[1] |
Liu P, Liu R, Xu Y, Zhang C, Niu Q, et al. 2023. DNA cytosine methylation dynamics and functional roles in horticultural crops. Horticulture Research 10:d170 doi: 10.1093/hr/uhad170 |
[2] |
Paudel L, Kerr S, Prentis P, Tanurdžić M, Papanicolaou A, et al. 2022. Horticultural innovation by viral-induced gene regulation of carotenogenesis. Horticulture Research 9:uhab008 doi: 10.1093/hr/uhab008 |
[3] |
Shi M, Wang C, Wang P, Yun F, Liu Z, et al. 2023. Role of methylation in vernalization and photoperiod pathway: a potential flowering regulator? Horticulture Research 10:uhad17 doi: 10.1093/hr/uhad174 |
[4] |
Cuerda-Gil D, Slotkin RK. 2016. Non-canonical RNA-directed DNA methylation. Nature Plants 2:16163 doi: 10.1038/nplants.2016.163 |
[5] |
Margis R, Fusaro AF, Smith NA, Curtin SJ, Watson JM, et al. 2006. The evolution and diversification of Dicers in plants. FEBS Letters 580:2442−50 doi: 10.1016/j.febslet.2006.03.072 |
[6] |
Kurihara Y, Watanabe Y. 2004. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proceedings of the National Academy of Sciences of the United States of America 101:12753−58 doi: 10.1073/pnas.0403115101 |
[7] |
Jia J, Ji R, Li Z, Yu Y, Nakano M, et al. 2020. Soybean DICER-LIKE2 regulates seed coat color via production of primary 22-nucleotide small interfering RNAs from long inverted repeats. The Plant Cell 32:3662−73 doi: 10.1105/tpc.20.00562 |
[8] |
Taochy C, Gursanscky NR, Cao J, Fletcher SJ, Dressel U, et al. 2017. A genetic screen for impaired systemic rnai highlights the crucial role of DICER-LIKE 2. Plant Physiology 175:1424−1437 doi: 10.1104/pp.17.01181 |
[9] |
Wu YY, Hou BH, Lee WC, Lu SH, Yang CJ, et al. 2017. DCL2- and RDR6-dependent transitive silencing of SMXL4 and SMXL5 in Arabidopsis dcl4 mutants causes defective phloem transport and carbohydrate over-accumulation. The Plant Journal 90:1064−78 doi: 10.1111/tpj.13528 |
[10] |
Matzke MA, Mosher RA. 2014. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nature Reviews Genetics 15:394−408 doi: 10.1038/nrg3683 |
[11] |
Wang Q, Xue Y, Zhang L, Zhong Z, Feng S, et al. 2021. Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation. Science 374:1152−57 doi: 10.1126/science.abl4546 |
[12] |
Liu Y, Teng C, Xia R, Meyers BC. 2020. PhasiRNAs in plants: their biogenesis, genic sources, and roles in stress responses, development, and reproduction. The Plant Cell 32:3059−80 doi: 10.1105/tpc.20.00335 |
[13] |
Teng C, Zhang H, Hammond R, Huang K, Meyers BC, Walbot V. 2020. Dicer-like 5 deficiency confers temperature-sensitive male sterility in maize. Nature Communications 11:2912 doi: 10.1038/s41467-020-16634-6 |
[14] |
Carbonell A, Carrington JC. 2015. Antiviral roles of plant ARGONAUTES. Current Opinion in Plant Biology 27:111−17 doi: 10.1016/j.pbi.2015.06.013 |
[15] |
Fang X, Qi Y. 2016. RNAi in plants: an argonaute-centered view. The Plant Cell 28:272−85 doi: 10.1105/tpc.15.00920 |
[16] |
Li Z, Li W, Guo M, Liu S, Liu L, et al. 2022. Origin, evolution and diversification of plant ARGONAUTE proteins. The Plant Journal 109:1086−97 doi: 10.1111/tpj.15615 |
[17] |
Zhang H, Xia R, Meyers BC, Walbot V. 2015. Evolution, functions, and mysteries of plant ARGONAUTE proteins. Current Opinion in Plant Biology 27:84−90 doi: 10.1016/j.pbi.2015.06.011 |
