title: Lineage-Specific Reductions of Plastid Genomes in an Orchid Tribe with Partially and Fully Mycoheterotrophic Species.
abstract: The plastid genome (plastome) of heterotrophic plants like mycoheterotrophs and parasites shows massive gene losses in consequence to the relaxation of functional constraints on photosynthesis. To understand the patterns of this convergent plastome reduction syndrome in heterotrophic plants, we studied 12 closely related orchids of three different lifeforms from the tribe Neottieae (Orchidaceae). We employ a comparative genomics approach to examine structural and selectional changes in plastomes within Neottieae. Both leafy and leafless heterotrophic species have functionally reduced plastid genome. Our analyses show that genes for the NAD(P)H dehydrogenase complex, the photosystems, and the RNA polymerase have been lost functionally multiple times independently. The physical reduction proceeds in a highly lineage-specific manner, accompanied by structural reconfigurations such as inversions or modifications of the large inverted repeats. Despite significant but minor selectional changes, all retained genes continue to evolve under purifying selection. All leafless Neottia species, including both visibly green and nongreen members, are fully mycoheterotrophic, likely evolved from leafy and partially mycoheterotrophic species. The plastomes of Neottieae span many stages of plastome degradation, including the longest plastome of a mycoheterotroph, providing invaluable insights into the mechanisms of plastome evolution along the transition from autotrophy to full mycoheterotrophy.
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Yan-Lei
authors.initials: YL
authors.lastname: Feng
authors.affiliation: Institute for Evolution and Biodiversity, University of Muenster, Germany.
authors.forename: Susann
authors.initials: S
authors.lastname: Wicke
authors.affiliation: Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun Township, Mengla County, Yunnan, China.
authors.forename: Jian-Wu
authors.initials: JW
authors.lastname: Li
authors.affiliation: Nanchang University, Jiangxi, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Han
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Choun-Sea
authors.initials: CS
authors.lastname: Lin
authors.affiliation: Key Laboratory of Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
authors.forename: De-Zhu
authors.initials: DZ
authors.lastname: Li
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Ting-Ting
authors.initials: TT
authors.lastname: Zhou
authors.affiliation: Chenshan Shanghai Botanical Garden, Shanghai, Songjiang, China.
authors.forename: Wei-Chang
authors.initials: WC
authors.lastname: Huang
authors.affiliation: National Resource Centre for Chinese Materia Medica, China Academy of Chinese Medical Science, Beijing, China.
authors.forename: Lu-Qi
authors.initials: LQ
authors.lastname: Huang
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China xiaohuajin@ibcas.ac.cn.
authors.forename: Xiao-Hua
authors.initials: XH
authors.lastname: Jin
mesh_terms: D019143:Evolution, Molecular; D054627:Genome, Plastid; D052836:Heterotrophic Processes / Q000235:genetics*; D009252:NADPH Dehydrogenase / Q000235:genetics; D029595:Orchidaceae / Q000235:genetics* / Q000378:metabolism; D010788:Photosynthesis / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics; D012641:Selection, Genetic
chemical_list: D010940:Plant Proteins; D009252:NADPH Dehydrogenase
keywords: Neottieae; Orchidaceae; heterotrophy; plastid genome reduction; relaxed selection