[1]

Cheng X, Xie T, Yang L, Shen H. 2022. Effects of ascorbic acid on physiological characteristics during somatic embryogenesis of Fraxinus mandshurica. International Journal of Molecular Sciences 24:289

doi: 10.3390/ijms24010289
[2]

Nielsen LR, Nagy NE, Piqueras S, Kosawang C, Thygesen LG, et al. 2022. Host–pathogen interactions in leaf petioles of common ash and manchurian ash infected with Hymenoscyphus fraxineus. Microorganisms 10:375

doi: 10.3390/microorganisms10020375
[3]

Cipollini D, Wang Q, Whitehill JGA, Powell JR, Bonello P, et al. 2011. Distinguishing defensive characteristics in the phloem of ash species resistant and susceptible to emerald ash borer. Journal of Chemical Ecology 37:450−459

doi: 10.1007/s10886-011-9954-z
[4]

Hu LJ, Uchiyama K, Shen HL, Saito Y, Tsuda Y, et al. 2008. Nuclear DNA microsatellites reveal genetic variation but a lack of phylogeographical structure in an endangered species, Fraxinus mandshurica, across north-east China. Annals of Botany 102:195−205

doi: 10.1093/aob/mcn074
[5]

Larionov MV, Volodkin AA, Volodkina OA, Lebedev EV, Khanbabayeva OE, et al. 2022. Features of the territorial distribution, composition and structure of phytocenoses with the participation of Fraxinus excelsior, their resource qualities, ecological and economic importance (southeastern part of the east European Plain). Life 13:93

doi: 10.3390/life13010093
[6]

Meger J, Ulaszewski B, Pałucka M, Kozioł C, Burczyk J. 2024. Genomic prediction of resistance to Hymenoscyphus fraxineus in common ash (Fraxinus excelsior L.) populations. Evolutionary Applications 17:e13694

doi: 10.1111/eva.13694
[7]

Sahraei SE, Cleary M, Stenlid J, Brandström Durling M, Elfstrand M. 2020. Transcriptional responses in developing lesions of european common ash (Fraxinus excelsior) reveal genes responding to infection by Hymenoscyphus fraxineus. BMC Plant Biology 20:455

doi: 10.1186/s12870-020-02656-1
[8]

Stocks JJ, Metheringham CL, Plumb WJ, Lee SJ, Kelly LJ, et al. 2019. Genomic basis of European ash tree resistance to ash dieback fungus. Nature Ecology & Evolution 3:1686−1696

doi: 10.1038/s41559-019-1036-6
[9]

Parvez S, Asif M, Ahmad A, Javaid I, Rasheed MZ, et al. 2025. Tracing the path from conservation to expansion evolutionary insights into NLR genes in oleaceae. BMC Plant Biology 25:259

doi: 10.1186/s12870-025-06233-2
[10]

Jones JDG, Staskawicz BJ, Dangl JL. 2024. The plant immune system: from discovery to deployment. Cell 187:2095−2116

doi: 10.1016/j.cell.2024.03.045
[11]

Wang J, Song W, Chai J. 2023. Structure, biochemical function, and signaling mechanism of plant NLRs. Molecular Plant 16:75−95

doi: 10.1016/j.molp.2022.11.011
[12]

Huot B, Yao J, Montgomery BL, He SY. 2014. Growth–defense tradeoffs in plants: a balancing act to optimize fitness. Molecular Plant 7:1267−1287

doi: 10.1093/mp/ssu049
[13]

Li W, Lin YJC, Chen YL, Zhou C, Li S, et al. 2024. Woody plant cell walls: fundamentals and utilization. Molecular Plant 17:112−140

doi: 10.1016/j.molp.2023.12.008
[14]

Liao H, Fang Y, Yin J, He M, Wei Y, et al. 2025. Rice transcription factor bHLH25 confers resistance to multiple diseases by sensing H2O2. Cell Research 35:205−219

doi: 10.1038/s41422-024-01058-4
[15]

