Fuchs J, Jovtchev G, Schubert I. The chromosomal distribution of histone methylation marks in gymnosperms differs from that of angiosperms. Chromosom Res. 2008;16(6):891–8.
Article
CAS
Google Scholar
Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin Y-C, Scofield DG, et al. The Norway spruce genome sequence and conifer genome evolution. Nature. 2013;497:579.
Article
CAS
Google Scholar
Zimin A, Stevens KA, Crepeau MW, Holtz-Morris A, Koriabine M, Marcais G, et al. Sequencing and assembly of the 22-gb loblolly pine genome. Genetics. 2014;196(3):875–90.
Article
CAS
Google Scholar
Stevens KA, Wegrzyn JL, Zimin A, Puiu D, Crepeau M, Cardeno C, et al. Sequence of the sugar pine megagenome. Genetics. 2016;204(4):1613–26.
Article
CAS
Google Scholar
Wegrzyn JL, Liechty JD, Stevens KA, Wu LS, Loopstra CA, Vasquez-Gross HA, et al. Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics. 2014;196(3):891–909.
Article
CAS
Google Scholar
Wessler SR. Transposable elements and the evolution of gene expression. Symp Soc Exp Biol. 1998;51:115–22.
CAS
PubMed
Google Scholar
Martínez G, Slotkin RK. Developmental relaxation of transposable element silencing in plants: functional or byproduct? Curr Opin Plant Biol. 2012;15(5):496–502.
Article
Google Scholar
Wessler SR, Bureau TE, White SE. LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Curr Opin Genet Dev. 1995;5(6):814–21.
Article
CAS
Google Scholar
Grandbastien M-A, Lucas H, Morel J-B, Mhiri C, Vernhettes S, Casacuberta J. The expression of the tobacco Tnt1 retrotransposon is linked to plant defense responses. Genetica. 1997;100(1):241–52.
Article
CAS
Google Scholar
Baucom RS, Estill JC, Leebens-Mack J, Bennetzen JL. Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Res. 2009;19(2):243–54.
Article
CAS
Google Scholar
Bennetzen JL. Transposable element contributions to plant gene and genome evolution. Plant Mol Biol. 2000;42(1):251–69.
Article
CAS
Google Scholar
Feschotte C. The contribution of transposable elements ot the evolution of regulatory networks. Nat Rev Genet. 2008;9(5):397–405.
Article
CAS
Google Scholar
Galindo-González L, Mhiri C, Deyholos MK, Grandbastien MA. LTR-retrotransposons in plants: engines of evolution. Gene. 2017;626(April):14–25.
Article
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
Google Scholar
Piriyapongsa J, Jordan IK. Dual coding of siRNAs and miRNAs by plant transposable elements. RNA. 2008;14(5):814–21.
Article
CAS
Google Scholar
Ito H. Small RNAs and regulation of transposons in plants. Genes Genet Syst. 2013;88(1):3–7.
Article
CAS
Google Scholar
Li Y, Li C, Xia J, Jin Y. Domestication of transposable elements into MicroRNA genes in plants. PLoS ONE. 2011;6(5):e19212.
Article
CAS
Google Scholar
Wang D, Qu Z, Yang L, Zhang Q, Liu ZH, Do T, et al. Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in plants. Plant J. 2017;90(1):133–46.
Article
CAS
Google Scholar
Zinad HS, Natasya I, Werner A. Natural antisense transcripts at the interface between host genome and mobile genetic elements. Front Microbiol. 2017;8:1–9.
Article
Google Scholar
Rubio-Piña JA, Zapata-Pérez O. Isolation of total RNA from tissues rich in polyphenols and polysaccharides of mangrove plants. Electron J Biotechnol. 2011. https://doi.org/10.2225/vol14-issue5-fulltext-10.
Article
Google Scholar
D’haene B, Vandesompele J, Hellemans J. Accurate and objective copy number profiling using real-time quantitative PCR. Methods. 2010;50(4):262–70.
Article
Google Scholar
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, et al. Primer3–new capabilities and interfaces. Nucleic Acids Res. 2012;40(15):e115.
Article
CAS
Google Scholar
Andersen CL, Jensen JL, Orntoft TF. Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res. 2004;64(15):5245–50.
Article
CAS
Google Scholar
Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper–Excel-based tool using pair-wise correlations. Biotechnol Lett. 2004;26(6):509–15.
Article
CAS
Google Scholar
Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001;29(9):45e–45.
Article
Google Scholar
McCune B, Mefford MJ. PC-ORD multivariate analysis of ecological data version 5.10. Gleneden Beach: MjM Software; 2006.
Google Scholar
Voronova A, Belevich V, Korica A, Rungis D. Retrotransposon distribution and copy number variation in gymnosperm genomes. Tree Genet Genomes. 2017;13(4):88.
Article
Google Scholar
McClintock B. The significance of responses of the genome to challenge. Science. 1984;226(4676):792–801.
Article
CAS
Google Scholar
Wessler SR. Plant retrotransposons: turned on by stress. Curr Biol. 1996;6(8):959–61.
