De novo assembly and annotation of the Zhe-Maidong (Ophiopogon japonicus (L.f.) Ker-Gawl) transcriptome in different growth stages

Huijun Liu,Huan Chen,Tingzhang Wang,Ying Wang,Xuhui Ying,Rongrong Wu

doi:10.1038/s41598-017-03937-w

Abstract

Zhe-Maidong (Ophiopogon japonicus (L.f.) Ker-Gawl) is a traditional medicinal herb in the family Liliaceae that has significant pharmacological effects on immunity and cardiovascular disease. In this study, three different growth stages of Zhe-Maidong were investigated using RNA-seq, and a total of 16.4 Gb of raw data was obtained. After filtering and assembling, 96,738 unigenes with an average length of 605.3 bp were ultimately generated. A total of 77,300 unigenes were annotated using information from five databases, including the NT, NR, SwissProt, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases. Additionally, the mechanisms of flavonoid, saponin and polysaccharide biosynthesis and of accumulation at different stages of tuber development were also characterized. From the first to third years, the contents of flavonoids, saponins and polysaccharides all increased, whereas the expression levels of related genes decreased in the flavonoid and saponin pathways and first increased and then decreased in the polysaccharide pathway. The results of this study provide the most comprehensive expressed sequence resource for Zhe-Maidong and will expand the available O. japonicus gene library and facilitate further genome-wide research and analyses of this species.

Highlights

Zhe-Maidong (ZMD), known as Ophiopogon japonicus (L.f.) Ker-Gawl, is an evergreen perennial in the Liliaceae family and a famous Chinese traditional medicinal herb
The longest transcript of each gene was selected as the unigene, and 96,738 unigenes were generated with an average length of 605.3 bp and an N50 length of 859 bp (Table 1)
Based on SwissProt database annotation, 254, 135 and 236 unigenes were identified that were related to the biosynthesis of flavonoids, saponins and polysaccharides, respectively

Summary

Introduction

Zhe-Maidong (ZMD), known as Ophiopogon japonicus (L.f.) Ker-Gawl, is an evergreen perennial in the Liliaceae family and a famous Chinese traditional medicinal herb. As a result of the rapid development of generation sequencing, RNA sequencing (RNA-seq) is a useful method for studying the metabolic pathways of medicinal components and related gene expression in different samples or tissues, such as flavonoid biosynthesis in Carthamus tinctorius[14], Pueraria lobata[15] and Polygonum cuspidatum[16]; saponin biosynthesis in Asparagus racemosus[17], Panax japonicus[18], Panax notoginseng[19] and Panax quinquefolius[20]; glycyrrhizin biosynthesis in Glycyrrhiza uralensis[21]; and fatty acid biosynthesis in Eucommia ulmoides[22]. The results of this study can serve as a guide for the development of breeding strategies

Methods

Results

Conclusion