Lin H, Wang M, Chen Y, Nomura K, Hui S, et al. 2022. An MKP-MAPK protein phosphorylation cascade controls vascular immunity in plants. Science Advances 8:eabg8723

doi: 10.1126/sciadv.abg8723
[16]

Huff M, Seaman J, Wu D, Zhebentyayeva T, Kelly LJ, et al. 2022. A high-quality reference genome for Fraxinus pennsylvanica for ash species restoration and research. Molecular Ecology Resources 22:1284−1302

doi: 10.1111/1755-0998.13545
[17]

Liu JN, Yan L, Chai Z, Liang Q, Dong Y, et al. 2025. Pan-genome analyses of 11 Fraxinus species provide insights into salt adaptation in ash trees. Plant Communications 6:101137

doi: 10.1016/j.xplc.2024.101137
[18]

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
[19]

Murray MG, Thompson WF. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research 8:4321−4325

doi: 10.1093/nar/8.19.4321
[20]

Cavallari MM, Siqueira MVBM, Val TM, Pavanelli JC, Monteiro M, et al. 2014. A modified acidic approach for DNA extraction from plant species containing high levels of secondary metabolites. Genetics and Molecular Research 13:6497−6502

doi: 10.4238/2014.august.25.13
[21]

Lieberman-Aiden E, Van Berkum NL, Williams L, Imakaev M, Ragoczy T, et al. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289−293

doi: 10.1126/science.1181369
[22]

Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, et al. 2014. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159:1665−1680

doi: 10.1016/j.cell.2014.11.021
[23]

Lajoie BR, Van Berkum NL, Sanyal A, Dekker J. 2009. My5C: web tools for chromosome conformation capture studies. Nature Methods 6:690−691

doi: 10.1038/nmeth1009-690
[24]

Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, et al. 2012. Hi–C: a comprehensive technique to capture the conformation of genomes. Methods 58:268−276

doi: 10.1016/j.ymeth.2012.05.001
[25]

Eid J, Fehr A, Gray J, Luong K, Lyle J, et al. 2009. Real-time DNA sequencing from single polymerase molecules. Science 323:133−138

doi: 10.1126/science.1162986
[26]

Kim HM, Jeon S, Chung O, Jun JH, Kim HS, et al. 2021. Comparative analysis of 7 short-read sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing. GigaScience 10:giab014

doi: 10.1093/gigascience/giab014
[27]

Wenger AM, Peluso P, Rowell WJ, Chang P-C, Hall RJ, et al. 2019. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nature Biotechnology 37:1155−1162

doi: 10.1038/s41587-019-0217-9
[28]

Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884−i890

doi: 10.1093/bioinformatics/bty560
[29]

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
[30]

Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, et al. 2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 33:290−295

doi: 10.1038/nbt.3122
[31]

Liao Y, Smyth GK, Shi W. 2014. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923−930

doi: 10.1093/bioinformatics/btt656
[32]

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
[33]

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
[34]

Huynh-Thu VA, Irrthum A, Wehenkel L, Geurts P. 2010. Inferring regulatory networks from expression data using tree-based methods. PLoS One 5:e12776

doi: 10.1371/journal.pone.0012776
[35]

Cheng H, Concepcion GT, Feng X, Zhang H, Li H. 2021. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nature Methods 18:170−175

doi: 10.1038/s41592-020-01056-5
[36]

Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, et al. 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356:92−95

doi: 10.1126/science.aal3327
[37]

Durand NC, Shamim MS, Machol I, Rao SSP, Huntley MH, et al. 2016. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Systems 3:95−98

doi: 10.1016/j.cels.2016.07.002
[38]

Ranallo-Benavidez TR, Jaron KS, Schatz MC. 2020. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nature Communications 11:1432

doi: 10.1038/s41467-020-14998-3
[39]

Rhie A, Walenz BP, Koren S, Phillippy AM. 2020. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biology 21:245

doi: 10.1186/s13059-020-02134-9
[40]

