验证了其传统分类学地位。与其他已测序被子植物相比，转录表达比较分析显示，参与印楝萜类化合物生物合成通路的已知基因呈现特异性表达或上调表达。通过对印楝基因组与转录组的分析，本研究鉴定出了重复序列元件、核苷酸组成特征以及不同器官的基因表达谱。 结论 本研究针对印楝基因组与转录组的工作，将为生物活性化合物合成相关代谢通路的解析、楝科不同物种间的比较进化研究提供参考模型，并有助于后续楝科物种的基因组注释工作。对印楝中印楝素合成相关分子通路的深入解析，将为环境友好型生物农药的规模化生产奠定基础。