[18] |
Garcia-Ruiz H, Carbonell A, Hoyer JS, Fahlgren N, Gilbert KB, et al. 2015. Roles and programming of arabidopsis argonaute proteins during Turnip mosaic virus infection. PLOS Pathogens 11:e1004755 doi: 10.1371/journal.ppat.1004755 |
[19] |
Wang XB, Jovel J, Udomporn P, Wang Y, Wu Q, et al. 2011. The 21-Nucleotide, but not 22-nucleotide, viral secondary small interfering rnas direct potent antiviral defense by two cooperative argonautes in Arabidopsis thaliana. The Plant Cell 23:1625−38 doi: 10.1105/tpc.110.082305 |
[20] |
Brosseau C, Moffett P. 2015. Functional and genetic analysis identify a role for arabidopsis argonaute5 in antiviral RNA silencing. The Plant Cell 27:1742−54 doi: 10.1105/tpc.15.00264 |
[21] |
Tucker MR, Okada T, Hu Y, Scholefield A, Taylor JM, et al. 2012. Somatic small RNA pathways promote the mitotic events of megagametogenesis during female reproductive development in Arabidopsis. Development 139:1399−404 doi: 10.1242/dev.075390 |
[22] |
Yu Y, Ji L, Le BH, Zhai J, Chen J, et al. 2021. Correction: ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis. PLOS Biology 19:e3001120 doi: 10.1371/journal.pbio.3001120 |
[23] |
Zhu H, Hu F, Wang R, Zhou X, Sze SH, et al. 2011. Arabidopsis argonaute10 specifically sequesters MIR166/165 to regulate shoot apical meristem development. Cell 145:242−56 doi: 10.1016/j.cell.2011.03.024 |
[24] |
Gao M, Wei W, Li MM, Wu YS, Ba Z, et al. 2014. Ago2 facilitates Rad51 recruitment and DNA double-strand break repair by homologous recombination. Cell Research 24:532−41 doi: 10.1038/cr.2014.36 |
[25] |
Schuck J, Gursinsky T, Pantaleo V, Burgyán J, Behrens SE. 2013. AGO/RISC-mediated antiviral RNA silencing in a plant in vitro system. Nucleic Acids Research 41:5090−103 doi: 10.1093/nar/gkt193 |
[26] |
Zhang X, Zhao H, Gao S, Wang WC, Katiyar-Agarwal S, et al. 2011. Arabidopsis Argonaute 2 regulates innate immunity via miRNA393-mediated silencing of a golgi-localized SNARE gene, MEMB12. Molecular Cell 42:356−66 doi: 10.1016/j.molcel.2011.04.010 |
[27] |
Zhang Z, Liu X, Guo X, Wang XJ, Zhang X. 2016. Arabidopsis AGO3 predominantly recruits 24-nt small RNAs to regulate epigenetic silencing. Nature Plants 2:16049 doi: 10.1038/nplants.2016.49 |
[28] |
Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, et al. 2007. Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. The Plant Cell 19:926−42 doi: 10.1105/tpc.107.050062 |
[29] |
Duan CG, Zhang H, Tang K, Zhu X, Qian W, et al. 2014. Specific but interdependent functions for Arabidopsis AGO4 and AGO6 in RNA-directed DNA methylation. The EMBO Journal 34:581−92 doi: 10.15252/embj.201489453 |
[30] |
Olmedo-Monfil V, Durán-Figueroa N, Arteaga-Vázquez M, Demesa-Arévalo E, Autran D, et al. 2010. Control of female gamete formation by a small RNA pathway in Arabidopsis. Nature 464:628−32 doi: 10.1038/nature08828 |
[31] |
Zheng X, Zhu J, Kapoor A, Zhu JK. 2007. Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing. The EMBO Journal 26:1691−701 doi: 10.1038/sj.emboj.7601603 |
[32] |
