| [1] |
Cosgrove DJ. 2005. Growth of the plant cell wall. Nature Reviews Molecular Cell Biology 6:850−61 doi: 10.1038/nrm1746 |
| [2] |
Luo L, Li L. 2022. Molecular understanding of wood formation in trees. Forestry Research 2:5 doi: 10.48130/FR-2022-0005 |
| [3] |
Eklöf JM, Brumer H. 2010. The XTH gene family: an update on enzyme structure, function, and phylogeny in xyloglucan remodeling. Plant Physiology 153:456−66 doi: 10.1104/pp.110.156844 |
| [4] |
Shinohara N, Nishitani K. 2021. Cryogenian origin and subsequent diversification of the plant cell-wall enzyme XTH family. Plant and Cell Physiology 62:1874−89 doi: 10.1093/pcp/pcab093 |
| [5] |
Johansson P, Brumer H, III, Baumann MJ, Kallas ÅM, Henriksson H, et al. 2004. Crystal structures of a poplar xyloglucan endotransglycosylase reveal details of transglycosylation acceptor binding. The Plant Cell 16:874−86 doi: 10.1105/tpc.020065 |
| [6] |
Okazawa K, Sato Y, Nakagawa T, Asada K, Kato I, et al. 1993. Molecular cloning and cDNA sequencing of endoxyloglucan transferase, a novel class of glycosyltransferase that mediates molecular grafting between matrix polysaccharides in plant cell walls. The Journal of Bioloxal Chemistry 268:25364−68 doi: 10.1016/S0021-9258(19)74400-7 |
| [7] |
Yokoyama R, Nishitani K. 2001. A comprehensive expression analysis of all members of a gene family encoding cell-wall enzymes allowed us to predict cis-regulatory regions involved in cell-wall construction in specific organs of Arabidopsis. Plant and Cell Physiology 42:1025−33 doi: 10.1093/pcp/pce154 |
| [8] |
Zhang J, He P, Xu X, Lu Z, Cui P, et al. 2023. Genome-wide identification and expression analysis of the xyloglucan endotransglucosylase/hydrolase gene family in sweet potato [Ipomoea batatas (L.) Lam]. International Journal of Molecular Sciences 24:775 doi: 10.3390/ijms24010775 |
| [9] |
Yokoyama R, Rose JKC, Nishitani K. 2004. A surprising diversity and abundance of xyloglucan endotransglucosylase/hydrolases in rice. Classification and expression analysis. Plant Physiology 134:1088−99 doi: 10.1104/pp.103.035261 |
| [10] |
Nawaz MA, Rehman HM, Imtiaz M, Baloch FS, Lee JD, et al. 2017. Systems identification and characterization of cell wall reassembly and degradation related genes in Glycine max (L.) Merill, a bioenergy legume. Scientific Reports 7:10862 doi: 10.1038/s41598-017-11495-4 |
| [11] |
Zhang C, He M, Jiang Z, Liu L, Pu J, et al. 2022. The xyloglucan endotransglucosylase/hydrolase gene XTH22/TCH4 regulates plant growth by disrupting the cell wall komeostasis in Arabidopsis under boron deficiency. International Journal of Molecular Sciences 23:1250 doi: 10.3390/ijms23031250 |
| [12] |
Du H, Hu X, Yang W, Hu W, Yan W, et al. 2021. ZmXTH, a xyloglucan endotransglucosylase/hydrolase gene of maize, conferred aluminum tolerance in Arabidopsis. Journal of Plant Physiology 266:153520 doi: 10.1016/j.jplph.2021.153520 |
| [13] |
Han Y, Han S, Ban Q, He Y, Jin M, et al. 2017. Overexpression of persimmon DkXTH1 enhanced tolerance to abiotic stress and delayed fruit softening in transgenic plants. Plant Cell Reports 36:583−96 doi: 10.1007/s00299-017-2105-4 |
| [14] |
Borthakur D, Busov V, Cao XH, Du Q, Gailing O, et al. 2022. Current status and trends in forest genomics. Forestry Research 2:11 doi: 10.48130/FR-2022-0011 |
| [15] |
An Y, Liu Y, Liu Y, Lu M, Kang X, et al. 2021. Opportunities and barriers for biofuel and bioenergy production from poplar. Global Change Biology Bioenergy 13:905−13 doi: 10.1111/gcbb.12829 |
| [16] |
