[1] Boerjan W, Ralph J, Baucher M. 2003. Lignin biosynthesis. Annual Review of Plant Biology 54:519−46 doi: 10.1146/annurev.arplant.54.031902.134938
[2] Weng JK, Akiyama T, Bonawitz ND, Li X, Ralph J, et al. 2010. Convergent evolution of syringyl lignin biosynthesis via distinct pathways in the lycophyte Selaginella and flowering plants. The Plant Cell 22:1033−45 doi: 10.1105/tpc.109.073528
[3] Poovaiah CR, Nageswara-Rao M, Soneji JR, Baxter HL, Stewart CN. 2014. Altered lignin biosynthesis using biotechnology to improve lignocellulosic biofuel feedstocks. Plant Biotechnology Journal 12:1163−73 doi: 10.1111/pbi.12225
[4] Zhao Q, Dixon RA. 2014. Altering the cell wall and its impact on plant disease: from forage to bioenergy. Annual Review of Phytopathology 52:69−91 doi: 10.1146/annurev-phyto-082712-102237
[5] Barros J, Serk H, Granlund I, Pesquet E. 2015. The cell biology of lignification in higher plants. Annals of Botany 115:1053−74 doi: 10.1093/aob/mcv046
[6] Uzal EN, Gómez Ros LV, Pomar F, Bernal MA, Paradela A, et al. 2009. The presence of sinapyl lignin in Ginkgo biloba cell cultures changes our views of the evolution of lignin biosynthesis. Physiologia Plantarum 135:196−213 doi: 10.1111/j.1399-3054.2008.01185.x
[7] Bonawitz ND, Chapple C. 2010. The Genetics of lignin biosynthesis: connecting genotype to phenotype. Annual Review of Genetics 44:337−63 doi: 10.1146/annurev-genet-102209-163508
[8] Zhao Q. 2016. Lignification: flexibility, biosynthesis and regulation. Trends in Plant Science 21:713−21 doi: 10.1016/j.tplants.2016.04.006
[9] Shi R, Sun YH, Li Q, Heber S, Sederoff R, et al. 2010. Towards a systems approach for lignin biosynthesis in Populus trichocarpa: transcript abundance and specificity of the monolignol biosynthetic genes. Plant and Cell Physiology 51:144−63 doi: 10.1093/pcp/pcp175
[10] Weng JK, Chapple C. 2010. The origin and evolution of lignin biosynthesis. New Phytologist 187:273−85 doi: 10.1111/j.1469-8137.2010.03327.x
[11] Wang JP, Liu B, Sun Y, Chiang VL, Sederoff RR. 2019. Enzyme-enzyme interactions in monolignol biosynthesis. Frontiers in Plant Science 9:1942 doi: 10.3389/fpls.2018.01942
[12] Balmant KM, Noble JD, Alves FC, Dervinis C, Conde D, et al. 2020. Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis in Populus deltoides. Genome Research 30:1131−43 doi: 10.1101/gr.261438.120
[13] Zhang J, Yuan H, Li Y, Chen Y, Liu G, et al. 2020. Genome sequencing and phylogenetic analysis of allotetraploid Salix matsudana Koidz. Horticulture Research 7:201
[14] Dai X, Hu Q, Cai Q, Feng K, Ye N, et al. 2014. The willow genome and divergent evolution from poplar after the common genome duplication. Cell Research 24:1274−7 doi: 10.1038/cr.2014.83
[15] Chen Y, Jiang Y, Chen Y, Feng W, Liu G, et al. 2020. Uncovering candidate genes responsive to salt stress in Salix matsudana (Koidz) by transcriptomic analysis. PloS One 15:e0236129 doi: 10.1371/journal.pone.0236129
[16] Wheeler TJ, Eddy SR. 2013. nhmmer: DNA homology search with profile HMMs. Bioinformatics 29:2487−9 doi: 10.1093/bioinformatics/btt403
[17] Li X, Liu G, Geng Y, Wu M, Pei W, et al. 2017. A genome-wide analysis of the small auxin-up RNA (SAUR) gene family in cotton. BMC Genomics 18:815 doi: 10.1186/s12864-017-4224-2
[18] Liu G, Liu J, Pei W, Li X, Wang N, et al. 2019. Analysis of the MIR160 gene family and the role of MIR160a_A05 in regulating fiber length in cotton. Planta 250:2147−58 doi: 10.1007/s00425-019-03271-7
