Rizhsky L, Liang H, Shuman J, Shulaev V, Davletova S, Mittler R. When defense pathways collide. The response of Arabidopsis to a combination of drought and heat stress. Plant Physiol. 2004;134(4):1683–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Atkinson NJ, Urwin PE. The interaction of plant biotic and abiotic stresses: from genes to the field. J Exp Bot. 2012;63(10):3523–43.
Article
CAS
PubMed
Google Scholar
Mittler R. Abiotic stress, the field environment and stress combination. Trends Plant Sci. 2006;11(1):15–9.
Article
CAS
PubMed
Google Scholar
Chan KX, Phua SY, Crisp P, McQuinn R, Pogson BJ. Learning the languages of the chloroplast: retrograde signaling and beyond. Annu Rev Plant Biol. 2016;67:25–53.
Article
CAS
PubMed
Google Scholar
Dhingra A, Bies DH, Lehner KR, Folta KM. Green light adjusts the plastid transcriptome during early photomorphogenic development. Plant Physiol. 2006;142(3):1256–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Martín G, Leivar P, Ludevid D, Tepperman JM, Quail PH, Monte E. Phytochrome and retrograde signalling pathways converge to antagonistically regulate a light-induced transcriptional network. Nat Commun. 2016;7:11431.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sun AZ, Guo FQ. Chloroplast retrograde regulation of heat stress responses in plants. Front Plant Sci. 2016;7:398.
PubMed
PubMed Central
Google Scholar
Chan KX, Mabbitt PD, Phua SY, Mueller JW, Nisar N, Gigolashvili T, Stroeher E, Grassl J, Arlt W, Estavillo GM, Jackson CJ, Pogson BJ. Sensing and signaling of oxidative stress in chloroplasts by inactivation of the SAL1 phosphoadenosine phosphatase. Proc Natl Acad Sci U S A. 2016;113(31):E4567–76.
Article
CAS
PubMed
PubMed Central
Google Scholar
Barkan A, Small I. Pentatricopeptide repeat proteins in plants. Annu Rev Plant Biol. 2014;65:415–42.
Article
CAS
PubMed
Google Scholar
Rédei GP. Extra-chromosomal mutability determined by a nuclear gene locus in Arabidopsis. Mut Res. 1973;18:149–62.
Article
Google Scholar
Sakamoto W, Kondo H, Murata M, Motoyoshi F. Altered mitochondrial gene expression in a maternal distorted leaf mutant of Arabidopsis induced by chloroplast mutator. Plant Cell. 1996;8(8):1377–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sandhu AP, Abdelnoor RV, Mackenzie SA. Transgenic induction of mitochondrial rearrangements for cytoplasmic male sterility in crop plants. Proc Natl Acad Sci U S A. 2007;104(6):1766–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao N, Xu X, Wamboldt Y, Mackenzie SA, Yang X, Hu Z, Yang J, Zhang M. MutS HOMOLOG1 silencing mediates ORF220 substoichiometric shifting and causes male sterility in Brassica juncea. J Exp Bot. 2016;67(1):435–44.
Article
CAS
PubMed
Google Scholar
Xu YZ, Santamaria Rde L, Virdi KS, Arrieta-Montiel MP, Razvi F, Li S, Ren G, Yu B, Alexander D, Guo L, Feng X, Dweikat IM, Clemente TE, Mackenzie SA. The chloroplast triggers developmental reprogramming when MutS HOMOLOG1 is suppressed in plants. Plant Physiol. 2012;159(2):710–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu YZ, Arrieta-Montiel MP, Virdi KS, de Paula WB, Widhalm JR, Basset GJ, Davila JI, Elthon TE, Elowsky CG, Sato SJ, Clemente TE, Mackenzie SA. MutS HOMOLOG1 is a nucleoid protein that alters mitochondrial and plastid properties and plant response to high light. Plant Cell. 2011;23(9):3428–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
de la Rosa Santamaria R, Shao MR, Wang G, Nino-Liu DO, Kundariya H, Wamboldt Y, Dweikat I, Mackenzie SA. MSH1-induced non-genetic variation provides a source of phenotypic diversity in Sorghum bicolor. PLoS One. 2014;9(10):e108407.