Hernández-Lagana E, Rodríguez-Leal D, Lúa J, Vielle-Calzada J. 2016. A multigenic network of argonaute4 clade members controls early megaspore formation in Arabidopsis. Genetics 204:1045−56 doi: 10.1534/genetics.116.188151 |
[33] |
Bélanger S, Zhan J, Meyers BC. 2023. Phylogenetic analyses of seven protein families refine the evolution of small RNA pathways in green plants. Plant Physiology 192:1183−203 doi: 10.1093/plphys/kiad141 |
[34] |
Wang S, Liang H, Xu Y, Li L, Wang H, et al. 2021. Genome-wide analyses across Viridiplantae reveal the origin and diversification of small RNA pathway-related genes. Communications Biology 4:412 doi: 10.1038/s42003-021-01933-5 |
[35] |
Li S, Wei L, Gao Q, Xu M, Wang Y, et al. 2024. Molecular and phylogenetic evidence of parallel expansion of anion channels in plants. Plant Physiology 194:2533−48 doi: 10.1093/plphys/kiad687 |
[36] |
Su L, Zhang T, Yang B, Dong T, Liu X, et al. 2023. Different evolutionary patterns of TIR1/AFBs and AUX/IAAs and their implications for the morphogenesis of land plants. BMC Plant Biology 23:265 doi: 10.1186/s12870-023-04253-4 |
[37] |
Wu Y, Wen J, Xia Y, Zhang L, Du H. 2022. Evolution and functional diversification of R2R3-MYB transcription factors in plants. Horticulture Research 9:uhac058 doi: 10.1093/hr/uhac058 |
[38] |
Nishiyama T, Sakayama H, de Vries J, Buschmann H, Saint-Marcoux D, et al. 2018. The chara genome: secondary complexity and implications for plant terrestrialization. Cell 174:448−64 doi: 10.1016/j.cell.2018.06.033 |
[39] |
Rensing SA. 2018. Great moments in evolution: the conquest of land by plants. Current Opinion in Plant Biology 42:49−54 doi: 10.1016/j.pbi.2018.02.006 |
[40] |
Alaba S, Piszczalka P, Pietrykowska H, Pacak AM, Sierocka I, et al. 2015. The liverwort Pellia endiviifolia shares microtranscriptomic traits that are common to green algae and land plants. New Phytologist 206:352−67 doi: 10.1111/nph.13220 |
[41] |
Axtell MJ, Snyder JA, Bartel DP. 2007. Common functions for diverse small RNAs of land plants. The Plant Cell 19:1750−69 doi: 10.1105/tpc.107.051706 |
[42] |
Fattash I, Voß B, Reski R, Hess WR, Frank W. 2007. Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution. BMC Plant Biology 7:13 doi: 10.1186/1471-2229-7-13 |
[43] |
Lin PC, Lu CW, Shen BN, Lee GZ, Bowman JL, et al. 2016. Identification of miRNAs and their targets in the liverwort Marchantia polymorpha by integrating RNA-Seq and degradome analyses. Plant and Cell Physiology 57:339−58 doi: 10.1093/pcp/pcw020 |
[44] |
Dong Q, Hu B, Zhang C. 2022. MicroRNAs and their roles in plant development. Frontiers in Plant Science 13:824240 doi: 10.3389/fpls.2022.824240 |
[45] |
Zhan J, Meyers BC. 2023. Plant Small RNAs: Their biogenesis, regulatory roles, and functions. Annual Review of Plant Biology 74:21−51 doi: 10.1146/annurev-arplant-070122-035226 |
[46] |
Conant GC, Birchler JA, Pires JC. 2014. Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time. Current Opinion in Plant Biology 19:91−98 doi: 10.1016/j.pbi.2014.05.008 |
[47] |
Liu S, Liu Y, Yang X, Tong C, Edwards D, et al. 2014. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nature Communications 5:3930 doi: 10.1038/ncomms4930 |
[48] |
