title: The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family.
abstract: The NAD(P)H dehydrogenase complex is encoded by 11 ndh genes in plant chloroplast (cp) genomes. However, ndh genes are truncated or deleted in some autotrophic Epidendroideae orchid cp genomes. To determine the evolutionary timing of the gene deletions and the genomic locations of the various ndh genes in orchids, the cp genomes of Vanilla planifolia, Paphiopedilum armeniacum, Paphiopedilum niveum, Cypripedium formosanum, Habenaria longidenticulata, Goodyera fumata and Masdevallia picturata were sequenced; these genomes represent Vanilloideae, Cypripedioideae, Orchidoideae and Epidendroideae subfamilies. Four orchid cp genome sequences were found to contain a complete set of ndh genes. In other genomes, ndh deletions did not correlate to known taxonomic or evolutionary relationships and deletions occurred independently after the orchid family split into different subfamilies. In orchids lacking cp encoded ndh genes, non cp localized ndh sequences were identified. In Erycina pusilla, at least 10 truncated ndh gene fragments were found transferred to the mitochondrial (mt) genome. The phenomenon of orchid ndh transfer to the mt genome existed in ndh-deleted orchids and also in ndh containing species.
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: JJ
authors.lastname: Chen
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: 1] Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan [2] Academia Sinica Biotechnology Center in Southern Taiwan, Tainan, Taiwan.
authors.forename: Ming-Tsair
authors.initials: MT
authors.lastname: Chan
authors.affiliation: Departments of Biochemistry and Pathology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA.
authors.forename: Henry
authors.initials: H
authors.lastname: Daniell
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Wan-Jung
authors.initials: WJ
authors.lastname: Chang
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Chen-Tran
authors.initials: CT
authors.lastname: Hsu
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: De-Chih
authors.initials: DC
authors.lastname: Liao
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Fu-Huei
authors.initials: FH
authors.lastname: Wu
authors.affiliation: Institute of Biomedical Sciences, National Chung-Hsing University, Taichung, Taiwan.
authors.forename: Sheng-Yi
authors.initials: SY
authors.lastname: Lin
authors.affiliation: Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan.
authors.forename: Chen-Fu
authors.initials: CF
authors.lastname: Liao
authors.affiliation: Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
authors.forename: Michael K
authors.initials: MK
authors.lastname: Deyholos
authors.affiliation: 1] Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada [2] Department of Medicine, University of Alberta, Edmonton AB, Canada [3] BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China.
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
authors.affiliation: Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
authors.forename: Victor A
authors.initials: VA
authors.lastname: Albert
authors.affiliation: Department of Life Sciences, Tzu Chi University, Hualien, Taiwan.
authors.forename: Ming-Lun
authors.initials: ML
authors.lastname: Chou
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Chun-Yi
authors.initials: CY
authors.lastname: Chen
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Ming-Che
authors.initials: MC
authors.lastname: Shih
mesh_terms: D002874:Chromosome Mapping; D019295:Computational Biology; D004251:DNA Transposable Elements; D019143:Evolution, Molecular; D017353:Gene Deletion; D023061:Gene Order; D061125:Genes, Chloroplast; D054628:Genome, Chloroplast; D054629:Genome, Mitochondrial; D023281:Genomics; D005810:Multigene Family; D009154:Mutation; D016366:Open Reading Frames; D029595:Orchidaceae / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny
chemical_list: D004251:DNA Transposable Elements