Article
PubMed
PubMed Central
CAS
Google Scholar
Yang X, Kundariya H, Xu YZ, Sandhu A, Yu J, Hutton SF, Zhang M, Mackenzie SA. MutS HOMOLOG1-derived epigenetic breeding potential in tomato. Plant Physiol. 2015;168(1):222–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shedge V, Davila J, Arrieta-Montiel MP, Mohammed S, Mackenzie SA. Extensive rearrangement of the Arabidopsis mitochondrial genome elicits cellular conditions for thermotolerance. Plant Physiol. 2010;152(4):1960–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Virdi KS, Wamboldt Y, Kundariya H, Laurie JD, Keren I, Kumar KR, Block A, Basset G, Luebker S, Elowsky C, Day PM, Roose JL, Bricker TM, Elthon T, Mackenzie SA. MSH1 is a plant organellar DNA binding and thylakoid protein under precise spatial regulation to alter development. Mol Plant. 2016;9(2):245–60.
Article
CAS
PubMed
Google Scholar
Virdi KS, Laurie JD, Xu YZ, Yu J, Shao MR, Sanchez R, Kundariya H, Wang D, Riethoven JJ, Wamboldt Y, Arrieta-Montiel MP, Shedge V, Mackenzie SA. Arabidopsis MSH1 mutation alters the epigenome and produces heritable changes in plant growth. Nat Commun. 2015;6:6386.
Article
CAS
PubMed
PubMed Central
Google Scholar
Slotkin RK, Martienssen R. Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet. 2007;8(4):272–85.
Article
CAS
PubMed
Google Scholar
Yong-Villalobos L, González-Morales SI, Wrobel K, Gutiérrez-Alanis D, Cervantes-Peréz SA, Hayano-Kanashiro C, Oropeza-Aburto A, Cruz-Ramírez A, Martínez O, Herrera-Estrella L. Methylome analysis reveals an important role for epigenetic changes in the regulation of the Arabidopsis response to phosphate starvation. Proc Natl Acad Sci U S A. 2015;112(52):E7293–302.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR. Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci U S A. 2012;109(32):E2183–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kinoshita T, Seki M. Epigenetic memory for stress response and adaptation in plants. Plant Cell Physiol. 2014;55(11):1859–63.
Article
CAS
PubMed
Google Scholar
James AB, Syed NH, Bordage S, Marshall J, Nimmo GA, Jenkins GI, Herzyk P, Brown JW, Nimmo HG. Alternative splicing mediates responses of the Arabidopsis circadian clock to temperature changes. Plant Cell. 2012;24(3):961–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shikata H, Hanada K, Ushijima T, Nakashima M, Suzuki Y, Matsushita T. Phytochrome controls alternative splicing to mediate light responses in Arabidopsis. Proc Natl Acad Sci U S A. 2014;111(52):18781–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol. 2013;31(1):46–53.
Article
CAS
PubMed
Google Scholar
Vitting-Seerup K, Porse BT, Sandelin A, Waage J. spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. BMC Bioinformatics. 2014;15:81.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hartley SW, Mullikin JC. Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq. Nucleic Acids Res. 2016;44(15):e127.
PubMed
PubMed Central
Google Scholar
Baker KE, Parker R. Nonsense-mediated mRNA decay: terminating erroneous gene expression. Curr Opin Cell Biol. 2004;16(3):293–9.
Article
CAS
PubMed
Google Scholar
Thimm O, Bläsing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY, Stitt M. MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 2004;37(6):914–39.
Article
CAS
PubMed
Google Scholar
Suárez-López P, Wheatley K, Robson F, Onouchi H, Valverde F, Coupland G. CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis. Nature. 2001;410(6832):1116–20.
