Thompson AR, Vierstra RD. Autophagic recycling: lessons from yeast help define the process in plants. Curr Opin Plant Biol. 2005;8(2):165–73.
Article
CAS
PubMed
Google Scholar
Yoshimoto K, Takano Y, Sakai Y. Autophagy in plants and phytopathogens. FEBS Lett. 2010;584(7):1350–8.
Article
CAS
PubMed
Google Scholar
Kanki T, Wang K, Baba M, Bartholomew CR, Lynch-Day MA, Du Z, Geng JF, Mao K, Yang ZF, Yen WL, et al. A Genomic Screen for Yeast Mutants Defective in Selective Mitochondria Autophagy. Mol Biol Cell. 2009;20(22):4730–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yao ZY, Delorme-Axford E, Backues SK, Klionsky DJ. Atg41/Icy2 regulates autophagosome formation. Autophagy. 2015;11(12):2288–99.
Article
CAS
PubMed
Google Scholar
Mizushima N. Autophagy: process and function. Gene Dev. 2007;21(22):2861–73.
Article
CAS
PubMed
Google Scholar
Okamoto K, Kondo-Okamoto N, Ohsumi Y. Mitochondria-anchored receptor Atg32 mediates degradation of mitochondria via selective autophagy. Dev Cell. 2009;17(1):87–97.
Article
CAS
PubMed
Google Scholar
Suzuki K, Kondo C, Morimoto M, Ohsumi Y. Selective transport of alpha-mannosidase by autophagic pathways identification of a novel receptor, Atg34p. J Biol Chem. 2010;285(39):30019–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tsukada M, Ohsumi Y. Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Lett. 1993;333(1–2):169–74.
Article
CAS
PubMed
Google Scholar
Thumm M, Egner R, Koch B, Schlumpberger M, Straub M, Veenhuis M, Wolf DH. Isolation of autophagocytosis mutants of Saccharomyces cerevisiae. FEBS Lett. 1994;349(2):275–80.
Article
CAS
PubMed
Google Scholar
Harding TM, Morano KA, Scott SV, Klionsky DJ. Isolation and Characterization of yeast mutants in the cytoplasm to vacuole protein targeting pathway. J Cell Biol. 1995;131(3):591–602.
Article
CAS
PubMed
Google Scholar
Noda T, Suzuki K, Ohsumi Y. Yeast autophagosomes: de novo formation of a membrane structure. Trends Cell Bio. 2002;12(5):231–5.
Article
CAS
Google Scholar
Wang CW, Klionsky DJ. The molecular mechanism of autophagy. Mol Med. 2003;9(3–4):65–76.
PubMed
PubMed Central
Google Scholar
Klionsky DJ, Cregg JM, Dunn WA, Emr SD, Sakai Y, Sandoval IV, Sibirny A, Subramani S, Thumm M, Veenhuis M, et al. A unified nomenclature for yeast autophagy-related genes. Dev Cell. 2003;5(4):539–45.
Article
CAS
PubMed
Google Scholar
Su W, Ma HJ, Liu C, Wu JX, Yang JS. Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4. Mol Biol Rep. 2006;33(4):273–8.
Article
CAS
PubMed
Google Scholar
Chung T, Suttangkakul A, Vierstra RD. The ATG autophagic conjugation system in maize: ATG transcripts and abundance of the ATG8-lipid adduct are regulated by development and nutrient availability. Plant Physiol. 2009;149(1):220–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xia KF, Liu T, Ouyang J, Wang R, Fan T, Zhang MY. Genome-wide identification, classification, and expression analysis of autophagy-associated gene homologues in rice (Oryza sativa L.). DNA Res. 2011;18(5):363–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li FQ, Chung T, Pennington JG, Federico ML, Kaeppler HF, Kaeppler SM, Otegui MS, Vierstra RD. Autophagic Recycling Plays a Central Role in Maize Nitrogen Remobilization. Plant Cell. 2015;27(5):1389–408.
