doi:10.48130/forres-0026-0003

[1]

Lev-Yadun S, Ne'eman G. 2006. Color changes in old aposematic thorns, spines, and prickles. Israel Journal of Plant Sciences 54:327−334

doi: 10.1007/978-3-319-42096-7_28

[2]

Zhong MC, Jiang XD, Yang GQ, Cui WH, Suo ZQ, et al. 2021. Rose without prickle: genomic insights linked to moisture adaptation. National Science Review 8:nwab092

doi: 10.1093/nsr/nwab092

[3]

Zhou N, Simonneau F, Thouroude T, Hibrand-Saint Oyant L, Foucher F. 2021. Morphological studies of rose prickles provide new insights. Horticulture Research 8:221

doi: 10.1038/s41438-021-00689-7

[4]

Zhao Z, Chai M, Sun L, Cong L, Jiang Q, et al. 2021. Identification of a gene responsible for seedpod spine formation and other phenotypic alterations using whole-genome sequencing analysis in Medicago truncatula. Journal of Experimental Botany 72:7769−7777

doi: 10.1093/jxb/erab359

[5]

Yang S, Cai Y, Liu X, Dong M, Zhang Y, et al. 2018. A CsMYB6-CsTRY module regulates fruit trichome initiation in cucumber. Journal of Experimental Botany 69:1887−1902

doi: 10.1093/jxb/ery047

[6]

Liu Y, Wang X, Li Z, Tu J, Lu YN, et al. 2023. Regulation of capsule spine formation in castor. Plant Physiology 192:1028−1045

doi: 10.1093/plphys/kiad149

[7]

Charles-Dominique T, Davies TJ, Hempson GP, Bezeng BS, Daru BH, et al. 2016. Spiny plants, mammal browsers, and the origin of African savannas. Proceedings of the National Academy of Sciences of the United States of America 113:E5572−E5579

doi: 10.1073/pnas.1607493113

[8]

Zhang F, Rossignol P, Huang T, Wang Y, May A, et al. 2020. Reprogramming of stem cell activity to convert thorns into branches. Current Biology 30:2951−2961

doi: 10.1016/j.cub.2020.05.068

[9]

Armani M, Charles-Dominique T, Barton KE, Tomlinson KW. 2019. Developmental constraints and resource environment shape early emergence and investment in spines in saplings. Annals of Botany 124:1133−1142

doi: 10.1093/aob/mcz152

[10]

Ren J, Duan Y, Li R, Zhang X, Shi Y, et al. 2025. Transcriptional regulation of thorn tip sclerification in plants. Proceedings of the National Academy of Sciences of the United States of America 122:e2510775122

doi: 10.1073/pnas.2510775122

[11]

Grünewald H, Böhm C, Quinkenstein A, Grundmann P, Eberts J, et al. 2009. Robinia pseudoacacia L.: a lesser known tree species for biomass production. BioEnergy Research 2:123−133

doi: 10.1007/springerreference_69293

[12]

Cierjacks A, Kowarik I, Joshi J, Hempel S, Ristow M, et al. 2013. Biological flora of the British Isles: Robinia pseudoacacia. Journal of Ecology 101:1623−1640

doi: 10.1111/1365-2745.12162

[13]

Guo Q, Wang JX, Su LZ, Lv W, Sun YH, et al. 2017. Development and evaluation of a novel set of EST-SSR markers based on transcriptome sequences of black locust (Robinia pseudoacacia L.). Genes 8:177

doi: 10.3390/genes8070177

[14]

Liang H, Xue Y, Li Z, Wang S, Wu X, et al. 2018. Soil moisture decline following the plantation of Robinia pseudoacacia forests: evidence from the Loess Plateau. Forest Ecology and Management 412:62−69

doi: 10.1016/j.foreco.2018.01.041

[15]

Yuan Y, Zhao Z, Niu S, Li X, Wang Y, et al. 2018. Reclamation promotes the succession of the soil and vegetation in opencast coal mine: a case study from Robinia pseudoacacia reclaimed forests, Pingshuo mine, China. CATENA 165:72−79

doi: 10.1016/j.catena.2018.01.025

[16]

Wang X, Zhong Z, Li W, Liu W, Zhang X, et al. 2020. Effects of Robinia pseudoacacia afforestation on aggregate size distribution and organic C dynamics in the central Loess Plateau of China: a chronosequence approach. Journal of Environmental Management 268:110558

doi: 10.1016/j.jenvman.2020.110558

[17]

Liu H, Wu S, Li A, Ruan J. 2021. SMARTdenovo: a de novo assembler using long noisy reads. Gigabyte 2021:1−9

doi: 10.46471/gigabyte.15

[18]

Jung Y, Han D. 2022. BWA-MEME: BWA-MEM emulated with a machine learning approach. Bioinformatics 38:2404−2413

doi: 10.1093/bioinformatics/btac137

[19]

Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, et al. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963

doi: 10.1371/journal.pone.0112963

[20]

Pryszcz LP, Gabaldón T. 2016. Redundans: an assembly pipeline for highly heterozygous genomes. Nucleic Acids Research 44(12):e113

doi: 10.1093/nar/gkw294

[21]

Deamer D, Akeson M, Branton D. 2016. Three decades of nanopore sequencing. Nature Biotechnology 34:518−524

doi: 10.1038/nbt.3423

[22]

Beier S, Thiel T, Münch T, Scholz U, Mascher M. 2017. MISA-web: a web server for microsatellite prediction. Bioinformatics 33:2583−2585

doi: 10.1093/bioinformatics/btx198

[23]

Xu Z, Wang H. 2007. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Research 35:W265−W268

doi: 10.1093/nar/gkm286

[24]

Chen F, Mackey AJ, Stoeckert CJ Jr, Roos DS. 2006. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Research 34:D363−D368

doi: 10.1093/nar/gkj123

[25]

Eddy SR. 1998. Profile hidden Markov models. Bioinformatics 14:755−763

doi: 10.1093/bioinformatics/14.9.755

[26]

Schiavinato M, Marcet‐Houben M, Dohm JC, Gabaldón T, Himmelbauer H. 2020. Parental origin of the allotetraploid tobacco Nicotiana benthamiana. The Plant Journal 102:541−554

doi: 10.1111/tpj.14648

[27]

Puttick MN. 2019. MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees. Bioinformatics 35:5321−5322

doi: 10.1093/bioinformatics/btz554

[28]

De Bie T, Cristianini N, Demuth JP, Hahn MW. 2006. CAFE: a computational tool for the study of gene family evolution. Bioinformatics 22:1269−1271

doi: 10.1093/bioinformatics/btl097

[29]

Zhao Y, Liu R, Xu Y, Wang M, Zhang J, et al. 2019. AGLF provides C-function in floral organ identity through transcriptional regulation of AGAMOUS in Medicago truncatula. Proceedings of the National Academy of Sciences of the United States of America 116:5176−5181

doi: 10.1073/pnas.1820468116

[30]

Huang X, Wang W, Gong T, Wickell D, Kuo LY, et al. 2022. The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence. Nature Plants 8:500−512

doi: 10.1038/s41477-022-01146-6

[31]

Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792−1797

doi: 10.1093/nar/gkh340

[32]

Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312−1313

doi: 10.1093/bioinformatics/btu033

[33]

Letunic I, Bork P. 2021. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Research 49:W293−W96

doi: 10.1093/nar/gkab301

[34]

Jordon‐Thaden IE, Chanderbali AS, Gitzendanner MA, Soltis DE. 2015. Modified CTAB and TRIzol protocols improve RNA extraction from chemically complex Embryophyta. Applications in Plant Sciences 3:apps.1400105

doi: 10.3732/apps.1400105

[35]

Zhu FY, Chen MX, Ye NH, Qiao WM, Gao B, et al. 2018. Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants. Plant Methods 14:69

doi: 10.1186/s13007-018-0337-0

[36]

Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. 2019. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnology 37:907−915

doi: 10.1038/s41587-019-0201-4

[37]

Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15:550

doi: 10.1186/s13059-014-0550-8

[38]

Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N. 2012. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Research 40:37−52

doi: 10.1093/nar/gkr688

[39]

Wang J, Zhang P, Lu Y, Li Y, Zheng Y, et al. 2019. piRBase: a comprehensive database of piRNA sequences. Nucleic Acids Research 47:D175−D80

doi: 10.1093/nar/gky1043

[40]

Sluiter A, Hames B, Ruiz R, Scarlata C, Sluiter J, et al. 2008. Determination of structural carbohydrates and lignin in biomass. Laboratory Analytical Procedure (LAP). Technical Report. National Renewable Energy Laboratory (NREL). Golden, Colorado, USA. https://docs.nrel.gov/docs/gen/fy13/42618.pdf

[41]

Kim H, Ralph J. 2010. Solution-state 2D NMR of ball-milled plant cell wall gels in DMSO-d6/pyridine-d5. Organic & Biomolecular Chemistry 8:576−591

doi: 10.1039/B916070A

[42]

Mansfield SD, Kim H, Lu F, Ralph J. 2012. Whole plant cell wall characterization using solution-state 2D NMR. Nature Protocols 7:1579−1589

doi: 10.1038/nprot.2012.064

[43]

Chang YM, Lin HH, Liu WY, Yu CP, Chen HJ, et al. 2019. Comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes. Proceedings of the National Academy of Sciences of the United States of America 116:3091−3099

doi: 10.1073/pnas.1817621116

[44]

Parra G, Bradnam K, Korf I. 2007. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23:1061−1067

doi: 10.1093/bioinformatics/btm071

[45]

