title: Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids.
abstract: The chloroplast NAD(P)H dehydrogenase-like (NDH) complex consists of about 30 subunits from both the nuclear and chloroplast genomes and is ubiquitous across most land plants. In some orchids, such as Phalaenopsis equestris, Dendrobium officinale and Dendrobium catenatum, most of the 11 chloroplast genome-encoded ndh genes (cp-ndh) have been lost. Here we investigated whether functional cp-ndh genes have been completely lost in these orchids or whether they have been transferred and retained in the nuclear genome. Further, we assessed whether both cp-ndh genes and nucleus-encoded NDH-related genes can be lost, resulting in the absence of the NDH complex. Comparative analyses of the genome of Apostasia odorata, an orchid species with a complete complement of cp-ndh genes which represents the sister lineage to all other orchids, and three published orchid genome sequences for P. equestris, D. officinale and D. catenatum, which are all missing cp-ndh genes, indicated that copies of cp-ndh genes are not present in any of these four nuclear genomes. This observation suggests that the NDH complex is not necessary for some plants. Comparative genomic/transcriptomic analyses of currently available plastid genome sequences and nuclear transcriptome data showed that 47 out of 660 photoautotrophic plants and all the heterotrophic plants are missing plastid-encoded cp-ndh genes and exhibit no evidence for maintenance of a functional NDH complex. Our data indicate that the NDH complex can be lost in photoautotrophic plant species. Further, the loss of the NDH complex may increase the probability of transition from a photoautotrophic to a heterotrophic life history.
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Choun-Sea
authors.initials: CS
authors.lastname: Lin
authors.affiliation: Institute of Biomedical Sciences, National Chung-Hsing University, Taichung, Taiwan.
authors.forename: Jeremy J W
authors.initials: JJW
authors.lastname: Chen
authors.affiliation: Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Chi-Chou
authors.initials: CC
authors.lastname: Chiu
authors.affiliation: Department of Bioinformatics and Medical Engineering, Asia University, Taichung City, Taiwan.
authors.forename: Han C W
authors.initials: HCW
authors.lastname: Hsiao
authors.affiliation: Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan.
authors.forename: Chen-Jui
authors.initials: CJ
authors.lastname: Yang
authors.affiliation: Institute of Botany, Chinese Academy of Sciences, Beijing, China.
authors.forename: Xiao-Hua
authors.initials: XH
authors.lastname: Jin
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, GA, USA.
authors.forename: James
authors.initials: J
authors.lastname: Leebens-Mack
authors.affiliation: Department of Biology, Pennsylvania State University, State College, PA, USA.
authors.forename: Claude W
authors.initials: CW
authors.lastname: de Pamphilis
authors.affiliation: Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan.
authors.forename: Yao-Ting
authors.initials: YT
authors.lastname: Huang
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Ling-Hung
authors.initials: LH
authors.lastname: Yang
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Wan-Jung
authors.initials: WJ
authors.lastname: Chang
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Kui
authors.affiliation: Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
authors.affiliation: Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan.
authors.forename: Jer-Ming
authors.initials: JM
authors.lastname: Hu
authors.affiliation: Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan.
authors.forename: Wen
authors.initials: W
authors.lastname: Wang
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Ming-Che
authors.initials: MC
authors.lastname: Shih
mesh_terms: D054628:Genome, Chloroplast / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D029595:Orchidaceae / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics*
chemical_list: D010940:Plant Proteins
keywords: 
  Apostasia odorata
  ; NDH complex; gene loss; orchid; photoautotrophic plant