Article
CAS
PubMed
PubMed Central
Google Scholar
Il Kwon S, Park OK. Autophagy in plants. J Plant Biol. 2008;51(5):313–20.
Article
Google Scholar
Zhou XM, Zhao P, Wang W, Zou J, Cheng TH, Peng XB, Sun MX. A comprehensive, genome-wide analysis of autophagy-related genes identified in tobacco suggests a central role of autophagy in plant response to various environmental cues. DNA Res. 2015;22(4):245–57.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu Y, Schiff M, Czymmek K, Talloczy Z, Levine B, Dinesh-Kumar SP. Autophagy regulates programmed cell death during the plant innate immune response. Cell. 2005;121(4):567–77.
Article
CAS
PubMed
Google Scholar
Xiang Y, Contento AL, Bassham D. Disruption of autophagy results in constitutive oxidative stress in Arabidopsis. Autophagy. 2007;3(3):257–8.
Article
Google Scholar
Xiong Y, Contento AL, Nguyen PQ, Bassham DC. Degradation of oxidized proteins by autophagy during oxidative stress in Arabidopsis. Plant Physiol. 2007;143(1):291–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chung T, Phillips AR, Vierstra RD. ATG8 lipidation and ATG8-mediated autophagy in Arabidopsis require ATG12 expressed from the differentially controlled ATG12A and ATG12B loci. Plant J. 2010;62(3):483–93.
Article
CAS
PubMed
Google Scholar
Wada S, Hayashida Y, Izumi M, Kurusu T, Hanamata S, Kanno K, Kojima S, Yamaya T, Kuchitsu K, Makino A, et al. Autophagy Supports Biomass Production and Nitrogen Use Efficiency at the Vegetative Stage in Rice. Plant Physiol. 2015;168(1):60–U721.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xiong Y, Contento AL, Bassham DC. AtATG18a is required for the formation of autophagosomes during nutrient stress and senescence in Arabidopsis thaliana. Plant J. 2005;42(4):535–46.
Article
CAS
PubMed
Google Scholar
Doelling JH, Walker JM, Friedman EM, Thompson AR, Vierstra RD. The APG8/12-activating enzyme APG7 is required for proper nutrient recycling and senescence in Arabidopsis thaliana. J Biol Chem. 2002;277(36):33105–14.
Article
CAS
PubMed
Google Scholar
Thompson AR, Doelling JH, Suttangkakul A, Vierstra RD. Autophagic nutrient recycling in Arabidopsis directed by the ATG8 and ATG12 conjugation pathways. Plant Physiol. 2005;138(4):2097–110.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bassham DC. Plant autophagy-more than a starvation response. Curr Opin Plant Biol. 2007;10(6):587–93.
Article
CAS
PubMed
Google Scholar
Hanaoka H, Noda T, Shirano Y, Kato T, Hayashi H, Shibata D, Tabata S, Ohsumi Y. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene. Plant Physiol. 2002;129(3):1181–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xie ZP, Nair U, Klionsky DJ. Atg8 controls phagophore expansion during autophagosome formation. Mol Biol Cell. 2008;19(8):3290–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nakatogawa H, Ichimura Y, Ohsumi Y. Atg8, a ubiquitin-like protein required for autophagosome formation, mediates membrane tethering and hemifusion. Cell. 2007;130(1):165–78.
Article
CAS
PubMed
Google Scholar
Yoshimoto K, Hanaoka H, Sato S, Kato T, Tabata S, Noda T, Ohsumi Y. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy. Plant Cell. 2004;16(11):2967–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Woo J, Park E, Dinesh-Kumar SP. Differential processing of Arabidopsis ubiquitin-like Atg8 autophagy proteins by Atg4 cysteine proteases (vol 111, pg 863, 2013). Proc Natl Acad Sci U S A. 2014;111(25):9325.
Google Scholar
Slavikova S, Shy G, Yao YL, Giozman R, Levanony H, Pietrokovski S, Elazar Z, Galili G. The autophagy-associated Atg8 gene family operates both under favourable growth conditions and under starvation stresses in Arabidopsis plants. J Exp Bot. 2005;56(421):2839–49.
