The Genome of Dendrobium officinale Illuminates the Biology of the Important Traditional Chinese Orchid Herb

Abstract

Dendrobium officinale Kimura et Migo is a traditional Chinese orchid herb that has both ornamental value and a broad range of therapeutic effects. Here, we report the first de novo assembled 1.35 Gb genome sequences for D. officinale by combining the second-generation Illumina Hiseq 2000 and third-generation PacBio sequencing technologies. We found that orchids have a complete inflorescence gene set and have some specific inflorescence genes. We observed gene expansion in gene families related to fungus symbiosis and drought resistance. We analyzed biosynthesis pathways of medicinal components of D. officinale and found extensive duplication of SPS and SuSy genes, which are related to polysaccharide generation, and that the pathway of D. officinale alkaloid synthesis could be extended to generate 16-epivellosimine. The D. officinale genome assembly demonstrates a new approach to deciphering large complex genomes and, as an important orchid species and a traditional Chinese medicine, the D. officinale genome will facilitate future research on the evolution of orchid plants, as well as the study of medicinal components and potential genetic breeding of the dendrobe.

Building a Genetic Manipulation Tool Box for Orchid Biology: Identification of Constitutive Promoters and Application of CRISPR/Cas9 in the Orchid, Dendrobium officinale

“…For CRISPR/Cas9, the available genome sequence of host species could help select target sites with low off-target efficiency and increase the efficiency and accuracy of genome editing. Currently, there are only published genome sequences of two orchid species: Dendrobium officinale (Yan et al, 2015; Zhang G.Q. et al, 2016) and Phalaenopsis equestris (Cai et al, 2015).…”

Whole-Transcriptome Selection and Evaluation of Internal Reference Genes for Expression Analysis in Protocorm Development of Dendrobium officinale Kimura et Migo

“…officinale like many other Dendrobium species, has been exploited to near extinction and is now classified as one of the rare and endangered medicinal plants of China [30,36]. Studies on D .…”

“…In this study, a GNOM and AP2 gene from D . officinale [30] was used to validate the IRGs in protocorm development. RT-qPCR primer pairs of GNOM were designed as that the forward primer is 5’-CTTGTTTTCGGGTTGTTCAT-3’ and the reverse 5’-GTTTGCCATTGCTTTTGCTA-3’.…”

Transcriptomic landscape of Dendrobium huoshanense and its genes related to polysaccharide biosynthesis

“…Employing transcriptomic approaches to collect and analyze bioinformation for understanding its genetic makeup and biosynthetic pathways of important secondary metabolites is a practical way to better protect and utilize this medicinal resource by using biotechnologies to produce products of interest in the future. By far, studies on genomic and transcriptomic level of Dendrobium plants have been confined to a few species such as D. officinal and D. nobile [13,15,16]. To our best knowledge, no transcriptomic report on D. huoshanense was retrieved up to date.…”