[1]

Rockwood DL, Naidu CV, Carter DR, Rahmani M, Spriggs TA, et al. 2004. Short-rotation woody crops and phytoremediation: opportunities for agroforestry? Agroforestry Systems 61:51−63

doi: 10.1023/B:AGFO.0000028989.72186.e6
[2]

Stettler RF, Bradshaw HD Jr, Heilman PE, Hinckley TM. 1996. Biology of Populus and its implications for management and conservation. Forest Science 43:457−458

doi: 10.1093/forestscience/43.3.457
[3]

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
[4]

Kim M, Xi H, Park S, Yun Y, Park J. 2021. Genome-wide comparative analyses of GATA transcription factors among seven Populus genomes. Scientific Reports 11:16578

doi: 10.1038/s41598-021-95940-5
[5]

Zhang S, Wu Z, Ma D, Zhai J, Han X, et al. 2022. Chromosome-scale assemblies of the male and female Populus euphratica genomes reveal the molecular basis of sex determination and sexual dimorphism. Communications Biology 5:1186

doi: 10.1038/s42003-022-04145-7
[6]

Shi T, Zhang X, Hou Y, Jia C, Dan X, et al. 2024. The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees. Molecular Plant 17:725−746

doi: 10.1016/j.molp.2024.03.009
[7]

Bradshaw HD, Ceulemans R, Davis J, Stettler R. 2000. Emerging model systems in plant biology: poplar (Populus) as a model forest tree. Journal of Plant Growth Regulation 19:306−313

doi: 10.1007/s003440000030
[8]

Guo Y, Qi Y, Yang G, Feng Y, Ding X, et al. 2024. A genome-wide identification of miPEPs in hybrid poplar reveals regulatory functions of miPEP166i in adventitious root elongation. Industrial Crops and Products 210:118150

doi: 10.1016/j.indcrop.2024.118150
[9]

Wang S, Tian L, Liu H, Li X, Zhang J, et al. 2020. Large-scale discovery of non-conventional peptides in maize and Arabidopsis through an integrated peptidogenomic pipeline. Molecular Plant 13:1078−1093

doi: 10.1016/j.molp.2020.05.012
[10]

Tian D, Liu Y, Tian L, Wan M, Zheng B, et al. 2019. Involvement of Populus CLEL peptides in root development. Tree Physiology 39:1907−1921

doi: 10.1093/treephys/tpz084
[11]

Zhu Y, Song D, Zhang R, Luo L, Cao S, et al. 2020. A xylem-produced peptide PtrCLE20 inhibits vascular cambium activity in Populus. Plant Biotechnology Journal 18:195−206

doi: 10.1111/pbi.13187
[12]

Kucukoglu M, Chaabouni S, Zheng B, Mähönen AP, Helariutta Y, et al. 2020. Peptide encoding Populus CLV3/ESR-RELATED 47 (PttCLE47) promotes cambial development and secondary xylem formation in hybrid aspen. New Phytologist 226:75−85

doi: 10.1111/nph.16331
[13]

Tavormina P, De Coninck B, Nikonorova N, De Smet I, Cammue BPA. 2015. The plant peptidome: an expanding repertoire of structural features and biological functions. The Plant Cell 27:2095−2118

doi: 10.1105/tpc.15.00440
[14]

Guo Y, Feng YF, Yang GG, Jia Y, He J, et al. 2024. Allele-specific DNA methylation and gene expression during shoot organogenesis in tissue culture of hybrid poplar. Horticulture Research 11:uhae027

doi: 10.1093/hr/uhae027
[15]

von Arnim AG, Jia Q, Vaughn JN. 2014. Regulation of plant translation by upstream open reading frames. Plant Science 214:1−12

doi: 10.1016/j.plantsci.2013.09.006
[16]

Fang E, Wang X, Wang J, Hu A, Song H, et al. 2020. Therapeutic targeting of YY1/MZF1 axis by MZF1-uPEP inhibits aerobic glycolysis and neuroblastoma progression. Theranostics 10:1555−1571

doi: 10.7150/thno.37383
[17]

Qiu D, Bai S, Ma J, Zhang L, Shao F, et al. 2019. The genome of Populus alba x Populus tremula var. glandulosa clone 84K. DNA Research 26:423−431

doi: 10.1093/dnares/dsz020
[18]

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 195:652−670

doi: 10.1093/plphys/kiae078
[19]

Pei MS, Liu HN, Wei TL, Yu YH, Guo DL. 2022. Large-scale discovery of non-conventional peptides in grape (Vitis vinifera L.) through peptidogenomics. Horticulture Research 9:uhac023

doi: 10.1093/hr/uhac023
[20]