Article
PubMed
Google Scholar
Valverde F. CONSTANS and the evolutionary origin of photoperiodic timing of flowering. J Exp Bot. 2011;62(8):2453–63.
Article
CAS
PubMed
Google Scholar
da Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57.
Article
CAS
Google Scholar
Ransbotyn V, Yeger-Lotem E, Basha O, Acuna T, Verduyn C, Gordon M, Chalifa-Caspi V, Hannah MA, Barak S. A combination of gene expression ranking and co-expression network analysis increases discovery rate in large-scale mutant screens for novel Arabidopsis thaliana abiotic stress genes. Plant Biotechnol J. 2015;13(4):501–13.
Article
CAS
PubMed
Google Scholar
Sham A, Moustafa K, Al-Ameri S, Al-Azzawi A, Iratni R, AbuQamar S. Identification of Arabidopsis candidate genes in response to biotic and abiotic stresses using comparative microarrays. PLoS One. 2015;10(5):e0125666.
Article
PubMed
PubMed Central
CAS
Google Scholar
Leviatan N, Alkan N, Leshkowitz D, Fluhr R. Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana with tiling microarray. PLoS One. 2013;8(6):e66511.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rivas-San Vicente M, Plasencia J. Salicylic acid beyond defense: its role in plant growth and development. J Exp Bot. 2011;62(10):3321–38.
Article
CAS
PubMed
Google Scholar
Wrzaczek M, Brosché M, Kangasjärvi J. ROS signaling loops - production, perception, regulation. Curr Opin Plant Biol. 2013;16(5):575–82.
Article
CAS
PubMed
Google Scholar
Herrera-Vásquez A, Salinas P, Holuigue L. Salicylic acid and reactive oxygen species interplay in the transcriptional control of defense genes expression. Front Plant Sci. 2015;6:171.
Article
PubMed
PubMed Central
Google Scholar
Zhu Z, Xu F, Zhang Y, Cheng YT, Wiermer M, Li X, Zhang Y. Arabidopsis resistance protein SNC1 activates immune responses through association with a transcriptional corepressor. Proc Natl Acad Sci U S A. 2010;107(31):13960–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
MacQueen A, Bergelson J. Modulation of R-gene expression across environments. J Exp Bot. 2016;67(7):2093–105.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kawakatsu T, Huang SS, Jupe F, Sasaki E, Schmitz RJ, Urich MA, Castanon R, Nery JR, Barragan C, He Y, Chen H, Dubin M, Lee CR, Wang C, Bemm F, Becker C, O’Neil R, O’Malley RC, Quarless DX, 1001 Genomes Consortium, Schork NJ, Weigel D, Nordborg M, Ecker JR. Epigenomic diversity in a global collection of Arabidopsis thaliana accessions. Cell. 2016;166(2):492–505.
Article
CAS
PubMed
Google Scholar
Kindgren P, Kremnev D, Blanco NE, de Dios Barajas López J, Fernández AP, Tellgren-Roth C, Kleine T, Small I, Strand A. The plastid redox insensitive 2 mutant of Arabidopsis is impaired in PEP activity and high light-dependent plastid redox signaling to the nucleus. Plant J. 2012;70(2):279–91.
Article
CAS
PubMed
Google Scholar
Mochizuki N, Brusslan JA, Larkin R, Nagatani A, Chory J. Arabidopsis genomes uncoupled 5 (GUN5) mutant reveals the involvement of Mg-chelatase H subunit in plastid-to-nucleus signal transduction. Proc Natl Acad Sci U S A. 2001;98(4):2053–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Van Aken O, Whelan J. Comparison of transcriptional changes to chloroplast and mitochondrial perturbations reveals common and specific responses in Arabidopsis. Front Plant Sci. 2012;3:281.
PubMed
PubMed Central
Google Scholar
Para A, Farré EM, Imaizumi T, Pruneda-Paz JL, Harmon FG, Kay SA. PRR3 Is a vascular regulator of TOC1 stability in the Arabidopsis circadian clock. Plant Cell. 2007;19(11):3462–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Greenham K, McClung CR. Integrating circadian dynamics with physiological processes in plants. Nat Rev Genet. 2015;16(10):598–610.