Zhang B, Zhu W, Diao S, Wu X, Lu J, et al. 2019. The poplar pangenome provides insights into the evolutionary history of the genus. Communications Biology 2:215 doi: 10.1038/s42003-019-0474-7 |
| [17] |
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32:268−74 doi: 10.1093/molbev/msu300 |
| [18] |
Subramanian B, Gao S, Lercher MJ, Hu S, Chen WH. 2019. Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees. Nucleic Acids Research 47:W270−W275 doi: 10.1093/nar/gkz357 |
| [19] |
Hu B, Jin J, Guo AY, Zhang H, Luo J, et al. 2015. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics 31:1296−97 doi: 10.1093/bioinformatics/btu817 |
| [20] |
Li Y, Kui LW, Liu Z, Allan AC, Qin S, et al. 2020. Genome-wide analysis and expression profiles of the StR2R3-MYB transcription factor superfamily in potato (Solanum tuberosum L.). International Journal of Biological Macromolecules 148:817−32 doi: 10.1016/j.ijbiomac.2020.01.167 |
| [21] |
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 |
| [22] |
Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, et al. 2002. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Research 30:325−27 doi: 10.1093/nar/30.1.325 |
| [23] |
Chow CN, Lee TY, Hung YC, Li GZ, Tseng KC, et al. 2019. PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. Nucleic Acids Research 47:D1155−D1163 doi: 10.1093/nar/gky1081 |
| [24] |
Wang Y, Tang H, DeBarry JD, Tan X, Li J, et al. 2012. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research 40:e49 doi: 10.1093/nar/gkr1293 |
| [25] |
Chen Y, Wu K, Zhang L, Wu F, Jiang C, et al. 2024. Comprehensive analysis of Cytokinin response factors revealed PagCRF8 regulates leaf development in Populus alba × P. glandulosa. Industrial Crops and Products 212:118361 doi: 10.1016/j.indcrop.2024.118361 |
| [26] |
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, et al. 2009. CIRCOS: an information aesthetic for comparative genomics. Genome Research 19:1639−45 doi: 10.1101/gr.092759.109 |
| [27] |
Zhang J, Wang X, Wang HT, Qiao Z, Yao T, et al. 2024. Overexpression of REDUCED WALL ACETYLATION C increases xylan acetylation and biomass recalcitrance in Populus. Plant Physiology 194:243−57 doi: 10.1093/plphys/kiad377 |
| [28] |
Wang X, Yuan W, Yuan X, Jiang C, An Y, et al. 2024. Comparative analysis of PLATZ transcription factors in six poplar species and analysis of the role of PtrPLATZ14 in leaf development. International Journal of Biological Macromolecules 263:130471 doi: 10.1016/j.ijbiomac.2024.130471 |
| [29] |
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 13:2498−504 doi: 10.1101/gr.1239303 |
| [30] |
Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. 2011. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27:431−32 doi: 10.1093/bioinformatics/btq675 |
| [31] |
Evans LM, Slavov GT, Rodgers-Melnick E, Martin J, Ranjan P, et al. 2014. Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations. Nature Genetics 46:1089−96 doi: 10.1038/ng.3075 |
| [32] |
Yu CS, Lin CJ, Hwang JK. 2004. Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Science 13:1402−06 doi: 10.1110/ps.03479604 |
| [33] |
Cheng Z, Zhang X, Yao W, Gao Y, Zhao K, et al. 2021. Genome-wide identification and expression analysis of the xyloglucan endotransglucosylase/hydrolase gene family in poplar. BMC Genomics 22:804 doi: 10.1186/s12864-021-08134-8 |
| [34] |
Nishitani K. 2005. Division of roles among members of the XTH gene family in plants. Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology 139:98−101 doi: 10.1080/11263500500055924 |
| [35] |
Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, et al. 2006. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596−604 doi: 10.1126/science.1128691 |
