Digital RNA-seq transcriptome plus tissue anatomy analyses reveal the developmental mechanism of the calabash-shaped root in Tetrastigma hemsleyanum

Abstract

Tetrastigma hemsleyanum is a liana plant with promising medicinal and ornamental values. Its calabash-shaped roots (CRs) are served as a traditional Chinese herb. However, it takes a long growth period to form CRs. In the present study, three types of architectural roots, including fine roots (FRs), bar-shaped roots (BRs) and CRs, were employed as materials, and the characteristics of histo-anatomy and digital RNA-seq transcriptome profiles were analyzed. Among the three types of roots, the vascular bundles in FRs were intact, while some of the vascular bundles degenerated in BRs, and only few traces of vascular bundles existed in CRs. Meanwhile, no obvious cell inclusions were found in the cytoplasm of FRs, while a few inclusions were found in BRs, and abundant inclusions were detected in CRs, which might be the main source of medicinal components in roots. The transcriptome profiles and qRT-PCR validation indicated that seven up-regulated genes encoding xyloglucan glycosyltransferase, ACC oxidase, CYP711A1, SHORT-ROOT transcript factor, galacturonosyltransferas, WAT1 and WRKY, and two down-regulated genes encoded LRR receptor-like serine/threonine-protein kinase and CYP83B1, were probably involved in the formation and development of CRs. Besides, GO terms of intrinsic component of membrane, integral component of membrane, cell periphery, membrane part, plasma membrane, membrane, intrinsic component of plasma membrane, cellular chemical homeostasis, and plasma membrane part were probably related to the formation of CRs. KEGG pathways related to the development of CRs probably included MAPK signaling pathway-plant, plant hormone signal transduction, and circadian rhythm-plant. Our finding suggested a probable mode for the formation of CRs.

Integrative Analysis of the Transcriptome and Metabolome Reveals the Developmental Mechanisms and Metabolite Biosynthesis of the Tuberous Roots of Tetrastigma hemsleyanum

“…However, seasonal variation may not fully reflect the changes across the whole growth period of SYQ. Additionally, Xiang et al [ 18 ] used digital RNA-seq transcriptome profiling to reveal the developmental mechanism of calabash-shaped SYQ roots. However, there has so far been a lack of analyses conducted on the connections between key genes and metabolites.…”

Combined treatment with anti‐PSMA CAR NK‐92 cell and anti‐PD‐L1 monoclonal antibody enhances the antitumour efficacy against castration‐resistant prostate cancer

“…At least 3 × 10 6 cells were collected from each cell type. According to previously reported methods, 17 , 18 , 19 , 20 total RNA was extracted, and cDNA libraries were constructed using KC‐Digit RNA technology (Seq Health Tech Co., Ltd.). Sequencing was performed on an Illumina NovaSeq 6000, and the statistical quantification was conducted using the feature counts software (Subread‐1.5.1; Bioconductor).…”