[19] Zhang J, Yuan H, Yang Q, Li M, Wang Y, et al. 2017. The genetic architecture of growth traits in Salix matsudana under salt stress. Horticulture Research 4:17024 doi: 10.1038/hortres.2017.24
[20] Pertea M, Pertea GM, Antonescu CM, Chang T, Mendell JT, et al. 2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 33:290−5 doi: 10.1038/nbt.3122
[21] Young MD, Wakefield Mj, Smyth Gk, Oshlack A. 2010. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 11:R14 doi: 10.1186/gb-2010-11-2-r14
[22] Liu G, Wu M, Pei W, Li X, Wang N, et al. 2019. A comparative analysis of small RNAs between two Upland cotton backcross inbred lines with different fiber length: Expression and distribution. The Crop Journal 7:198−208 doi: 10.1016/j.cj.2018.08.004
[23] Sundell D, Street NR, Kumar M, Mellerowicz EJ, Kucukoglu M, et al. 2017. AspWood: high-spatial-resolution transcriptome profiles reveal uncharacterized modularity of wood formation in Populus tremula. The Plant Cell 29:1585−604 doi: 10.1105/tpc.17.00153
[24] 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
[25] Gunasekara C, Subramanian A, Avvari JVRK, Li B, Chen S, et al. 2016. ExactSearch: a web-based plant motif search tool. Plant Methods 12:26 doi: 10.1186/s13007-016-0126-6
[26] Kumari S, Nie J, Chen H, Ma H, Stewart R, et al. 2012. Evaluation of gene association methods for coexpression network construction and biological knowledge discovery. PLoS One 7:e50411 doi: 10.1371/journal.pone.0050411
[27] Hefer CA, Mizrachi E, Myburg AA, Douglas CJ, Mansfield SD. 2015. Comparative interrogation of the developing xylem transcriptomes of two wood-forming species: Populus trichocarpa and Eucalyptus grandis. New Phytologist 206:1391−405 doi: 10.1111/nph.13277
[28] Wang JP, Matthews ML, Williams CM, Shi R, Yang C, et al. 2018. Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis. Nature Communications 9:1579 doi: 10.1038/s41467-018-03863-z
[29] Shen H, Mazarei M, Hisano H, Escamilla-Trevino L, Fu C, et al. 2013. A genomics approach to deciphering lignin biosynthesis in switchgrass. The Plant Cell 25:4342−61 doi: 10.1105/tpc.113.118828
[30] Seyfferth C, Wessels B, Jokipii-Lukkari S, Sundberg B, Delhomme N, et al. 2018. Ethylene-related gene expression networks in wood formation. Frontiers in Plant Science 9:272 doi: 10.3389/fpls.2018.00272
[31] Immanen J, Nieminen K, Smolander OP, Kojima M, Alonso Serra J, et al. 2016. Cytokinin and auxin display distinct but interconnected distribution and signaling profiles to stimulate cambial activity. Current Biology 26:1990−7 doi: 10.1016/j.cub.2016.05.053
[32] Bhalerao RP, Fischer U. 2014. Auxin gradients across wood - instructive or incidental? Physiologia Plantarum 151:43−51 doi: 10.1111/ppl.12134
[33] Morreel K, Goeminne G, Storme V, Sterck L, Ralph J, et al. 2006. Genetical metabolomics of flavonoid biosynthesis in Populus: a case study. The Plant Journal 47:224−37 doi: 10.1111/j.1365-313X.2006.02786.x
[34] Kuzmin E, VanderSluis B, Nguyen Ba AN, Wang W, Koch EN, et al. 2020. Exploring whole-genome duplicate gene retention with complex genetic interaction analysis. Science 368:eaaz5667 doi: 10.1126/science.aaz5667
[35] Keane OM, Toft C, Carretero-Paulet L, Jones GW, Fares MA. 2014. Preservation of genetic and regulatory robustness in ancient gene duplicates of Saccharomyces cerevisiae. Genome Research 24:1830−41 doi: 10.1101/gr.176792.114
