Bailey T L, Boden M, Buske F A, Frith M, Grant C E, Clementi L, Ren J Y, Li W W, Noble W L. 2009. MEME Suite: tools for motif discovery and searching. Nucleic Acids Research , 37 (S2): W202–W208..

Battchikova N, Wei L Z, Du L Y, Bersanini L, Aro E M, Ma W M. 2011. Identification of novel Ssl0352 protein (NdhS), essential for efficient operation of cyclic electron transport around photosystem I, in NADPH: plastoquinone oxidoreductase (NDH-1) complexes of Synechocystis sp. PCC 6803. Journal of Biological Chemistry , 286 (42): 36992–37001..

Bertelli C M, Unsworth R K F. 2018. Light stress responses by the eelgrass, Zostera marina (L). Frontiers in Environmental Science , 6 : 39..

Braukmann T W A, Kuzmina M, Stefanović S. 2009. Loss of all plastid NDH genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogeny. Current Genetics , 55 (3): 323–337..

Burrows P A, Sazanov L A, Svab Z, Maliga P, Nixon P J. 1998. Identification of a functional respiratory complex in chloroplasts through analysis of tobacco mutants containing disrupted plastid NDH genes. The EMBO Journal , 17 (4): 868–876..

Chateigner-Boutin A L, Small I. 2010. Plant RNA editing. RNA Biology , 7 (2): 213–219..

Chen C J, Chen H, Zhang Y, Thomas H R, Frank M H, He Y H, Xia R. 2020. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant , 13 (8): 1194–1202..

Chen H Y, Deng L K, Jiang Y, Lu P, Yu J N. 2011. RNA editing sites exist in protein-coding genes in the chloroplast genome of Cycas taitungensis . Journal of Integrative Plant Biology , 53 (12): 961–970..

Efremov R G, Baradaran R, Sazanov L A. 2010. The architecture of respiratory complex I. Nature , 465 (7297): 441–445..

Essemine J, Qu M N, Mi H L, Zhu X G. 2016. Response of chloroplast NAD(P)H dehydrogenase-mediated cyclic electron flow to a shortage or lack in ferredoxin-Quinone oxidoreductase-dependent pathway in rice following short-term heat stress. Frontiers in Plant Science , 7 : 383..

Fan X Y, Zhang J, Li W J, Peng L W. 2015. The NdhV subunit is required to stabilize the chloroplast NADH dehydrogenase-like complex in Arabidopsis . The Plant Journal: For Cell and Molecular Biology , 82 (2): 221–231..

Gao F D, Zhao J H, Wang X Z, Qin S, Wei L Z, Ma W M. 2016. NdhV is a subunit of NADPH dehydrogenase essential for cyclic electron transport in Synechocystis sp. Strain PCC 6803. Plant Physiology , 170 (2): 752–760..

He X, Zhang J. 2005. Gene complexity and gene duplicability. Current Biology Cb , 15 (11): 1016–1021..

He Z H, Zheng F F, Wu Y Z, Li Q H, Lv J, Fu P C, Mi H L. 2015. NDH-1L interacts with ferredoxin via the subunit NdhS in Thermosynechococcus elongatus . Photosynthesis Research , 126 (2–3): 341–349..

Hein A, Polsakiewicz M, Knoop V. 2016. Frequent chloroplast RNA editing in early-branching flowering plants: pilot studies on angiosperm-wide coexistence of editing sites and their nuclear specificity factors. BMC Evolutionary Biology , 16 (1): 23..

Horvath E M, Peter S O, Joët T, Rumeau D, Cournac L, Horváth G V, Kavanagh T A, Schäfer C, Peltier G, Medgyesy P. 2000. Targeted inactivation of the plastid ndhB gene in tobacco results in an enhanced sensitivity of photosynthesis to moderate stomatal closure. Plant Physiology , 123 (4): 1337–1350..

Ifuku K, Endo T, Shikanai T, Aro E M. 2011. Structure of the chloroplast NADH dehydrogenase-like complex: nomenclature for nuclear-encoded subunits. Plant & Cell Physiology , 52 (9): 1560–1568..

Iles W J D, Smith S Y, Graham S W. 2013. A well-supported phylogenetic framework for the monocot order Alismatales reveals multiple losses of the plastid NADH dehydrogenase complex and a strong long-branch effect. In : Wilkin P, Mayo S J eds. Early Events in Monocot Evolution. Cambridge: Cambridge University Press.

Ishikawa N, Takabayashi A, Ishida S, Hano Y, Endo T, Sato F. 2008. NDF6: a thylakoid protein specific to terrestrial plants is essential for activity of chloroplastic NAD(P)H dehydrogenase in Arabidopsis . Plant and Cell Physiology , 49 (7): 1066–1073..