Article
CAS
PubMed
Google Scholar
Lai AG, Doherty CJ, Mueller-Roeber B, Kay SA, Schippers JH, Dijkwel PP. CIRCADIAN CLOCK-ASSOCIATED 1 regulates ROS homeostasis and oxidative stress responses. Proc Natl Acad Sci U S A. 2012;109(42):17129–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lepage É, Zampini É, Brisson N. Plastid genome instability leads to reactive oxygen species production and plastid-to-nucleus retrograde signaling in Arabidopsis. Plant Physiol. 2013;163(2):867–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou M, Wang W, Karapetyan S, Mwimba M, Marqués J, Buchler NE, Dong X. Redox rhythm reinforces the circadian clock to gate immune response. Nature. 2015;523(7561):472–6.
Article
PubMed
PubMed Central
CAS
Google Scholar
Covington MF, Harmer SL. The circadian clock regulates auxin signaling and responses in Arabidopsis. PLoS Biol. 2007;5(8):e222.
Article
PubMed
PubMed Central
CAS
Google Scholar
Arana MV, Marín-de la Rosa N, Maloof JN, Blázquez MA, Alabadí D. Circadian oscillation of gibberellin signaling in Arabidopsis. Proc Natl Acad Sci U S A. 2011;108(22):9292–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Atamian HS, Harmer SL. Circadian regulation of hormone signaling and plant physiology. Plant Mol Biol. 2016;91(6):691–702.
Article
CAS
PubMed
Google Scholar
Wood NT, Haley A, Viry-Moussaïd M, Johnson CH, van der Luit AH, Trewavas AJ. The calcium rhythms of different cell types oscillate with different circadian phases. Plant Physiol. 2001;125(2):787–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mazars C, Thuleau P, Lamotte O, Bourque S. Cross-talk between ROS and calcium in regulation of nuclear activities. Mol Plant. 2010;3(4):706–18.
Article
CAS
PubMed
Google Scholar
Mühlenbock P, Szechynska-Hebda M, Plaszczyca M, Baudo M, Mateo A, Mullineaux PM, Parker JE, Karpinska B, Karpinski S. Chloroplast signaling and LESION SIMULATING DISEASE1 regulate crosstalk between light acclimation and immunity in Arabidopsis. Plant Cell. 2008;20(9):2339–56.
Article
PubMed
PubMed Central
CAS
Google Scholar
Baxter A, Mittler R, Suzuki N. ROS as key players in plant stress signaling. J Exp Bot. 2014;65(5):1229–40.
Article
CAS
PubMed
Google Scholar
Zhang C, Xie Q, Anderson RG, Ng G, Seitz NC, Peterson T, McClung CR, McDowell JM, Kong D, Kwak JM, Lu H. Crosstalk between the circadian clock and innate immunity in Arabidopsis. PLoS Pathog. 2013;9(6):e1003370.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sanchez A, Shin J, Davis SJ. Abiotic stress and the plant circadian clock. Plant Signal Behav. 2011;6(2):223–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Luesse DR, Wilson ME, Haswell ES. RNA sequencing analysis of the msl2msl3, crl, and ggps1 mutants indicates that diverse sources of plastid dysfunction do not alter leaf morphology through a common signaling pathway. Front Plant Sci. 2015;6:1148.
Article
PubMed
PubMed Central
Google Scholar
Hotto AM, Schmitz RJ, Fei Z, Ecker JR, Stern DB. Unexpected diversity of chloroplast noncoding RNAs as revealed by deep sequencing of the Arabidopsis transcriptome. G3 (Bethesda). 2011;1(7):559–70.
Article
CAS
Google Scholar
Woodson JD, Perez-Ruiz JM, Schmitz RJ, Ecker JR, Chory J. Sigma factor-mediated plastid retrograde signals control nuclear gene expression. Plant J. 2013;73(1):1–13.
