Abstract
Cornus officinalis is one of the most widely used medicinal plants in China and other East Asian countries to cure diseases such as liver, kidney, cardiovascular diseases and frequent urination for thousands of years. It is a Level 3 protected species, and is one of the 42 national key protected wild species of animals and plants in China. However, the genetics and molecular biology of C. officinalis are poorly understood, which has hindered research on the molecular mechanism of its metabolism and utilization. Hence, enriching its genomic data and information is very important. In recent years, the fast-growing technology of next generation sequencing has provided an effective path to gain genomic information from nonmodel species. This study is the first to explore the leaf and fruit tissue transcriptome of C. officinalis using the Illumina HiSeq 4000 platform. A total of 57,954,134 and 60,971,652 clean reads from leaf and fruit were acquired, respectively (GenBank number SRP115440). The pooled reads from all two libraries were assembled into 56,392 unigenes with an average length 856 bp. Among these, 41,146 unigenes matched with sequences in the NCBI nonredundant protein database. The Gene Ontology database assigned 24,336 unigenes with biological process (83.26%), cellular components (53.58%), and molecular function (83.93%). In addition, 10,808 unigenes were assigned a KOG functional classification by the KOG database. Searching against the KEGG pathway database indicated that 18,435 unigenes were mapped to 371 KEGG pathways. Moreover, the edgeR database identified 4,585 significant differentially expressed genes (DEGs), of which 1,392 were up-regulated and 3,193 were down-regulated in fruit tissue compared with leaf tissue. Finally, we explored 581 transcription factors with 50 transcription factor gene families. Most DEGs and transcription factors were related to terpene biosynthesis and secondary metabolic regulation. This study not only represented the first de novo transcriptomic analysis of C. officinalis but also provided fundamental information on its genes and biosynthetic pathway. These findings will help us explore the molecular metabolism mechanism of terpene biosynthesis in C. officinalis.
Highlights
C. officinalis Siebold et Zucc. (Cornaceae) is a deciduous tree widely distributed in China, Korea and Japan [1, 2]
The cDNA library was constructed from the fruits and leaves of C. officinalis using TruseqTM RNA sample preparation kit
Since the genome of C. officinalis is not available, we performed de novo assembly of the transcripts
Summary
C. officinalis Siebold et Zucc. (Cornaceae) is a deciduous tree widely distributed in China, Korea and Japan [1, 2]. C. officinalis is classified as a food and medicinal plant by the Ministry of Health of the People’s Re- public of China. It is the main ingredient of a medicine named Liu wei di huang pill. Corni Fructus has been used to treat various diseases, including vertigo, tinnitus, cardiovascular disease, frequent urination, oxidative stress, and acute myocardial ischemia [3, 5, 11]. It can regulate the immune system [12,13,14]. The previous results show that iridoid glucosides are its main active substance [3, 5, 10]
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