Comparative transcriptome analysis identifies putative genes involved in secondary metabolite biosynthesis in Euphorbia maculata

Euphorbia maculata L. is an annual plant, belonging to Euphorbiaceae family that can produce anti-inflammatory and biologically important compounds like terpenoids, tannins and polyphenols. Despite the importance of E maculata, there is very limited genetic information. In this study, we conducted full-length cDNA characterization using the SMRT sequencing of PacBio to investigate comprehensive reference gene information and isoform copy number in metabolite biosynthesis. In addition, we sequenced E. maculata transcriptomes obtained from leaves, roots and stems using Illumina short read to identify differential expressed genes in the metabolite biosynthesis pathways. PacBio generated 62 million polymerase read out of which 81,433 high quality reads were obtained that were further processed to reconstruct a genome of 20,722 reads. Of the total genes, 44% were having at least two or more isoforms. More than 92% of unigenes were successfully annotated in various databases like Nr, Pfam, GO and KEGG. Plant transcription factors (TF) database annotated 1,564 putative E. maculata unigenes in 46 TF families, of which, ARF and MYB-related were among the highest annotated. Multiple candidate genes encoding for enzymes in tocopherol biosynthesis, polyphenol and flavonol biosynthetic pathways were identified. Our transcriptome data and related findings would provide valuable genetic resources for studying various biochemical processes of E maculata, particularly the biosynthesis of terpenoids

斑地锦（Euphorbia maculata L.）为一年生草本植物，隶属于大戟科（Euphorbiaceae），可合成具有抗炎活性及重要生物学功能的萜类（terpenoids）、鞣质（tannins）与多酚（polyphenols）等化合物。尽管斑地锦具有重要研究价值，但目前针对其的遗传信息仍十分匮乏。本研究采用太平洋生物科学（PacBio）平台的单分子实时（SMRT）测序技术开展全长cDNA鉴定，以解析代谢生物合成通路中的完整参考基因信息及异构体拷贝数情况。此外，本研究利用Illumina短读长测序技术对斑地锦的叶、根、茎转录组进行测序，以筛选代谢生物合成通路中的差异表达基因。PacBio测序共产生6200万条聚合酶读段，经筛选后获得81433条高质量读段，经进一步处理后组装得到包含20722条读段的转录本集合。在所有基因中，44%的基因至少拥有2个及以上的异构体。超过92%的单基因（unigenes）可在Nr、Pfam、GO及KEGG等多个数据库中获得成功注释。利用植物转录因子（TF）数据库，共在46个转录因子家族中注释得到1564个斑地锦推定单基因，其中注释数量最多的家族为ARF及MYB相关家族。本研究还鉴定得到多个编码生育酚（tocopherol）、多酚及黄酮醇生物合成通路相关酶的候选基因。本研究产生的转录组数据及相关研究结果，将为斑地锦多种生化过程的研究，尤其是萜类化合物的生物合成研究，提供宝贵的遗传资源。