Data from: De novo genome assembly of Camptotheca acuminata, a natural source of the anti-cancer compound camptothecin

Camptotheca acuminata is 1 of a limited number of species that produce camptothecin, a pentacyclic quinoline alkaloid with anti-cancer activity due to its ability to inhibit DNA topoisomerase. While transcriptome studies have been performed previously with various camptothecin-producing species, no genome sequence for a camptothecin-producing species is available to date. We generated a high-quality de novo genome assembly for C. acuminata representing 403 174 860 bp on 1394 scaffolds with an N50 scaffold size of 1752 kbp. Quality assessments of the assembly revealed robust representation of the genome sequence including genic regions. Using a novel genome annotation method, we annotated 31 825 genes encoding 40 332 gene models. Based on sequence identity and orthology with validated genes from Catharanthus roseus as well as Pfam searches, we identified candidate orthologs for genes potentially involved in camptothecin biosynthesis. Extensive gene duplication including tandem duplication was widespread in the C. acuminata genome, with 2571 genes belonging to 997 tandem duplicated gene clusters. To our knowledge, this is the first genome sequence for a camptothecin-producing species, and access to the C. acuminata genome will permit not only discovery of genes encoding the camptothecin biosynthetic pathway but also reagents that can be used for heterologous expression of camptothecin and camptothecin analogs with novel pharmaceutical applications.喜树（Camptotheca acuminata）是少数能够合成喜树碱（camptothecin）的物种之一。喜树碱是一种五环喹啉生物碱（pentacyclic quinoline alkaloid），可通过抑制DNA拓扑异构酶（DNA topoisomerase）发挥抗癌活性。此前已有针对多种产喜树碱物种的转录组研究（transcriptome studies），但截至目前，尚无任何产喜树碱物种的基因组序列可供使用。 本研究为喜树（C. acuminata）构建了高质量的从头（de novo）基因组组装，该组装包含1394个支架（scaffold），总长度达403174860 bp，支架N50长度为1752 kbp。对该组装的质量评估结果显示，其可完整覆盖包括基因区域在内的基因组序列。 我们采用一种新型基因组注释方法，共注释得到31825个基因，编码40332个基因模型（gene models）。基于与长春花（Catharanthus roseus）已验证基因的序列一致性和直系同源性，结合Pfam数据库（Pfam）搜索，我们鉴定出了可能参与喜树碱生物合成的候选直系同源基因。 研究发现，包括串联重复（tandem duplication）在内的大规模基因重复事件在喜树基因组中广泛存在，共有2571个基因隶属于997个串联重复基因簇。据我们所知，这是首个产喜树碱物种的基因组序列；获取喜树基因组资源，不仅可助力发掘编码喜树碱生物合成通路的相关基因，还能为可用于异源表达（heterologous expression）喜树碱及具有新型药用价值的喜树碱类似物的试剂开发提供支撑。