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

Liang Yan; Xiao Wang; Hui Liu; Yang Tian; Jinmin Lian; Ruijuan Yang; Shumei Hao; Xuanjun Wang; Shengchao Yang; Qiye Li; Shuai Qi; Ling Kui; Moses Okpekum; Xiao Ma; Jiajin Zhang; Zhaoli Ding; Guojie Zhang; Wen Wang; Yang Dong; Jun Sheng

doi:10.1016/j.molp.2014.12.011

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

Mol Plant. 2015 Jun;8(6):922-34. doi: 10.1016/j.molp.2014.12.011. Epub 2014 Dec 24.

Authors

Liang Yan¹, Xiao Wang², Hui Liu², Yang Tian³, Jinmin Lian⁴, Ruijuan Yang⁵, Shumei Hao⁶, Xuanjun Wang⁷, Shengchao Yang⁷, Qiye Li⁴, Shuai Qi⁸, Ling Kui², Moses Okpekum², Xiao Ma⁷, Jiajin Zhang⁹, Zhaoli Ding², Guojie Zhang⁴, Wen Wang², Yang Dong¹⁰, Jun Sheng¹¹

Affiliations

¹ College of Life Science, Jilin University, Changchun 130012, China; Pu'er Institute of Pu-er Tea, Pu'er 665000, China.
² State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China.
³ College of Life Science, Jilin University, Changchun 130012, China; Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China.
⁴ China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China.
⁵ Pu'er Institute of Pu-er Tea, Pu'er 665000, China.
⁶ Yunnan University, Kunming 650091, China.
⁷ Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China.
⁸ Agri-Biotech Lab, Kunming 650502, China.
⁹ School of Science and Information Engineering, Yunnan Agricultural University, Kunming 650201, China.
¹⁰ State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China; Laboratory of Applied Genomics and Synthetic Biology, College of Life Science, Kunming University of Science and Technology, Kunming 650500, China. Electronic address: loyalyang@163.com.
¹¹ College of Life Science, Jilin University, Changchun 130012, China; Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China. Electronic address: shengj@ynau.edu.cn.

PMID: 25825286
DOI: 10.1016/j.molp.2014.12.011

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.

Keywords: Dendrobium officinale; Illunima; PacBio; genome; orchid plant.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
Dendrobium / classification
Dendrobium / genetics*
Genome, Plant*
Medicine, Chinese Traditional
Molecular Sequence Data
Phylogeny
Plant Proteins / genetics
Plants, Medicinal / classification
Plants, Medicinal / genetics*

Substances

Plant Proteins