Fukuda H, Ohashi-Ito K. 2019. Vascular tissue development in plants. Current Topics in Developmental Biology 131:141−160

doi: 10.1016/bs.ctdb.2018.10.005

[46]

Ohtani M, Akiyoshi N, Takenaka Y, Sano R, Demura T. 2017. Evolution of plant conducting cells: perspectives from key regulators of vascular cell differentiation. Journal of Experimental Botany 68:17−26

doi: 10.1093/jxb/erw473

[47]

Kubo M, Udagawa M, Nishikubo N, Horiguchi G, Yamaguchi M, et al. 2005. Transcription switches for protoxylem and metaxylem vessel formation. Genes & Development 19:1855−1860

doi: 10.1101/gad.1331305

[48]

Yamaguchi M, Goué N, Igarashi H, Ohtani M, Nakano Y, et al. 2010. Vascular-related nac-domain6 and vascular-related nac-domain7 effectively induce transdifferentiation into xylem vessel elements under control of an induction system. Plant Physiology 153:906−914

doi: 10.1104/pp.110.154013

[49]

Tan TT, Endo H, Sano R, Kurata T, Yamaguchi M, et al. 2018. Transcription factors VND1-VND3 contribute to cotyledon xylem vessel formation. Plant Physiology 176:773−789

doi: 10.1104/pp.17.00461

[50]

Zhong R, Demura T, Ye ZH. 2006. SND1, a NAC domain transcription factor, is a key regulator of secondary wall synthesis in fibers of Arabidopsis. The Plant Cell 18:3158−3170

doi: 10.1105/tpc.106.047399

[51]

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

[52]

Luo L, Li L. 2022. Molecular understanding of wood formation in trees. Forestry Research 2:5

doi: 10.48130/fr-2022-0005

[53]

Xiang X, Zhou X, Zi H, Wei H, Cao D, et al. 2023. Populus cathayana genome and population resequencing provide insights into its evolution and adaptation. Horticulture Research 11:uhad255

doi: 10.1093/hr/uhad255

[54]

Hu H, Wang J, Nie S, Zhao J, Batley J, et al. 2024. Plant pangenomics, current practice and future direction. Agriculture Communications 2:100039

doi: 10.1016/j.agrcom.2024.100039

[55]

Yatsu LY, Espelie KE, Kolattukudy PE. 1983. Ultrastructural and chemical evidence that the cell wall of green cotton fiber is suberized. Plant Physiology 73:521−524

doi: 10.1104/pp.73.2.521

[56]

Legay S, Guerriero G, André C, Guignard C, Cocco E, et al. 2016. MdMyb93 is a regulator of suberin deposition in russeted apple fruit skins. New Phytologist 212:977−991

doi: 10.1111/nph.14170

[57]

Wu Z, Wang N, Hisano H, Cao Y, Wu F, et al. 2019. Simultaneous regulation of F5H in COMT-RNAi transgenic switchgrass alters effects of COMT suppression on syringyl lignin biosynthesis. Plant Biotechnology Journal 17:836−845

doi: 10.1111/pbi.13019

[58]

Yang W, Duan H, Yu K, Hou S, Kang Y, et al. 2024. Integrative dissection of lignin composition in Tartary buckwheat seed hulls for enhanced dehulling efficiency. Advanced Science 11:2400916

doi: 10.1002/advs.202400916

[59]

Zhong R, Ye ZH. 2015. The Arabidopsis NAC transcription factor NST2 functions together with SND1 and NST1 to regulate secondary wall biosynthesis in fibers of inflorescence stems. Plant Signaling & Behavior 10:e989746

doi: 10.4161/15592324.2014.989746

[60]

Zhang Q, Luo F, Zhong Y, He J, Li L. 2020. Modulation of NAC transcription factor NST1 activity by XYLEM NAC DOMAIN1 regulates secondary cell wall formation in Arabidopsis. Journal of Experimental Botany 71:1449−1458

doi: 10.1093/jxb/erz513

[61]

Zhou J, Zhong R, Ye ZH. 2014. Arabidopsis NAC domain proteins, VND1 to VND5, are transcriptional regulators of secondary wall biosynthesis in vessels. PLoS One 9:e105726

doi: 10.1371/journal.pone.0105726

[62]

Ramachandran P, Augstein F, Mazumdar S, Van Nguyen T, Minina EA, et al. 2021. Abscisic acid signaling activates distinct VND transcription factors to promote xylem differentiation in Arabidopsis. Current Biology 31:3153−3161

doi: 10.1016/j.cub.2021.04.057

[63]

Wang H, Wang ZX, Tian HY, Zeng YL, Xue H, et al. 2025. The miR172a–SNB module orchestrates both induced and adult-plant resistance to multiple diseases via MYB30-mediated lignin accumulation in rice. Molecular Plant 18:59−75

doi: 10.1016/j.molp.2024.11.015