Jobson R W, Qiu Y L. 2008. Did RNA editing in plant organellar genomes originate under natural selection or through genetic drift? Biology Direct , 3 (1): 43..

Kim H T, Chase M W. 2017. Independent degradation in genes of the plastid ndh gene family in species of the orchid genus Cymbidium (Orchidaceae; Epidendroideae). PLoS One , 12 (11): e0187318..

Kofer W, Koop H U, Wanner G, Steinmüller K. 1998. Mutagenesis of the genes encoding subunits A, C, H, I, J and K of the plastid NAD(P)H-plastoquinone-oxidoreductase in tobacco by polyethylene glycolmediated plastome transformation. Molecular and General Genetics MGG , 258 (1–2): 166–173..

Krogh A, Larsson B, Von Heijne G, Sonnhammer E L L. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of Molecular Biology , 305 (3): 567–580..

Larkin M A, Blackshields G, Brown N P, Chenna R, McGettigan P A, McWilliam H, Valentin F, Wallace I M, Wilm A, Lopez R, Thompson J D, Gibson T J, Higgins D G. 2007. Clustal W and Clustal X version 2.0. Bioinformatics , 23 (21): 2947–2948..

Larkum A W D, Davey P A, Kuo J, Ralph P J, Raven J A. 2017. Carbon-concentrating mechanisms in seagrasses. Journal of Experimental Botany , 68 (14): 3773–3784..

Lee H T, Golicz A A, Bayer P E, Severn-Ellis A A, Chan C K K, Batley J, Kendrick G A, Edwards D. 2018. Genomic comparison of two independent seagrass lineages reveals habitat-driven convergent evolution. Journal of Experimental Botany , 69 (15): 3689–3702..

Lemieux C, Otis C, Turmel M. 2000. Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution. Nature , 403 (6770): 649–652..

Les D H, Cleland M A, Waycott M. 1997. Phylogenetic studies in Alismatidae, Ⅱ: evolution of marine angiosperms (seagrasses) and hydrophily. Systematic Botany , 22 (3): 443–463..

Li X G, Duan W, Meng Q W, Zou Q, Zhao S J. 2004. The function of chloroplastic NAD(P)H dehydrogenase in tobacco during chilling stress under low irradiance. Plant and Cell Physiology , 45 (1): 103–108..

Lin C S, Chen J J W, Chiu C C, Hsiao H C W, Yang C J, Jin X H, Leebens-Mack J, De Pamphilis C W, Huang Y T, Yang L H, Chang W J, Kui L, Wong G K S, Hu J M, Wang W, Shih M C. 2017. Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids. The Plant Journal , 90 (5): 994–1006..

Maier R M, Neckermann K, Igloi G L, Kössel H. 1995. Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. Journal of Molecular Biology , 251 (5): 614–628..

Matsubayashi T, Wakasugi T, Shinozaki K, Yamaguchi-Shinozaki K, Zaita N, Hidaka T, Meng B Y, Ohto C, Tanaka M, Kato A, Maruyama T, Sugiura M. 1987. Six chloroplast genes ( ndhA-F ) homologous to human mitochondrial genes encoding components of the respiratory chain NADH dehydrogenase are actively expressed: determination of the splice sites in ndhA and ndhB pre-mRNAs. Molecular and General Genetics MGG , 210 (3): 385–393..

Munekage Y, Hashimoto M, Miyake C, Tomizawa K I, Endo T, Tasaka M, Shikanai T. 2004. Cyclic electron flow around photosystem I is essential for photosynthesis. Nature , 429 (6991): 579–582..

Ogawa T. 1991. A gene homologous to the subunit-2 gene of NADH dehydrogenase is essential to inorganic carbon transport of Synechocystis PCC6803. Proceedings of the National Academy of Sciences of the United States of America , 88 (10): 4275–4279..

Ohyama K, Fukuzawa H, Kohchi T, Shirai H, Sano T, Sano S, Umesono K, Shiki Y, Takeuchi M, Chang Z, Aota S I, Inokuchi H, Ozeki H. 1986. Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature , 322 (6079): 572–574..

Okegawa Y, Kagawa Y, Kobayashi Y, Shikanai T. 2008. Characterization of factors affecting the activity of photosystem I Cyclic electron transport in chloroplasts. Plant and Cell Physiology , 49 (5): 825–834..

Olsen J L, Rouzé P, Verhelst B, Lin Y C, Bayer T, Collen J, Dattolo E, De Paoli E, Dittami S, Maumus F, Michel G, Kersting A, Lauritano C, Lohaus R, Töpel M, Tonon T, Vanneste K, Amirebrahimi M, Brakel J, Boström C, Chovatia M, Grimwood J, Jenkins J W, Jueterbock A, Mraz A, Stam W T, Tice H, Bornberg-Bauer E, Green P J, Pearson G A, Procaccini G, Duarte C M, Schmutz J, Reusch T B H, Van De Peer Y. 2016. The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Nature , 530 (7590): 331–335..