[36] Włoch W, Wilczek A, Jura-Morawiec J, Kojs P, Iqbal M. 2013. Modelling for rearrangement of fusiform initials during radial growth of the vascular cambium in Pinus sylvestris L. Trees 27:879−93 doi: 10.1007/s00468-013-0842-8
[37] Wilczek A, Jura-Morawiec J, Kojs P, Iqbal M, Włoch W. 2011. Correlation of intrusive growth of cambial initials to rearrangement of rays in the vascular cambium. IAWA J 32:313−31 doi: 10.1163/22941932-90000060
[38] Oraby HF, Ramadan MF. 2015. Impact of suppressing the caffeic acidO-methyltransferase (COMT) gene on lignin, fiber, and seed oil composition in Brassica napus transgenic plants. European Food Research and Technology 240:931−8 doi: 10.1007/s00217-014-2397-3
[39] Wang YJ, Sheng LP, Zhang HR, Du XP, An C, et al. 2017. CmMYB19 over-expression improves aphid tolerance in Chrysanthemum by promoting lignin synthesis. International Journal Of Molecular Sciences 18:619 doi: doi.org/10.3390/ijms18030619
[40] Gui J, Lam PY, Tobimatsu Y, Sun J, Huang C, et al. 2020. Fibre-specific regulation of lignin biosynthesis improves biomass quality in Populus. New Phytologist 226:1074−87 doi: 10.1111/nph.16411
[41] Peng X, Sun S, Wen J, Yin W, Sun R. 2014. Structural characterization of lignins from hydroxycinnamoyl transferase (HCT) down-regulated transgenic poplars. Fuel 134:485−92 doi: 10.1016/j.fuel.2014.05.069
[42] Xia X, Tang Y, Wei M, Zhao D. 2018. Effect of paclobutrazol application on plant photosynthetic performance and leaf greenness of Herbaceous Peony. Horticulturae 4:5 doi: 10.3390/horticulturae4010005
[43] Xie M, Zhang J, Tschaplinski TJ, Tuskan GA, Chen JG, et al. 2018. Regulation of lignin biosynthesis and its role in growth-defense tradeoffs. Frontiers in Plant Science 9:1427 doi: 10.3389/fpls.2018.01427
[44] Ohtani M, Demura T. 2019. The quest for transcriptional hubs of lignin biosynthesis: beyond the NAC-MYB-gene regulatory network model. Current Opinion in Biotechnology 56:82−7 doi: 10.1016/j.copbio.2018.10.002
[45] Zhang J, Gao G, Chen J, Taylor G, Cui K, et al. 2011. Molecular features of secondary vascular tissue regeneration after bark girdling in Populus. New Phytologist 192:869−84 doi: 10.1111/j.1469-8137.2011.03855.x
[46] Pesquet E, Tuominen H. 2011. Ethylene stimulates tracheary element differentiation in Zinnia elegans cell cultures. New Phytologist 190:138−49 doi: 10.1111/j.1469-8137.2010.03600.x
[47] Felten J, Vahala J, Love J, Gorzsás A, Rüggeberg M, et al. 2018. Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen. New Phytologist 218:999−1014 doi: 10.1111/nph.15078
[48] Harkey AF, Yoon GM, Seo DH, DeLong A, Muday GK. 2019. Light modulates ethylene synthesis, signaling, and downstream transcriptional networks to control plant development. Frontiers in Plant Science 10:1094 doi: 10.3389/fpls.2019.01094
[49] Love J, Björklund S, Vahala J, Hertzberg M, Kangasjärvi J, et al. 2009. Ethylene is an endogenous stimulator of cell division in the cambial meristem of Populus. Proceedings Of The National Academy Of Sciences Of The United States Of America 106:5984−9 doi: 10.1073/pnas.0811660106
[50] Andersson-Gunnerås S, Hellgren JM, Björklund S, Regan S, Moritz T, et al. 2003. Asymmetric expression of a poplar ACC oxidase controls ethylene production during gravitational induction of tension wood. The Plant Journal 34:339−49 doi: 10.1046/j.1365-313X.2003.01727.x