Article
CAS
Google Scholar
Grandbastien MA. LTR retrotransposons, handy hitchhikers of plant regulation and stress response. Biochim Biophys Acta Gene Regul Mech. 2015;1849(4):403–16.
Article
CAS
Google Scholar
Capy P, Gasperi G, Biémont C, Bazin C. Stress and transposable elements: co-evolution or useful parasites? Heredity (Edinb). 2000;85(2):101–6.
Article
CAS
Google Scholar
Butelli E, Licciardello C, Zhang Y, Liu J, Mackay S, Bailey P, et al. Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges. Plant Cell. 2012;24(3):1242–55.
Article
CAS
Google Scholar
Rocheta M, Carvalho L, Viegas W, Morais-Cecílio L. Corky, a gypsy-like retrotransposon is differentially transcribed in Quercus suber tissues. BMC Res Notes. 2012;5:1–6.
Article
Google Scholar
Matsunaga W, Ohama N, Tanabe N, Masuta Y, Masuda S, Mitani N, et al. A small RNA mediated regulation of a stress-activated retrotransposon and the tissue specific transposition during the reproductive period in Arabidopsis. Front Plant Sci. 2015;6(February):1–12.
Google Scholar
Witte C-P, Le QH, Bureau T, Kumar A. Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. Proc Natl Acad Sci. 2001;98(24):13778–83.
Article
CAS
Google Scholar
Kalendar R, Vicient CM, Peleg O, Anamthawat-Jonsson K, Bolshoy A, Schulman AH. Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes. Genetics. 2004;166(3):1437–50.
Article
CAS
Google Scholar
Kapranov P, St. Laurent G. Dark matter RNA: existence, function, and controversy. Front Genet. 2012;3:1–9.
Google Scholar
Tapia G, Verdugo I, Yañez M, Ahumada I, Theoduloz C, Cordero C, et al. Involvement of ethylene in stress-induced expression of the TLC1.1 retrotransposon from Lycopersicon chilense Dun. Plant Physiol. 2005;138(4):2075–86.
Article
CAS
Google Scholar
Kossack DS, Kinlaw CS. IFG, a gypsy-like retrotransposon in Pinus (Pinaceae), has an extensive history in pines. Plant Mol Biol. 1999;39(3):417–26.
Article
CAS
Google Scholar
Testing Martinsson O. Scots pine for resistance to Lophodermium needle cast. Uppsala: College of Forestry, Swedish University of Agricultural Sciences; 1979.
Google Scholar
Gregory SC, Redfern D. Disease and disorders of forest trees Forestry C. Forestry Commission: Scotland; 1998.
Google Scholar
Minter DW. Lophodermium on Pines. Mycol Pap. 1981;147:1–54.
Google Scholar
Rack K. Studies on needle-cast of Scots pine I-III. 2. Pflanz Krankheiten. 1963;70(3):137–46.
Google Scholar
Ortiz-García S, Gernandt DS, Stone JK, Johnston PR, Chapela IH, Salas-Lizana R, et al. Phylogenetics of Lophodermium from pine. Mycologia. 2003;95(5):846–59.
Article
Google Scholar
Deckert RJ, Melville LH, Peterson RL. Structural features of a Lophodermium endophyte during the cryptic life-cycle phase in the foliage of Pinus strobus. Mycol Res. 2001;105(8):991–7.
Article
Google Scholar
Ponge J. The soil under the microscope: the optical examination of a small area of Scots pine litter. Budapset: Éditions Universitaires Européennes; 2010. https://doi.org/10.13140/RG.2.2.25335.83368.
Book
Google Scholar
Jansons A, Neimane U, Baumanis I. Needlecast resistance of Scots pine and possibilities of its improvement. Mezzinatne. 2008;18(51):3–18.
Google Scholar
Asiegbu FO, Adomas A, Stenlid J. Conifer root and butt rot caused by Heterobasidion annosum (Fr.) Bref. s.l. Mol Plant Pathol. 2005;6(4):395–409.
Article
Google Scholar
Govrin EM, Levine A. The hypersensitive response facilitates plant infection by the necrotrophic pathogen Botrytis cinerea. Curr Biol. 2000;10(13):751–7.
Article
CAS
Google Scholar
Nagy ED, Lee T-C, Ramakrishna W, Xu Z, Klein PE, SanMiguel P, et al. Fine mapping of the Pc locus of Sorghum bicolor, a gene controlling the reaction to a fungal pathogen and its host-selective toxin. Theor Appl Genet. 2007;114(6):961–70.
Article
CAS
Google Scholar
Thomma BP, Eggermont K, Penninckx IA, Mauch-Mani B, Vogelsang R, Cammue BP, et al. Separate jasmonate-dependent and salicylate-dependent defense-response pathways in Arabidopsis are essential for resistance to distinct microbial pathogens. Proc Natl Acad Sci USA. 1998;95(25):15107–11.
Article
CAS
Google Scholar
Weiberg A, Jin H. Small RNAs—the secret agents in the plant–pathogen interactions. Curr Opin Plant Biol. 2015;26:87–94.
Article
CAS
Google Scholar
Panaud O. Horizontal transfers of transposable elements in eukaryotes: the flying genes. C R Biol. 2016;339(7–8):296–9.
Article
Google Scholar