title: NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss.
abstract: BACKGROUND
  Key innovations have facilitated novel niche utilization, such as the movement of the algal predecessors of land plants into terrestrial habitats where drastic fluctuations in light intensity, ultraviolet radiation and water limitation required a number of adaptations. The NDH (NADH dehydrogenase-like) complex of Viridiplantae plastids participates in adapting the photosynthetic response to environmental stress, suggesting its involvement in the transition to terrestrial habitats. Although relatively rare, the loss or pseudogenization of plastid NDH genes is widely distributed across diverse lineages of photoautotrophic seed plants and mutants/transgenics lacking NDH function demonstrate little difference from wild type under non-stressed conditions. This study analyzes large transcriptomic and genomic datasets to evaluate the persistence and loss of NDH expression across plants.
  
  
  RESULTS
  Nuclear expression profiles showed accretion of the NDH gene complement at key transitions in land plant evolution, such as the transition to land and at the base of the angiosperm lineage. While detection of transcripts for a selection of non-NDH, photosynthesis related proteins was independent of the state of NDH, coordinate, lineage-specific loss of plastid NDH genes and expression of nuclear-encoded NDH subunits was documented in Pinaceae, gnetophytes, Orchidaceae and Geraniales confirming the independent and complete loss of NDH in these diverse seed plant taxa.
  
  
  CONCLUSIONS
  The broad phylogenetic distribution of NDH loss and the subtle phenotypes of mutants suggest that the NDH complex is of limited biological significance in contemporary plants. While NDH activity appears dispensable under favorable conditions, there were likely sufficiently frequent episodes of abiotic stress affecting terrestrial habitats to allow the retention of NDH activity. These findings reveal genetic factors influencing plant/environment interactions in a changing climate through 450 million years of land plant evolution.
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA. truhlman@austin.utexas.edu.
authors.forename: Tracey A
authors.initials: TA
authors.lastname: Ruhlman
authors.affiliation: Agricultural Biotechnology Research Center of Academia Sinica, Agricultural Technology Building, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan. yualbert@gate.sinica.edu.tw.
authors.forename: Wan-Jung
authors.initials: WJ
authors.lastname: Chang
authors.affiliation: Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan. jwchen@dragon.nchu.edu.tw.
authors.forename: Jeremy J W
authors.initials: JJ
authors.lastname: Chen
authors.affiliation: Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan. ythuang@cs.ccu.edu.tw.
authors.forename: Yao-Ting
authors.initials: YT
authors.lastname: Huang
authors.affiliation: Agricultural Biotechnology Research Center of Academia Sinica, Agricultural Technology Building, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan. mbmtchan@gate.sinica.edu.tw.
authors.forename: Ming-Tsair
authors.initials: MT
authors.lastname: Chan
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA. jinzhang.zj@gmail.com.
authors.forename: Jin
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Agricultural Biotechnology Research Center of Academia Sinica, Agricultural Technology Building, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan. derchyh@gate.sinica.edu.tw.
authors.forename: De-Chih
authors.initials: DC
authors.lastname: Liao
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA. chrisblazier@yahoo.com.
authors.forename: John C
authors.initials: JC
authors.lastname: Blazier
authors.affiliation: Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China. xiaohuajin@ibcas.ac.cn.
authors.forename: Xiaohua
authors.initials: X
authors.lastname: Jin
authors.affiliation: Agricultural Biotechnology Research Center of Academia Sinica, Agricultural Technology Building, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan. mcshih@gate.sinica.edu.tw.
authors.forename: Ming-Che
authors.initials: MC
authors.lastname: Shih
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA. jansen@austin.utexas.edu.|Department of Biological Science, Biotechnology Research Group, King Abdulaziz University, Jeddah, 21589, Saudi Arabia. jansen@austin.utexas.edu.
authors.forename: Robert K
authors.initials: RK
authors.lastname: Jansen
authors.affiliation: Agricultural Biotechnology Research Center of Academia Sinica, Agricultural Technology Building, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan. cslin99@gate.sinica.edu.tw.
authors.forename: Choun-Sea
authors.initials: CS
authors.lastname: Lin
mesh_terms: D002467:Cell Nucleus / Q000235:genetics; D060365:Chloroplast Proteins / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D018745:Genome, Plant; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D059467:Transcriptome; D057948:Viridiplantae / Q000235:genetics* / Q000378:metabolism
chemical_list: D060365:Chloroplast Proteins