Bedell JA, Korf I, Gish W. 2000. MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics 16:1040−1041

doi: 10.1093/bioinformatics/16.11.1040
[41]

Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, et al. 2020. RepeatModeler2 for automated genomic discovery of transposable element families. Proceedings of the National Academy of Sciences of the United States of America 117:9451−9457

doi: 10.1073/pnas.1921046117
[42]

Bao W, Kojima KK, Kohany O. 2015. Repbase update, a database of repetitive elements in eukaryotic genomes. Mobile DNA 6:11

doi: 10.1186/s13100-015-0041-9
[43]

Storer J, Hubley R, Rosen J, Wheeler TJ, Smit AF. 2021. The Dfam community resource of transposable element families, sequence models, and genome annotations. Mobile DNA 12:2

doi: 10.1186/s13100-020-00230-y
[44]

Ou S, Jiang N. 2018. LTR_retriever: a highly accurate and sensitive program for identification of long terminal repeat retrotransposons. Plant Physiology 176:1410−1422

doi: 10.1104/pp.17.01310
[45]

Ou S, Chen J, Jiang N. 2018. Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Research 46:e126

doi: 10.1093/nar/gky730
[46]

Lin Y, Ye C, Li X, Chen Q, Wu Y, et al. 2023. quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification. Horticulture Research 10:uhad127

doi: 10.1093/hr/uhad127
[47]

Holt C, Yandell M. 2011. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 12:491

doi: 10.1186/1471-2105-12-491
[48]

Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, et al. 2008. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biology 9:R7

doi: 10.1186/gb-2008-9-1-r7
[49]

Stanke M, Morgenstern B. 2005. AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Research 33:W465−W467

doi: 10.1093/nar/gki458
[50]

Korf I. 2004. Gene finding in novel genomes. BMC Bioinformatics 5:59

doi: 10.1186/1471-2105-5-59
[51]

Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M. 2008. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Research 18:1979−1990

doi: 10.1101/gr.081612.108
[52]

Kanehisa M, Furumichi M, Sato Y, Matsuura Y, Ishiguro-Watanabe M. 2025. KEGG: biological systems database as a model of the real world. Nucleic Acids Research 53:D672−D677

doi: 10.1093/nar/gkae909
[53]

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10:421

doi: 10.1186/1471-2105-10-421
[54]

Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25:955−964

doi: 10.1093/nar/25.5.955
[55]

Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, et al. 2015. Rfam 12.0: updates to the RNA families database. Nucleic Acids Research 43:D130−D137

doi: 10.1093/nar/gku1063
[56]

Nawrocki EP, Eddy SR. 2013. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29:2933−2935

doi: 10.1093/bioinformatics/btt509
[57]

Wang Y, Lu L, Li J, Li H, You Y, et al. 2022. A chromosome-level genome of Syringa oblata provides new insights into chromosome formation in Oleaceae and evolutionary history of lilacs. The Plant Journal 111:836−848

doi: 10.1111/tpj.15858
[58]

Rao G, Zhang J, Liu X, Lin C, Xin H, et al. 2021. De novo assembly of a new Olea europaea genome accession using nanopore sequencing. Horticulture Research 8:64

doi: 10.1038/s41438-021-00498-y
[59]

Sollars ESA, Harper AL, Kelly LJ, Sambles CM, Ramirez-Gonzalez RH, et al. 2017. Genome sequence and genetic diversity of European ash trees. Nature 541:212−216

doi: 10.1038/nature20786
[60]

The French–Italian Public Consortium for Grapevine Genome Characterization. 2007. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463−467

doi: 10.1038/nature06148
[61]

Daccord N, Celton JM, Linsmith G, Becker C, Choisne N, et al. 2017. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nature Genetics 49:1099−1106

doi: 10.1038/ng.3886
[62]

Kapoor B, Jenkins J, Schmutz J, Zhebentyayeva T, Kuelheim C, et al. 2023. A haplotype-resolved chromosome-scale genome for Quercus rubra L. provides insights into the genetics of adaptive traits for red oak species. G3: Genes, Genomes, Genetics 13:jkad209

doi: 10.1093/g3journal/jkad209
[63]