Zhang Z, Chen Y, Zhang J, Ma X, Li Y, et al. 2020. Improved genome assembly provides new insights into genome evolution in a desert poplar (Populus euphratica). Molecular Ecology Resources 20:781−794

doi: 10.1111/1755-0998.13142
[21]

Rice P, Longden I, Bleasby A. 2000. EMBOSS: the European molecular biology open software suite. Trends in Genetics 16:276−277

doi: 10.1016/S0168-9525(00)02024-2
[22]

Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841−842

doi: 10.1093/bioinformatics/btq033
[23]

Song QX, Lu X, Li QT, Chen H, Hu XY, et al. 2013. Genome-wide analysis of DNA methylation in Soybean. Molecular Plant 6:1961−1974

doi: 10.1093/mp/sst123
[24]

Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, et al. 2009. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25:1422−1423

doi: 10.1093/bioinformatics/btp163
[25]

Hao Z, Lv D, Ge Y, Shi J, Weijers D, et al. 2020. RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms. PeerJ Computer Science 6:e251

doi: 10.7717/peerj-cs.251
[26]

Kanehisa M, Furumichi M, Sato Y, Kawashima M, Ishiguro-Watanabe M. 2023. KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Research 51:D587−D592

doi: 10.1093/nar/gkac963
[27]

Kanehisa M, Goto S. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28:27−30

doi: 10.1093/nar/28.1.27
[28]

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
[29]

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
[30]

Luo S, Xiao B, Geng J, Hu S. 2024. multiMotif: a generalized tool for scanning and visualization of diverse and distant multiple motifs. Journal of Genetics and Genomics 51:1342−1345

doi: 10.1016/j.jgg.2024.07.003
[31]

van Wijk KJ, Leppert T, Sun Z, Guzchenko I, Debley E, et al. 2024. The Zea mays PeptideAtlas: a new maize community resource. Journal of Proteome Research 23:3984−4004

doi: 10.1021/acs.jproteome.4c00320
[32]

Lauressergues D, Couzigou JM, Clemente HS, Martinez Y, Dunand C, et al. 2015. Primary transcripts of microRNAs encode regulatory peptides. Nature 520:90−93

doi: 10.1038/nature14346
[33]

de Bang TC, Lundquist PK, Dai X, Boschiero C, Zhuang Z, et al. 2017. Genome-wide identification of Medicago peptides involved in macronutrient responses and nodulation. Plant Physiology 175:1669−1689

doi: 10.1104/pp.17.01096
[34]

Yadav DK, Srivastava GP, Singh A, Singh M, Yadav N, et al. 2024. Proteome-wide analysis reveals G protein-coupled receptor-like proteins in rice (Oryza sativa). Plant Signaling & Behavior 19:2365572

doi: 10.1080/15592324.2024.2365572
[35]

Fortunel C, Fine PVA, Baraloto C. 2012. Leaf, stem and root tissue strategies across 758 Neotropical tree species. Functional Ecology 26:1153−1161

doi: 10.1111/j.1365-2435.2012.02020.x
[36]

Speck T, Burgert I. 2011. Plant stems: functional design and mechanics. Annual Review of Materials Research 41:169−193

doi: 10.1146/annurev-matsci-062910-100425
[37]

Augstein F, Carlsbecker A. 2018. Getting to the roots: a developmental genetic view of root anatomy and function from Arabidopsis to lycophytes. Frontiers in Plant Science 9:1410

doi: 10.3389/fpls.2018.01410
[38]

Cleary S, Seoighe C. 2021. Perspectives on allele-specific expression. Annual Review of Biomedical Data Science 4:101−122

doi: 10.1146/annurev-biodatasci-021621-122219
[39]

Couzigou JM, Lauressergues D, Bécard G, Combier JP. 2015. miRNA-encoded peptides (miPEPs): a new tool to analyze the roles of miRNAs in plant biology. RNA Biology 12:1178−1180

doi: 10.1080/15476286.2015.1094601
[40]

Shikata H, Shibata M, Ushijima T, Nakashima M, Kong SG, et al. 2012. The RS domain of Arabidopsis splicing factor RRC1 is required for phytochrome B signal transduction. The Plant Journal 70:727−738

doi: 10.1111/j.1365-313X.2012.04937.x
[41]

Pawela A, Banasiak J, Biała W, Martinoia E, Jasiński M. 2019. MtABCG20 is an ABA exporter influencing root morphology and seed germination of Medicago truncatula. The Plant Journal 98:511−523

doi: 10.1111/tpj.14234
[42]

Teng S, Keurentjes J, Bentsink L, Koornneef M, Smeekens S. 2005. Sucrose-specific induction of anthocyanin biosynthesis in Arabidopsis requires the MYB75/PAP1 gene. Plant Physiology 139:1840−1852

doi: 10.1104/pp.105.066688