Pan X W, Cao D F, Xie F, Xu F, Su X D, Mi H L, Zhang X Z, Li M. 2020. Structural basis for electron transport mechanism of complex Ⅰ-like photosynthetic NAD(P)H dehydrogenase. Nature Communications , 11 (1): 610..

Peltier G, Cournac L. 2002. Chlororespiration. Annual Review of Plant Biology , 53 : 523–550..

Peng L W, Yamamoto H, Shikanai T. 2011. Structure and biogenesis of the chloroplast NAD(P)H dehydrogenase complex. Biochimica et Biophysica Acta (BBA)-Bioenergetics , 1807 (8): 945–953..

Peredo E L, King U M, Les D H. 2013. The plastid genome of Najas flexilis : adaptation to submersed environments is accompanied by the complete loss of the NDH complex in an aquatic angiosperm. PLoS One , 8 (7): e68591..

Qiao X, Li Q H, Yin H, Qi K J, Li L T, Wang R Z, Zhang S L, Paterson A H. 2019. Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants. Genome Biology , 20 (1): 38..

Reddy A S N, Marquez Y, Kalyna M, Barta A. 2013. Complexity of the alternative splicing landscape in plants. The Plant Cell , 25 (10): 3657–3683..

Robert X, Gouet P. 2014. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Research , 42 (1): 320–324..

Romano P, Gray J, Horton P, Luan S. 2005. Plant immunophilins: functional versatility beyond protein maturation. New Phytologist , 166 (3): 753–769..

Ruhlman T A, Chang W J, Chen J J W, Huang Y T, Chan M T, Zhang J, Liao D C, Blazier J C, Jin X H, Shih M C, Jansen R K, Lin C S. 2015. NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss. BMC Plant Biology , 15 (1): 100..

Rumeau D, Becuwe-Linka N, Beyly A, Louwagie M, Garin J, Peltier G. 2005. New subunits NDH-M, -N, and-O, encoded by nuclear genes, are essential for plastid NDH complex functioning in higher plants. The Plant Cell , 17 (1): 219–232..

Schubert N, Colombo-Pallota M F, Enríquez S. 2015. Leaf and canopy scale characterization of the photoprotective response to high-light stress of the seagrass Thalassia testudinum . Limnologyand Oceanography , 60 (1): 286–302..

Shikanai T. 2007. Cyclic electron transport around photosystem Ⅰ: genetic approaches. Annual Review of Plant Biology , 58 : 199–217..

Shikanai T. 2016. Chloroplast NDH: a different enzyme with a structure similar to that of respiratory NADH dehydrogenase. Biochimica et Biophysica Acta (BBA)-Bioenergetics , 1857 (7): 1015–1022..

Shikanai T, Endo T, Hashimoto T, Yamada Y, Asada K, Yokota A. 1998. Directed disruption of the tobacco ndhB gene impairs cyclic electron flow around photosystem I. Proceedings of the National Academy of Sciences of the United States of America , 95 (16): 9705–9709..

Shimizu H, Peng L W, Myouga F, Motohashi R, Shinozaki K, Shikanai T. 2008. CRR23/NdhL is a subunit of the chloroplast NAD(P)H dehydrogenase complex in Arabidopsis . Plant and Cell Physiology , 49 (5): 835–842..

Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayshida N, Matsubayasha T, Zaita N, Chunwongse J, Obokata J, Yamaguchi-Shinozaki K, Ohto C, Torazawa K, Meng B Y, Sugita M, Deno H, Kamogashira T, Yamada K, Kusuda J, Takaiwa F, Kata A, Tohdoh N, Shimada H, Sugiura M. 1986. The complete nucleotide sequence of the tobacco chloroplast genome. Plant Molecular Biology Reporter , 4 (3): 111–148..

Sirpiö S, Holmström M, Battchikova N, Aro E M. 2009. AtCYP20-2 is an auxiliary protein of the chloroplast NAD(P)H dehydrogenase complex. FEBS Letters , 583 (14): 2355–2358..

Staudt A C, Wenkel S. 2011. Regulation of protein function by 'microProteins'. EMBO Reports , 12 (1): 35–42..

Suorsa M, Sirpiö S, Aro E M. 2009. Towards characterization of the chloroplast NAD(P)H dehydrogenase complex. Molecular Plant , 2 (6): 1127–1140..

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution , 28 (10): 2731–2739..

