Wang Xin, Li Shutao, Li Jia, Li Changfu, Zhang Yansheng
CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.
Plant Cell Rep. 2015 May;34(5):733-43. doi: 10.1007/s00299-014-1733-1. Epub 2014 Dec 30.
Using Illumina sequencing technology, we have generated the large-scale transcriptome sequencing data and indentified many putative genes involved in isoflavones biosynthesis in Pueraria lobata. Pueraria lobata, a member of the Leguminosae family, is a traditional Chinese herb which has been used since ancient times. P. lobata root has extensive clinical usages, because it contains a rich source of isoflavones, including daidzin and puerarin. However, the knowledge of isoflavone metabolism and the characterization of corresponding genes in such a pathway remain largely unknown. In this study, de novo transcriptome of P. lobata root and leaf was sequenced using the Solexa sequencing platform. Over 140 million high-quality reads were assembled into 163,625 unigenes, of which about 43.1% were aligned to the Nr protein database. Using the RPKM (reads per kilo bases per million reads) method, 3,148 unigenes were found to be upregulated, and 2,011 genes were downregulated in the leaf as compared to those in the root. Towards a further understanding of these differentially expressed genes, Gene ontology enrichment and metabolic pathway enrichment analyses were performed. Based on these results, 47 novel structural genes were identified in the biosynthesis of isoflavones. Also, 22 putative UDP glycosyltransferases and 45 O-methyltransferases unigenes were identified as the candidates most likely to be involved in the tailoring processes of isoflavonoid downstream pathway. Moreover, MYB transcription factors were analyzed, and 133 of them were found to have higher expression levels in the roots than in the leaves. In conclusion, the de novo transcriptome investigation of these unique transcripts provided an invaluable resource for the global discovery of functional genes related to isoflavones biosynthesis in P. lobata.
利用Illumina测序技术，我们生成了大规模转录组测序数据，并鉴定出许多参与野葛异黄酮生物合成的推定基因。野葛是豆科植物的一员，是一种自古以来就被使用的传统中草药。野葛根有广泛的临床用途，因为它含有丰富的异黄酮来源，包括大豆苷和葛根素。然而，异黄酮代谢的知识以及该途径中相应基因的特征在很大程度上仍然未知。在本研究中，使用Solexa测序平台对野葛根和叶进行了从头转录组测序。超过1.4亿条高质量读段被组装成163,625个单基因，其中约43.1%与Nr蛋白质数据库比对。使用RPKM（每百万读段中每千碱基的读段数）方法，发现与根相比，叶中有3,148个单基因上调，2,011个基因下调。为了进一步了解这些差异表达基因，进行了基因本体富集和代谢途径富集分析。基于这些结果，在异黄酮生物合成中鉴定出47个新的结构基因。此外，鉴定出22个推定的UDP糖基转移酶和45个O-甲基转移酶单基因，它们最有可能参与异黄酮下游途径的修饰过程。此外，对MYB转录因子进行了分析，发现其中133个在根中的表达水平高于叶。总之，对这些独特转录本的从头转录组研究为全面发现与野葛异黄酮生物合成相关的功能基因提供了宝贵资源。