Article
CAS
PubMed
Google Scholar
Miura E, Kato Y, Sakamoto W. Comparative transcriptome analysis of green/white variegated sectors in Arabidopsis yellow variegated2: responses to oxidative and other stresses in white sectors. J Exp Bot. 2010;61(9):2433–45.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bermúdez MA, Páez-Ochoa MA, Gotor C, Romero LC. Arabidopsis S-sulfocysteine synthase activity is essential for chloroplast function and long-day light-dependent redox control. Plant Cell. 2010;22(2):403–16.
Article
PubMed
PubMed Central
Google Scholar
Laloi C, Stachowiak M, Pers-Kamczyc E, Warzych E, Murgia I, Apel K. Cross-talk between singlet oxygen- and hydrogen peroxide-dependent signaling of stress responses in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2007;104(2):672–7.
Article
CAS
PubMed
Google Scholar
Dietzel L, Gläßer C, Liebers M, Hiekel S, Courtois F, Czarnecki O, Schlicke H, Zubo Y, Börner T, Mayer K, Grimm B, Pfannschmidt T. Identification of early nuclear target genes of plastidial redox signals that trigger the long-term response of Arabidopsis to light quality shifts. Mol Plant. 2015;8(8):1237–52.
Article
CAS
PubMed
Google Scholar
Ng S, Ivanova A, Duncan O, Law SR, Van Aken O, De Clercq I, Wang Y, Carrie C, Xu L, Kmiec B, Walker H, Van Breusegem F, Whelan J, Giraud E. A membrane-bound NAC transcription factor, ANAC017, mediates mitochondrial retrograde signaling in Arabidopsis. Plant Cell. 2013;25(9):3450–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ng S, Giraud E, Duncan O, Law SR, Wang Y, Xu L, Narsai R, Carrie C, Walker H, Day DA, Blanco NE, Strand Å, Whelan J, Ivanova A. Cyclin-dependent kinase E1 (CDKE1) provides a cellular switch in plants between growth and stress responses. J Biol Chem. 2013;288(5):3449–59.
Article
CAS
PubMed
Google Scholar
Koussevitzky S, Nott A, Mockler TC, Hong F, Sachetto-Martins G, Surpin M, Lim J, Mittler R, Chory J. Signals from chloroplasts converge to regulate nuclear gene expression. Science. 2007;316(5825):715–9.
Article
CAS
PubMed
Google Scholar
Rubio-Somoza I, Weigel D. MicroRNA networks and developmental plasticity in plants. Trends Plant Sci. 2011;16(5):258–64.
Article
CAS
PubMed
Google Scholar
Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014;42(Database issue):D68–73.
Article
CAS
PubMed
Google Scholar
Chung PJ, Park BS, Wang H, Liu J, Jang IC, Chua NH. Light-inducible miR163 targets PXMT1 transcripts to promote seed germination and primary root elongation in Arabidopsis. Plant Physiol. 2016;170(3):1772–82.
CAS
PubMed
PubMed Central
Google Scholar
Ng DW, Zhang C, Miller M, Palmer G, Whiteley M, Tholl D, Chen ZJ. cis- and trans-Regulation of miR163 and target genes confers natural variation of secondary metabolites in two Arabidopsis species and their allopolyploids. Plant Cell. 2011;23(5):1729–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao B, Ge L, Liang R, Li W, Ruan K, Lin H, Jin Y. Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor. BMC Mol Biol. 2009;10:29.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhao M, Ding H, Zhu JK, Zhang F, Li WX. Involvement of miR169 in the nitrogen-starvation responses in Arabidopsis. New Phytol. 2011;190(4):906–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu MY, Zhang L, Li WW, Hu XL, Wang MB, Fan YL, Zhang CY, Wang L. Stress-induced early flowering is mediated by miR169 in Arabidopsis thaliana. J Exp Bot. 2014;65(1):89–101.
