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

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

Author information

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.

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

PMID:
25825286
DOI:
10.1016/j.molp.2014.12.011
[Indexed for MEDLINE]
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