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Plant J. 2017 Jun;90(5):994-1006. doi: 10.1111/tpj.13525. Epub 2017 Apr 11.

Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids.

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Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
Institute of Biomedical Sciences, National Chung-Hsing University, Taichung, Taiwan.
Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan.
Department of Bioinformatics and Medical Engineering, Asia University, Taichung City, Taiwan.
Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan.
Institute of Botany, Chinese Academy of Sciences, Beijing, China.
Department of Plant Biology, University of Georgia, Athens, GA, USA.
Department of Biology, Pennsylvania State University, State College, PA, USA.
Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China.
Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.


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.


Apostasia odorata ; NDH complex; gene loss; orchid; photoautotrophic plant

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