De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform

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.

Transcriptome Assembly and Gene Expression Analysis of Leaf and Rhizome tissues of Dioscorea opposita

“…suggesting that the assembled unigenes represented a wide diversity of transcripts in the D. opposita genome, similar to in many previous reports [52,53]. In the three GO categories, reproduction and metabolic processes were the most abundant classes in BP cell and cell part activity were the most abundant classes in CC, which was consistent with some previous research [17,51,52].…”

“…However, the proportion of annotated long sequences was signi cantly higher than that of annotated short sequences. Similar results have been reported for other species [17,51].…”

Morroniside Promotes PGC-1α-Mediated Cholesterol Efflux in Sodium Palmitate or High Glucose-Induced Mouse Renal Tubular Epithelial Cells

“…Therefore, exploring new strategies for the treatment of lipid metabolism disorder is of great significance in the prevention and control of DN. Cornus officinalis is a traditional Chinese medicine that has a certain therapeutic effect on liver and kidney diseases [ 20 ]. Several studies in recent years have documented that morroniside (MOR), an iridoid glycoside derived from Cornus officinalis Sieb.…”

Identification of Candidate Genes Associated with Pulp Color by Transcriptomic Analysis of ‘Huaxiu’ Plum (Prunus salicina Lindl.) during Fruit-Ripening

“…In total, 57,119 unigenes were assembled, with a mean length of 953 bp ( Table 1 ), which is comparable to 944 bp for sweet cherry ( P. avium L.) [ 47 ], and with the longer to the previously reported other species such as 872 bp for cultivar ‘Furongli’ ( P. salicina L.) [ 1 ] and 531 bp for Chinese bayberry ( Myrica rubra ) [ 48 ]. Approximately 61.6% of the unigenes were annotated to public databases (NR, Swiss-Prot, GO, COG, and KEGG), which means that more than one-third of the unigenes have no apparent homologs, with similar results seen in other no model plant species [ 49 ]. The unannotated unigenes could be plum-specific genes with novel functions, which may be related with some unique biosynthesis processes and pathways in the results.…”