Panchy N, Lehti-Shiu M, Shiu SH. 2016. Evolution of gene duplication in plants. Plant Physiology 171:2294−316 doi: 10.1104/pp.16.00523 |
[49] |
He S, Feng X. 2022. DNA methylation dynamics during germline development. Journal of Integrative Plant Biology 64:2240−51 doi: 10.1111/jipb.13422 |
[50] |
Melnyk CW, Molnar A, Bassett A, Baulcombe DC. 2011. Mobile 24 nt small RNAs direct transcriptional gene silencing in the root meristems of Arabidopsis thaliana. Current Biology 21:1678−83 doi: 10.1016/j.cub.2011.08.065 |
[51] |
Nielsen CPS, Arribas-Hernández L, Han L, Reichel M, Woessmann J, et al. 2024. Evidence for an RNAi-independent role of Arabidopsis DICER-LIKE2 in growth inhibition and basal antiviral resistance. The Plant Cell 36:2289−309 doi: 10.1093/plcell/koae067 |
[52] |
Parent JS, Bouteiller N, Elmayan T, Vaucheret H. 2015. Respective contributions of Arabidopsis DCL2 and DCL4 to RNA silencing. The Plant Journal 81:223−32 doi: 10.1111/tpj.12720 |
[53] |
Wu H, Li B, Iwakawa HO, Pan Y, Tang X, et al. 2020. Plant 22-nt siRNAs mediate translational repression and stress adaptation. Nature 581:89−93 doi: 10.1038/s41586-020-2231-y |
[54] |
Havecker ER, Wallbridge LM, Hardcastle TJ, Bush MS, Kelly KA, et al. 2010. The Arabidopsis RNA-directed dna methylation argonautes functionally diverge based on their expression and interaction with target loci. The Plant Cell 22:321−34 doi: 10.1105/tpc.109.072199 |
[55] |
Ortiz-Vasquez Q, León-Martínez G, Barragán-Rosillo C, González-Orozco E, Deans S, et al. 2023. Genomic methylation patterns in pre-meiotic gynoecia of wild-type and RdDM mutants of Arabidopsis. Frontiers in Plant Science 14:1123211 doi: 10.3389/fpls.2023.1123211 |
[56] |
He F, Xu C, Fu X, Shen Y, Guo L, et al. 2018. The MicroRNA390/TRANS-ACTING SHORT INTERFERING RNA3 module mediates lateral root growth under salt stress via the auxin pathway. Plant Physiology 177:775−91 doi: 10.1104/pp.17.01559 |
[57] |
Yin W, Xiao Y, Niu M, Meng W, Li L, et al. 2020. ARGONAUTE2 enhances grain length and salt tolerance by activating BIG GRAIN3 to modulate cytokinin distribution in rice. The Plant Cell 32:2292−306 doi: 10.1105/tpc.19.00542 |
[58] |
Birchler JA, Yang H. 2022. The multiple fates of gene duplications: Deletion, hypofunctionalization, subfunctionalization, neofunctionalization, dosage balance constraints, and neutral variation. The Plant Cell 34:2466−74 doi: 10.1093/plcell/koac076 |
[59] |
Paysan-Lafosse T, Blum M, Chuguransky S, Grego T, Pinto BL, et al. 2023. InterPro in 2022. Nucleic Acids Research 51:D418−D427 doi: 10.1093/nar/gkac993 |
[60] |
Price MN, Dehal PS, Arkin AP. 2010. FastTree 2 - approximately maximum-likelihood trees for large alignments. PLoS One 5:e9490 doi: 10.1371/journal.pone.0009490 |
[61] |
Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, et al. 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution 37:1530−34 doi: 10.1093/molbev/msaa015 |
[62] |
Tang H, Bowers JE, Wang X, Ming R, Alam M, et al. 2008. Synteny and collinearity in plant genomes. Science 320:486−88 doi: 10.1126/science.1153917 |
[63] |
Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, et al. 2020. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant 13:1194−202 doi: 10.1016/j.molp.2020.06.009 |