Li X, Cai K, Zhang Q, Pei X, Chen S, et al. 2022. The manchurian walnut genome: insights into juglone and lipid biosynthesis. GigaScience 11:giac057

doi: 10.1093/gigascience/giac057
[64]

Chen S, Wang Y, Yu L, Zheng T, Wang S, et al. 2021. Genome sequence and evolution of Betula platyphylla. Horticulture Research 8:37

doi: 10.1038/s41438-021-00481-7
[65]

Cheng CY, Krishnakumar V, Chan AP, Thibaud-Nissen F, Schobel S, et al. 2017. Araport11: a complete reannotation of the Arabidopsis thaliana reference genome. The Plant Journal 89:789−804

doi: 10.1111/tpj.13415
[66]

Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, et al. 2006. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596−1604

doi: 10.1126/science.1128691
[67]

Emms DM, Kelly S. 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biology 20:238

doi: 10.1186/s13059-019-1832-y
[68]

Han MV, Thomas GWC, Lugo-Martinez J, Hahn MW. 2013. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. Molecular Biology and Evolution 30:1987−1997

doi: 10.1093/molbev/mst100
[69]

Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30:772−780

doi: 10.1093/molbev/mst010
[70]

Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17:540−552

doi: 10.1093/oxfordjournals.molbev.a026334
[71]

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
[72]

Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24:1586−1591

doi: 10.1093/molbev/msm088
[73]

Kumar S, Stecher G, Suleski M, Hedges SB. 2017. TimeTree: a resource for timelines, timetrees, and divergence times. Molecular Biology and Evolution 34:1812−1819

doi: 10.1093/molbev/msx116
[74]

Sun P, Jiao B, Yang Y, Shan L, Li T, et al. 2022. WGDI: a user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes. Molecular Plant 15:1841−1851

doi: 10.1016/j.molp.2022.10.018
[75]

Tang H, Krishnakumar V, Zeng X, Xu Z, Taranto A, et al. 2024. JCVI: a versatile toolkit for comparative genomics analysis. iMeta 3:e211

doi: 10.1002/imt2.211
[76]

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−e49

doi: 10.1093/nar/gkr1293
[77]

Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, et al. 2018. MUMmer4: a fast and versatile genome alignment system. PLoS Computational Biology 14:e1005944

doi: 10.1371/journal.pcbi.1005944
[78]

Goel M, Sun H, Jiao WB, Schneeberger K. 2019. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biology 20:277

doi: 10.1186/s13059-019-1911-0
[79]

Qiao X, Li Q, Yin H, Qi K, Li L, et al. 2019. Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants. Genome Biology 20:38

doi: 10.1186/s13059-019-1650-2
[80]

Zhang Z. 2022. KaKs_Calculator 3.0: calculating selective pressure on coding and non-coding sequences. Genomics, Proteomics & Bioinformatics 20:536−540

doi: 10.1016/j.gpb.2021.12.002
[81]

Steuernagel B, Witek K, Krattinger SG, Ramirez-Gonzalez RH, Schoonbeek HJ, et al. 2020. The NLR-annotator tool enables annotation of the intracellular immune receptor repertoire. Plant Physiology 183:468−482

doi: 10.1104/pp.19.01273
[82]

Jones JDG, Vance RE, Dangl JL. 2016. Intracellular innate immune surveillance devices in plants and animals. Science 354:aaf6395

doi: 10.1126/science.aaf6395
[83]

El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, et al. 2019. The Pfam protein families database in 2019. Nucleic Acids Research 47:D427−D432

doi: 10.1093/nar/gky995
[84]

Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW. 2003. Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. The Plant Cell 15:809−834

doi: 10.1105/tpc.009308
[85]

Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, et al. 2012. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Research 40:D1202−D1210

doi: 10.1093/nar/gkr1090
[86]

Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, et al. 2017. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Research 45:D200−D203

doi: 10.1093/nar/gkw1129
[87]

Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. 2007. Clustal W and clustal X version 2.0. Bioinformatics 23:2947−2948

doi: 10.1093/bioinformatics/btm404
[88]

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 37:1530−1534

doi: 10.1093/molbev/msaa015
[89]

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−W296

doi: 10.1093/nar/gkab301
[90]

Eddy SR. 2011. Accelerated profile HMM searches. PLoS Computational Biology 7:e1002195

doi: 10.1371/journal.pcbi.1002195
[91]

Sparkes IA, Runions J, Kearns A, Hawes C. 2006. Rapid, transient expression of fluorescent fusion proteins in tobacco plants and generation of stably transformed plants. Nature Protocols 1:2019−2025

doi: 10.1038/nprot.2006.286
[92]

Gambino G, Perrone I, Gribaudo I. 2008. A rapid and effective method for RNA extraction from different tissues of grapevine and other woody plants. Phytochemical Analysis 19:520−525

doi: 10.1002/pca.1078
[93]

Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCᴛ method. Methods 25:402−408

doi: 10.1006/meth.2001.1262
[94]

Elfstrand M, Chen J, Cleary M, Halecker S, Ihrmark K, et al. 2021. Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires. BMC Genomics 22:503

doi: 10.1186/s12864-021-07837-2
[95]

Teufel F, Almagro Armenteros JJ, Johansen AR, Gíslason MH, Pihl SI, et al. 2022. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nature Biotechnology 40:1023−1025

doi: 10.1038/s41587-021-01156-3
[96]

Krogh A, Larsson B, Von Heijne G, Sonnhammer ELL. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of Molecular Biology 305:567−580

doi: 10.1006/jmbi.2000.4315
[97]

Sperschneider J, Dodds PN. 2022. EffectorP 3.0: prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes. Molecular Plant-Microbe Interactions 35:146−156

doi: 10.1094/MPMI-08-21-0201-R
[98]

Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210−3212

doi: 10.1093/bioinformatics/btv351
[99]

Tegenfeldt F, Kuznetsov D, Manni M, Berkeley M, Zdobnov EM, et al. 2025. OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes. Nucleic Acids Research 53:D516−D522

doi: 10.1093/nar/gkae987
[100]

Pastirčáková K, Adamčíková K, Barta M, Pažitný J, Hoťka P, et al. 2020. Host range of Hymenoscyphus fraxineus in Slovak arboreta. Forests 11:596

doi: 10.3390/f11050596
[101]

Nielsen LR, McKinney LV, Hietala AM, Kjær ED. 2017. The susceptibility of Asian, European and North American Fraxinus species to the ash dieback pathogen Hymenoscyphus fraxineus reflects their phylogenetic history. European Journal of Forest Research 136:59−73

doi: 10.1007/s10342-016-1009-0
[102]

Kowalski T, Bilański P, Holdenrieder O. 2015. Virulence of Hymenoscyphus albidus and H. fraxineus on Fraxinus excelsior and F. pennsylvanica. PLoS One 10:e0141592

doi: 10.1371/journal.pone.0141592
[103]

Fu M, Wang P, Liang R, Feng Q, Li C, et al. 2025. The coordinated response of xylem vessels and pits of Fraxinus mandshurica to drought during earlywood and latewood formation. Journal of Forestry Research 36:113

doi: 10.1007/s11676-025-01906-y
[104]

Zhong R, Richardson EA, Ye ZH. 2007. Two NAC domain transcription factors, SND1 and NST1, function redundantly in regulation of secondary wall synthesis in fibers of Arabidopsis. Planta 225:1603−1611

doi: 10.1007/s00425-007-0498-y
[105]

Fan BL, Chen LH, Chen LL. 2025. Analysis of gene expansion and defense-related genes in Anacardiaceae family from an evolutionary aspect. Frontiers in Plant Science 16:1638044

doi: 10.3389/fpls.2025.1638044
[106]