Tan Y, Zhang Q S, Zhao W, Liu Z, Ma M Y, Zhong M Y, Wang M X. 2020a. The highly efficient NDH-dependent photosystem I cyclic electron flow pathway in the marine angiosperm Zostera marina . Photosynthesis Research , 144 (1): 49–62..

Tan Y, Zhang Q S, Zhao W, Liu Z, Ma M Y, Zhong M Y, Wang M X, Xu B. 2020b. Chlororespiration serves as photoprotection for the photo-inactivated oxygen-evolving complex in Zostera marina , a marine angiosperm. Plant and Cell Physiology , 61 (8): 1517–1529..

Tillich M, Funk H T, Schmitz-Linneweber C, Poltnigg P, Sabater B, Martin M, Maier R M. 2005. Editing of plastid RNA in Arabidopsis thaliana ecotypes. The Plant Journal , 43 (5): 708–715..

Turmel M, Otis C, Lemieux C. 1999. The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: insights into the architecture of ancestral chloroplast genomes. Proceedings of the National Academy of Sciences of the United States of America , 96 (18): 10248–10253..

Ueda M, Kuniyoshi T, Yamamoto H, Sugimoto K, Ishizaki K, Kohchi T, Nishimura Y, Shikanai T. 2012. Composition and physiological function of the chloroplast NADH dehydrogenase-like complex in Marchantia polymorpha . The Plant Journal: for Cell and Molecular Biology , 72 (4): 683–693..

Uthaipaisanwong P, Chanprasert J, Shearman J R, Sangsrakru D, Yoocha T, Jomchai N, Jantasuriyarat C, Tragoonrung S, Tangphatsornruang S. 2012. Characterization of the chloroplast genome sequence of oil palm ( Elaeis guineensis Jacq.). Gene , 500 (2): 172–180..

Wang P, Ye J Y, Shen Y G, Mi H L. 2006. The role of chloroplast NAD(P)H dehydrogenase in protection of tobacco plant against heat stress. Science in China Series C: Life Sciences , 49 (4): 311–321..

Wang W, Zhang W, Wu Y, Maliga P, Messing J. 2015. RNA Editing in chloroplasts of Spirodela polyrhiza , an aquatic monocotelydonous species. PLoS One , 10 (10): e0140285..

Waycott M, Duarte C M, Carruthers T J B, Orth R J, Dennison W C, Olyarnik S, Calladine A, Fourqurean J W, Heck K L J, Hughes A R, Kendrick G A, Kenworthy W J, Short F T, Williams S L. 2009. Accelerating loss of seagrasses across the globe threatens coastal ecosystems. Proceedings of the National Academy of Sciences of the United States of America , 106 (30): 12377–12381..

Weng M L, Blazier J C, Govindu M, Jansen R K. 2014. Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates. Molecular Biology and Evolution , 31 (3): 645–659..

Wu C S, Wang Y N, Liu S M, Chaw S M. 2007. Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: insights into cpDNA evolution and phylogeny of extant seed plants. Molecular Biology and Evolution , 24 (6): 1366–1379..

Xing Q K, Guo J. 2018. Characterization of the complete chloroplast genome of the seagrass Zostera marina using Illumina sequencing technology. Conservation Genetics Resources , 10 (3): 419–422..

Xiong A S, Peng R H, Zhuang J, Gao F, Zhu B, Fu X Y, Xue Y, Jin X F, Tian Y S, Zhao W, Yao Q H. 2009. Gene duplication, transfer, and evolution in the chloroplast genome. Biotechnology Advances , 27 (4): 340–347..

Yang X Q, Zhang Q S, Zhang D, Sheng Z T. 2017. Light intensity dependent photosynthetic electron transport in eelgrass ( Zostera marina L.). Plant Physiology and Biochemistry , 113 : 168–176..

Zhang P P, Battchikova N, Paakkarinen V, Katoh H, Iwai M, Ikeuchi M, Pakrasi H B, Ogawa T, Aro E M. 2005. Isolation, subunit composition and interaction of the NDH-1 complexes from Thermosynechococcus elongatus BP-1. The Biochemical Journal , 390 (2): 513–520..

Zhang Y Y, Li B B, Xu Y Y, Li H, Li S S, Zhang D J, Mao Z W, Guo S Y, Yang C H, Weng Y X, Chong K. 2013. The cyclophilin CYP20-2 modulates the conformation of brassinazole-resistant1, which binds the promoter of flowering locus D to regulate flowering in Arabidopsis . The Plant Cell , 25 (7): 2504–2521..

Zhang Y Z, Ma J, Yang B X, Li R Y, Zhu W, Sun L L, Tian J K, Zhang L. 2014. The complete chloroplast genome sequence of Taxus chinensis var. mairei (Taxaceae): loss of an inverted repeat region and comparative analysis with related species. Gene , 540 (2): 201–209..