title: 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.
authors.affiliation: College of Life Science, Jilin University, Changchun 130012, China; Pu'er Institute of Pu-er Tea, Pu'er 665000, China.
authors.forename: Liang
authors.initials: L
authors.lastname: Yan
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Liu
authors.affiliation: College of Life Science, Jilin University, Changchun 130012, China; Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Tian
authors.affiliation: China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Jinmin
authors.initials: J
authors.lastname: Lian
authors.affiliation: Pu'er Institute of Pu-er Tea, Pu'er 665000, China.
authors.forename: Ruijuan
authors.initials: R
authors.lastname: Yang
authors.affiliation: Yunnan University, Kunming 650091, China.
authors.forename: Shumei
authors.initials: S
authors.lastname: Hao
authors.affiliation: Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China.
authors.forename: Xuanjun
authors.initials: X
authors.lastname: Wang
authors.affiliation: Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China.
authors.forename: Shengchao
authors.initials: S
authors.lastname: Yang
authors.affiliation: China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Qiye
authors.initials: Q
authors.lastname: Li
authors.affiliation: Agri-Biotech Lab, Kunming 650502, China.
authors.forename: Shuai
authors.initials: S
authors.lastname: Qi
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Kui
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China.
authors.forename: Moses
authors.initials: M
authors.lastname: Okpekum
authors.affiliation: Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Ma
authors.affiliation: School of Science and Information Engineering, Yunnan Agricultural University, Kunming 650201, China.
authors.forename: Jiajin
authors.initials: J
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China.
authors.forename: Zhaoli
authors.initials: Z
authors.lastname: Ding
authors.affiliation: China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Guojie
authors.initials: G
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China.
authors.forename: Wen
authors.initials: W
authors.lastname: Wang
authors.affiliation: 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.
authors.forename: Yang
authors.initials: Y
authors.lastname: Dong
authors.affiliation: 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.
authors.forename: Jun
authors.initials: J
authors.lastname: Sheng
mesh_terms: D001483:Base Sequence; D031667:Dendrobium / Q000145:classification / Q000235:genetics*; D018745:Genome, Plant; D008516:Medicine, Chinese Traditional; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D010946:Plants, Medicinal / Q000145:classification / Q000235:genetics*
chemical_list: D010940:Plant Proteins
keywords: Dendrobium officinale; Illunima; PacBio; genome; orchid plant