Differential Gene Expression between Leaf and Rhizome in Atractylodes lancea: A Comparative Transcriptome Analysis

Abstract

The rhizome of Atractylodes lancea is extensively used in the practice of Traditional Chinese Medicine because of its broad pharmacological activities. This study was designed to characterize the transcriptome profiling of the rhizome and leaf of Atractylodes lancea in an attempt to uncover the molecular mechanisms regulating rhizome formation and growth. Over 270 million clean reads were assembled into 92,366 unigenes, 58% of which are homologous with sequences in public protein databases (NR, Swiss-Prot, GO, and KEGG). Analysis of expression levels showed that genes involved in photosynthesis, stress response, and translation were the most abundant transcripts in the leaf, while transcripts involved in stress response, transcription regulation, translation, and metabolism were dominant in the rhizome. Tissue-specific gene analysis identified distinct gene families active in the leaf and rhizome. Differential gene expression analysis revealed a clear difference in gene expression pattern, identifying 1518 up-regulated genes and 3464 down-regulated genes in the rhizome compared with the leaf, including a series of genes related to signal transduction, primary and secondary metabolism. Transcription factor (TF) analysis identified 42 TF families, with 67 and 60 TFs up-regulated in the rhizome and leaf, respectively. A total of 104 unigenes were identified as candidates for regulating rhizome formation and development. These data offer an overview of the gene expression pattern of the rhizome and leaf and provide essential information for future studies on the molecular mechanisms of controlling rhizome formation and growth. The extensive transcriptome data generated in this study will be a valuable resource for further functional genomics studies of A. lancea.

Transcriptome Analysis of Secondary Metabolism Pathway, Transcription Factors, and Transporters in Response to Methyl Jasmonate in Lycoris aurea

“…Previously, the de novo transcriptome was sequenced to produce the EST (comprehensive expressed sequence tag) dataset for Lycoris aurea , which provides one perspective of the regulatory and synthesized molecular mechanisms of Amaryllidaceae-type alkaloids (Wang et al, 2013). On the other hand, the inspection of the comparative transcriptome files between two databases provides another method to investigate the secondary metabolites biosynthesis, or/and find the objective genes involved in Salvia miltiorrhiza, Catharanthus roseus , sweet cherry, Atractylodes lancea , and so on (Guo et al, 2013; Yu and Luca, 2013; Wei et al, 2015; Huang et al, 2016). …”

IDENTIFICATION OF GENES PREFERENTIALLY EXPRESSED IN MESOCARP TISSUE OF OIL PALM USING in silico ANALYSIS OF TRANSCRIPTS

“…Despite the differences in the results of RNAseq and RT-qPCR, these methods have been widely used in many gene expression studies. Huang et al (2016) identified differential expressed genes (DEG) that regulate rhizome formation and development in Atractylodes lancea through comparative transcriptome analysis. Gene expression analysis of 20 selected genes was verified using RT-qPCR and all genes show similar trend of the expression patterns in the transcriptome analysis and the RT-qPCR (Huang et al, 2016).…”

“…Huang et al (2016) identified differential expressed genes (DEG) that regulate rhizome formation and development in Atractylodes lancea through comparative transcriptome analysis. Gene expression analysis of 20 selected genes was verified using RT-qPCR and all genes show similar trend of the expression patterns in the transcriptome analysis and the RT-qPCR (Huang et al, 2016). Similar method was used by Le Yu and his group, where the transcriptome data of Populus euphratica Oliv.…”

Revealing the full-length transcriptome of caucasian clover rhizome development

“…Recently, high-throughput RNA sequencing (RNA-seq) technology has become a powerful and costefficient means to facilitate an understanding of differential gene expression and regulatory mechanisms, especially for plant species without a reference genome [8,9]. RNA-seq has been widely used in the study of rhizome transcriptomics, including in various rhizomatous species such as sorghum (Sorghum halepense and Sorghum propinquum) [10,11], bamboo (Phyllostachys praecox) [12], Oryza longIstam-inata [13][14][15], Equisetum hyemale L. [16], Panax ginseng [17], reed (Phragm ites-australis) [18], tropical lotus (Nelumbo nucifera) [19], CangZhu (Atractylodes Lace-a) [20], Ligusticum chuanxiong [21], ginger (Zingiber officinale) [22], and Miscanthus lutarioriparius [8].…”