| [36] |
Qiu D, Bai S, Ma J, Zhang L, Shao F, et al. 2019. The genome of Populus alba × Populus tremula var. glandulosa clone 84K. DNA Research 26:423−31 doi: 10.1093/dnares/dsz020 |
| [37] |
Carmi G, Bolshoy A. 2016. Gene-family extension measures and correlations. Life 6:30 doi: 10.3390/life6030030 |
| [38] |
O'Connor K, Hayes B, Hardner C, Nock C, Baten A, et al. 2020. Genome-wide association studies for yield component traits in a macadamia breeding population. BMC Genomics 21:199 doi: 10.1186/s12864-020-6575-3 |
| [39] |
Shi TL, Jia KH, Bao YT, Nie S, Tian XC, et al. 2024. High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar. Plant Physiology 195:652−70 doi: 10.1093/plphys/kiae078 |
| [40] |
Thessen A, Cooper L, Swetnam T, Hegde H, Reese J, et al. 2023. Using knowledge graphs to infer gene expression in plants. Frontiers in Artificial Intelligence 6:1201002 doi: 10.3389/frai.2023.1201002 |
| [41] |
Zhu J. 2016. Abiotic stress signaling and responses in plants. Cell 167:313−24 doi: 10.1016/j.cell.2016.08.029 |
| [42] |
Nakashima K, Yamaguchi-Shinozaki K. 2013. ABA signaling in stress-response and seed development. Plant Cell Reports 32:959−70 doi: 10.1007/s00299-013-1418-1 |
| [43] |
Han X, Zhao Y, Chen Y, Xu J, Jiang C, et al. 2022. Lignin biosynthesis and accumulation in response to abiotic stresses in woody plants. Forestry Research 2:9 doi: 10.48130/FR-2022-0009 |
| [44] |
De Caroli M, Manno E, Piro G, Lenucci MS. 2021. Ride to cell wall: Arabidopsis XTH11, XTH29 and XTH33 exhibit different secretion pathways and responses to heat and drought stress. The Plant Journal 107:448−66 doi: 10.1111/tpj.15301 |
| [45] |
Choi JY, Seo YS, Kim SJ, Kim WT, Shin JS. 2011. Constitutive expression of CaXTH3, a hot pepper xyloglucan endotransglucosylase/hydrolase, enhanced tolerance to salt and drought stresses without phenotypic defects in tomato plants (Solanum lycopersicum cv. Dotaerang). Plant Cell Reports 30:867−77 doi: 10.1007/s00299-010-0989-3 |
| [46] |
Holland C, Simmons TJ, Meulewaeter F, Hudson A, Fry SC. 2020. Three highly acidic Equisetum XTHs differ from hetero-trans-β-glucanase in donor substrate specificity and are predominantly xyloglucan homo-transglucosylases. Journal of Plant Physiology 251:153210 doi: 10.1016/j.jplph.2020.153210 |
| [47] |
Kaewthai N, Gendre D, Eklöf JM, Ibatullin FM, Ezcurra I, et al. 2013. Group III-A XTH genes of Arabidopsis encode predominant xyloglucan endohydrolases that are dispensable for normal growth. Plant Physiology 161:440−54 doi: 10.1104/pp.112.207308 |
| [48] |
Shin YK, Yum H, Kim ES, Cho H, Gothandam KM, et al. 2006. BcXTH1, a Brassica campestris homologue of Arabidopsis XTH9, is associated with cell expansion. Planta 224:32−41 doi: 10.1007/s00425-005-0189-5 |
| [49] |
Zhang H, Zhao Y, Zhu JK. 2020. Thriving under stress: how plants balance growth and the stress response. Developmental Cell 55:529−43 doi: 10.1016/j.devcel.2020.10.012 |
| [50] |
Zhang Y, Chen S, Xu L, Chu S, Yan X, et al. 2024. Transcription factor PagMYB31 positively regulates cambium activity and negatively regulates xylem development in poplar. The Plant Cell 36:1806−28 doi: 10.1093/plcell/koae040 |
| [51] |
Yang X, Lu M, Wang Y, Wang Y, Liu Z, et al. 2021. Response mechanism of plants to drought stress. Horticulturae 7:50 doi: 10.3390/horticulturae7030050 |
| [52] |
Kim TH, Böhmer M, Hu H, Nishimura N, Schroeder JI. 2010. Guard cell signal transduction network: advances in understanding abscisic acid, CO2 , and Ca2+ signaling. Annual Review of Plant Biology 61:561−91 doi: 10.1146/annurev-arplant-042809-112226 |