Article
CAS
PubMed
Google Scholar
Kuzuoglu-Ozturk D, Yalcinkaya OC, Akpinar BA, Mitou G, Korkmaz G, Gozuacik D, Budak H. Autophagy-related gene, TdAtg8, in wild emmer wheat plays a role in drought and osmotic stress response. Planta. 2012;236(4):1081–92.
Article
CAS
PubMed
Google Scholar
Slavikova S, Ufaz S, Avin-Wittenberg T, Levanony H, Galili G. An autophagy-associated Atg8 protein is involved in the responses of Arabidopsis seedlings to hormonal controls and abiotic stresses. J Exp Bot. 2008;59(14):4029–43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xia TM, Xiao D, Liu D, Chai WT, Gong QQ, Wang NN. Heterologous expression of ATG8c from soybean confers tolerance to nitrogen deficiency and increases yield in Arabidopsis. Plos One. 2012;7(5):e37217.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J, et al. Reference genome sequence of the model plant Setaria. Nat Biotechnol. 2012;30(6):555–61.
Article
CAS
PubMed
Google Scholar
Zhang GY, Liu X, Quan ZW, Cheng SF, Xu X, Pan SK, Xie M, Zeng P, Yue Z, Wang WL, et al. Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol. 2012;30(6):549–54.
Article
CAS
PubMed
Google Scholar
Jia GQ, Huang XH, Zhi H, Zhao Y, Zhao Q, Li WJ, Chai Y, Yang LF, Liu KY, Lu HY, et al. A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat Genet. 2013;45(8):957–61.
Article
CAS
PubMed
Google Scholar
Kellogg EA. Evolutionary history of the grasses. Plant Physiol. 2001;125(3):1198–205.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang YC, Mao LY, Wang H, Brocker C, Yin XJ, Vasiliou V, Fei ZJ, Wang XP. Genome-wide identification and analysis of grape aldehyde dehydrogenase (ALDH) gene superfamily. Plos One. 2012;7(2):e32153.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chardon F, Noel V, Masclaux-Daubresse C. Exploring NUE in crops and in Arabidopsis ideotypes to improve yield and seed quality. J Exp Bot. 2012;63(9):3401–12.
Article
CAS
PubMed
Google Scholar
Guiboileau A, Yoshimoto K, Soulay F, Bataille MP, Avice JC, Masclaux-Daubresse C. Autophagy machinery controls nitrogen remobilization at the whole-plant level under both limiting and ample nitrate conditions in Arabidopsis. New Phytol. 2012;194(3):732–40.
Article
CAS
PubMed
Google Scholar
Guiboileau A, Avila-Ospina L, Yoshimoto K, Soulay F, Azzopardi M, Marmagne A, Lothier J, Masclaux-Daubresse C. Physiological and metabolic consequences of autophagy deficiency for the management of nitrogen and protein resources in Arabidopsis leaves depending on nitrate availability. New Phytol. 2013;199(3):683–94.
Article
CAS
PubMed
Google Scholar
Vision TJ, Brown DG, Tanksley SD. The origins of genomic duplications in Arabidopsis. Science. 2000;290(5499):2114–7.
Article
CAS
PubMed
Google Scholar
Pennisi E. Evolutionary biology - Twinned genes live life in the fast lane. Science. 2000;290(5494):1065–6.
Article
CAS
PubMed
Google Scholar
Juretic N, Hoen DR, Huynh ML, Harrison PM, Bureau TE. The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Res. 2005;15(9):1292–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lyons E, Pedersen B, Kane J, Alam M, Ming R, Tang HB, Wang XY, Bowers J, Paterson A, Lisch D, et al. Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol. 2008;148(4):1772–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu G, Guo C, Shan H, Kong H. Divergence of duplicate genes in exon-intron structure. Proc Natl Acad Sci U S A. 2012;109(4):1187–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ahuja I, de Vos RC, Bones AM, Hall RD. Plant molecular stress responses face climate change. Trends Plant Sci. 2010;15(12):664–74.