Leister D. 2004. Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance genes. Trends in Genetics 20:116−122

doi: 10.1016/j.tig.2004.01.007
[107]

Michelmore RW, Meyers BC. 1998. Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Research 8:1113−1130

doi: 10.1101/gr.8.11.1113
[108]

Zhong R, Cui D, Ye ZH. 2019. Secondary cell wall biosynthesis. New Phytologist 221:1703−1723

doi: 10.1111/nph.15537
[109]

Zhong R, Lee C, Ye ZH. 2010. Functional characterization of poplar wood-associated NAC domain transcription factors. Plant Physiology 152:1044−1055

doi: 10.1104/pp.109.148270
[110]

Mitsuda N, Iwase A, Yamamoto H, Yoshida M, Seki M, et al. 2007. NAC transcription factors, NST1 and NST3, are key regulators of the formation of secondary walls in woody tissues of Arabidopsis. The Plant Cell 19:270−280

doi: 10.1105/tpc.106.047043
[111]

Marjamaa K, Kukkola EM, Fagerstedt KV. 2009. The role of xylem class III peroxidases in lignification. Journal of Experimental Botany 60:367−376

doi: 10.1093/jxb/ern278
[112]

Liu Q, Luo L, Zheng L. 2018. Lignins: biosynthesis and biological functions in plants. International Journal of Molecular Sciences 19:335

doi: 10.3390/ijms19020335
[113]

Vogt T. 2010. Phenylpropanoid biosynthesis. Molecular Plant 3:2−20

doi: 10.1093/mp/ssp106
[114]

Liu JJ, Houston S, Cruickshank M, Zamany A, Leal I, et al. 2025. Controlled inoculation provides insight into western redcedar resistance to multiple root- and butt-rot pathogens. Frontiers in Plant Science 16:1669570

doi: 10.3389/fpls.2025.1669570
[115]

Gao S, Zhao M, Sun S, Fan X, Yan J, et al. 2025. Development of an endogenous promoter-driven CRISPR/Cas9 system for genome editing in Fraxinus mandshurica. Forestry Research 5:e016

doi: 10.48130/forres-0025-0016
[116]

Xie J, Li M, Zeng J, Li X, Zhang D. 2022. Single-cell RNA sequencing profiles of stem-differentiating xylem in poplar. Plant Biotechnology Journal 20:417−419

doi: 10.1111/pbi.13763
[117]

Zhang SY, Zhao BG, Shen Z, Mei YC, Li G, et al. 2023. Integrating ATAC-seq and RNA-seq to identify differentially expressed genes with chromatin-accessible changes during photosynthetic establishment in Populus leaves. Plant Molecular Biology 113:59−74

doi: 10.1007/s11103-023-01375-z
[118]

Verdonk C, Gagalova K, Raffaele S, Derbyshire M. 2025. Learning the language of plant immunity: opportunities and challenges for AI-assisted modelling of fungal effector x host protein complexes. Computational and Structural Biotechnology Journal 27:2881−2889

doi: 10.1016/j.csbj.2025.06.048
[119]

Li LF, Cushman SA, He YX, Li Y. 2020. Genome sequencing and population genomics modeling provide insights into the local adaptation of weeping Forsythia. Horticulture Research 7:130

doi: 10.1038/s41438-020-00352-7
[120]

Borrelli GM, Mazzucotelli E, Marone D, Crosatti C, Michelotti V, et al. 2018. Regulation and evolution of NLR genes: a close interconnection for plant immunity. International Journal of Molecular Sciences 19:1662

doi: 10.3390/ijms19061662
[121]

Cesari S. 2018. Multiple strategies for pathogen perception by plant immune receptors. New Phytologist 219:17−24

doi: 10.1111/nph.14877
[122]

Zhang H, Zhao J, Zhang T, Wang G, Han Z, et al. 2025. Research progress of NAC transcription factors in woody plants. Frontiers in Plant Science 16:1592898

doi: 10.3389/fpls.2025.1592898