Weixiong Zhang1, Guoqiang Zhang2,3,4, Peng Zeng1, Yongqiang Zhang2,3,4,5, Hao Hu1, Zhongjian Liu5, Jing Cai6. 1. State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, 999078, Macau, China. 2. Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, 518114, Shenzhen, China. 3. Shenzhen Key Laboratory for Orchid Conservation and Utilization, 518114, Shenzhen, China. 4. National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, 518114, Shenzhen, China. 5. Key Laboratory of NFGA for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, 350002, Fuzhou, China. 6. School of Ecology and Environment, Northwestern Polytechnical University, 710129, Xi'an, China. jingcai@nwpu.edu.cn.
Abstract
BACKGROUND: The Orchidaceae family is one of the most diverse among flowering plants and serves as an important research model for plant evolution, especially "evo-devo" study on floral organs. Recently, sequencing of several orchid genomes has greatly improved our understanding of the genetic basis of orchid biology. To date, however, most sequenced genomes are from the Epidendroideae subfamily. To better elucidate orchid evolution, greater attention should be paid to other orchid lineages, especially basal lineages such as Apostasioideae. RESULTS: Here, we present a genome sequence of Apostasia ramifera, a terrestrial orchid species from the Apostasioideae subfamily. The genomes of A. ramifera and other orchids were compared to explore the genetic basis underlying orchid species richness. Genome-based population dynamics revealed a continuous decrease in population size over the last 100 000 years in all studied orchids, although the epiphytic orchids generally showed larger effective population size than the terrestrial orchids over most of that period. We also found more genes of the terpene synthase gene family, resistant gene family, and LOX1/LOX5 homologs in the epiphytic orchids. CONCLUSIONS: This study provides new insights into the adaptive evolution of orchids. The A. ramifera genome sequence reported here should be a helpful resource for future research on orchid biology.
BACKGROUND: The Orchidaceae family is one of the most diverse among flowering plants and serves as an important research model for plant evolution, especially "evo-devo" study on floral organs. Recently, sequencing of several orchid genomes has greatly improved our understanding of the genetic basis of orchid biology. To date, however, most sequenced genomes are from the Epidendroideae subfamily. To better elucidate orchid evolution, greater attention should be paid to other orchid lineages, especially basal lineages such as Apostasioideae. RESULTS: Here, we present a genome sequence of Apostasia ramifera, a terrestrial orchid species from the Apostasioideae subfamily. The genomes of A. ramifera and other orchids were compared to explore the genetic basis underlying orchid species richness. Genome-based population dynamics revealed a continuous decrease in population size over the last 100 000 years in all studied orchids, although the epiphytic orchids generally showed larger effective population size than the terrestrial orchids over most of that period. We also found more genes of the terpene synthase gene family, resistant gene family, and LOX1/LOX5 homologs in the epiphytic orchids. CONCLUSIONS: This study provides new insights into the adaptive evolution of orchids. The A. ramifera genome sequence reported here should be a helpful resource for future research on orchid biology.
Authors: Felipe A Simão; Robert M Waterhouse; Panagiotis Ioannidis; Evgenia V Kriventseva; Evgeny M Zdobnov Journal: Bioinformatics Date: 2015-06-09 Impact factor: 6.937