Article
CAS
PubMed
Google Scholar
Puranik S, Sahu PP, Mandal SN, Suresh BV, Parida SK, Prasad M. Comprehensive Genome-wide survey, genomic constitution and expression profiling of the NAC transcription factor family in foxtail millet (Setaria italic L.). Plos One. 2013;8(5):e64594.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhu JK. Cell signaling under salt, water and cold stresses. Curr Opin Plant Biol. 2001;4(5):401–6.
Article
CAS
PubMed
Google Scholar
Tsugane K, Kobayashi K, Niwa Y, Ohba Y, Wada K, Kobayashi H. A recessive arabidopsis mutant that grows photoautotrophically under salt stress shows enhanced active oxygen detoxification. Plant Cell. 1999;11(7):1195–206.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shin JH, Yoshimoto K, Ohsumi Y, Jeon JS, An G. OsATG10b, an autophagosome component, is needed for cell survival against oxidative stresses in rice. Mol Cells. 2009;27(1):67–74.
Article
CAS
PubMed
Google Scholar
Rose TL, Bonneau L, Der C, Marty-Mazars D, Marty F. Starvation-induced expression of autophagy-related genes in Arabidopsis. Biol Cell. 2006;98(1):53–67.
Article
CAS
PubMed
Google Scholar
Puranik S, Bahadur RP, Srivastava PS, Prasad M. Molecular cloning and characterization of a membrane associated NAC family gene, SiNAC from foxtail millet [Setaria italica (L.) P. Beauv.]. Mol Biotechnol. 2011;49(2):138–50.
Article
CAS
PubMed
Google Scholar
Puranik S, Jha S, Srivastava PS, Sreenivasulu N, Prasad M. Comparative transcriptome analysis of contrasting foxtail millet cultivars in response to short-term salinity stress. J Plant Physiol. 2011;168(3):280–7.
Article
CAS
PubMed
Google Scholar
Briesemeister S, Rahnenfuhrer J, Kohlbacher O. Going from where to why-interpretable prediction of protein subcellular localization. Bioinformatics. 2010;26(9):1232–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Briesemeister S, Rahnenfuhrer J, Kohlbacher O. YLoc-an interpretable web server for predicting subcellular localization. Nucleic Acids Res. 2010;38:W497–502.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28(10):2731–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Voorrips RE. MapChart: Software for the graphical presentation of linkage maps and QTLs. J Hered. 2002;93(1):77–8.
Article
CAS
PubMed
Google Scholar
Chen Z, Chen M, Xu ZS, Li LC, Chen XP, Ma YZ. Characteristics and expression patterns of the aldehyde dehydrogenase (ALDH) gene superfamily of foxtail millet (Setaria italica L.). Plos One. 2014;9(7):e101136.
Article
PubMed
Google Scholar
Lynch M, Conery JS. The evolutionary fate and consequences of duplicate genes. Science. 2000;290(5494):1151–5.
Article
CAS
PubMed
Google Scholar
Yang ZF, Gu SL, Wang XF, Li WJ, Tang ZX, Xu CW. Molecular evolution of the CPP-like gene family in plants: Insights from comparative genomics of Arabidopsis and rice. J Mol Evol. 2008;67(3):266–77.
Article
CAS
PubMed
Google Scholar
Hiei Y, Ohta S, Komari T, Kumashiro T. Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J. 1994;6(2):271–82.
Article
CAS
PubMed
Google Scholar
Li YL, Fan XR, Shen QR. The relationship between rhizosphere nitrification and nitrogen-use efficiency in rice plants. Plant Cell Environ. 2008;31(1):73–85.
PubMed
Google Scholar
Carlsson N, Borde A, Wolfel S, Akerman B, Larsson A. Quantification of protein concentration by the Bradford method in the presence of pharmaceutical polymers. Anal Biochem. 2011;411(1):116–21.
Article
CAS
PubMed
Google Scholar