Article
CAS
PubMed
Google Scholar
Olovnikov I, Aravin AA, Fejes Toth K. Small RNA in the nucleus: the RNA-chromatin ping-pong. Curr Opin Genet Dev. 2012;22(2):164–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sunkar R, Chinnusamy V, Zhu J, Zhu JK. Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci. 2007;12(7):301–9.
Article
CAS
PubMed
Google Scholar
Phillips JR, Dalmay T, Bartels D. The role of small RNAs in abiotic stress. FEBS Lett. 2007;581(19):3592–7.
Article
CAS
PubMed
Google Scholar
Huang J, Yang M, Zhang X. The function of small RNAs in plant biotic stress response. J Integr Plant Biol. 2016;58(4):312–27.
Article
CAS
PubMed
Google Scholar
Johnson NR, Yeoh JM, Coruh C, Axtell MJ. Improved placement of multi-mapping small RNAs. G3 (Bethesda). 2016;6(7):2103–11.
Article
Google Scholar
Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW. Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell. 2003;15(4):809–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Oliver KR, McComb JA, Greene WK. Transposable elements: powerful contributors to angiosperm evolution and diversity. Genome Biol Evol. 2013;5(10):1886–901.
Article
PubMed
PubMed Central
Google Scholar
Jarvis P, López-Juez E. Biogenesis and homeostasis of chloroplasts and other plastids. Nat Rev Mol Cell Biol. 2013;14(12):787–802.
Article
CAS
PubMed
Google Scholar
Millar AH, Whelan J, Soole KL, Day DA. Organization and regulation of mitochondrial respiration in plants. Annu Rev Plant Biol. 2011;62:79–104.
Article
CAS
PubMed
Google Scholar
Jacoby RP, Li L, Huang S, Pong Lee C, Millar AH, Taylor NL. Mitochondrial composition, function and stress response in plants. J Integr Plant Biol. 2012;54(11):887–906.
CAS
PubMed
Google Scholar
Shedge V, Arrieta-Montiel M, Christensen AC, Mackenzie SA. Plant mitochondrial recombination surveillance requires unusual RecA and MutS homologs. Plant Cell. 2007;19(4):1251–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kelliher T, Walbot V. Hypoxia triggers meiotic fate acquisition in maize. Science. 2012;337(6092):345–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Boyko A, Kovalchuk I. Genome instability and epigenetic modification–heritable responses to environmental stress? Curr Opin Plant Biol. 2011;14(3):260–6.
Article
PubMed
Google Scholar
Becker C, Hagmann J, Müller J, Koenig D, Stegle O, Borgwardt K, Weigel D. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature. 2011;480(7376):245–9.
Article
CAS
PubMed
Google Scholar
Schmitz RJ, Schultz MD, Lewsey MG, O’Malley RC, Urich MA, Libiger O, Schork NJ, Ecker JR. Transgenerational epigenetic instability is a source of novel methylation variants. Science. 2011;334(6054):369–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sanchez R, Mackenzie SA. Information thermodynamics of cytosine DNA methylation. PLoS One. 2016;11(3):e0150427.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sanchez R, Mackenzie SA. Genome-wide discriminatory information patterns of cytosine DNA methylation. Int J Mol Sci. 2016;17(6):E938.
Article
PubMed
Google Scholar
Probst AV, Mittelsten Scheid O. Stress-induced structural changes in plant chromatin. Curr Opin Plant Biol. 2015;27:8–16.
Article
CAS
PubMed
Google Scholar
Rodermel S. Arabidopsis variegation mutants. Arabidopsis Book. 2002;1:e0079.
Article
PubMed
PubMed Central
Google Scholar
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36.
Article
PubMed
PubMed Central
CAS
Google Scholar
Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, Stoeckert CJ, Hogenesch JB, Pierce EA. Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics. 2011;27(18):2518–28.
CAS
PubMed
PubMed Central
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21.
Article
CAS
PubMed
Google Scholar
Jin Y, Tam OH, Paniagua E, Hammell M. TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics. 2015;31(22):3593–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47.
Article
PubMed
PubMed Central
CAS
Google Scholar