[1]

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
[2]

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.11286
[3]

Yates TB, Feng K, Zhang J, Singan V, Jawdy SS, et al. 2021. The ancient salicoid genome duplication event: a platform for reconstruction of de novo gene evolution in Populus trichocarpa. Genome Biology and Evolution 13:evab198

doi: 10.1093/gbe/evab198
[4]

Schiffthaler B, Delhomme N, Bernhardsson C, Jenkins J, Jansson S, et al. 2019. An improved genome assembly of the European aspen Populus tremula. bioRxiv

doi: 10.1101/805614
[5]

Lin YC, Wang J, Delhomme N, Schiffthaler B, Sundström G, et al. 2018. Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen. Proceedings of the National Academy of Sciences of the United States of America 115:E10970−E10978

doi: 10.1073/pnas.1801437115
[6]

Liu S, Wang Z, Shi T, Dan X, Zhang Y, et al. 2023. Chromosomal-level genome assembly of Populus adenopoda. bioRxiv

doi: 10.1101/2023.07.11.548479
[7]

Long Z, Sang Y, Feng J, Shi T, Dan X, et al. 2023. Chromosomal-level genome assembly of Populus lasiocarpa. bioRxiv

doi: 10.1101/2023.07.11.548483
[8]

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
[9]

Ma T, Wang J, Zhou G, Yue Z, Hu Q, et al. 2013. Genomic insights into salt adaptation in a desert poplar. Nature Communications 4:2797

doi: 10.1038/ncomms3797
[10]

Li C, Xing H, Li C, Ren Y, Li H, et al. 2022. Chromosome-scale genome assembly provides insights into the molecular mechanisms of tissue development of Populus wilsonii. Communications Biology 5:1125

doi: 10.1038/s42003-022-04106-0
[11]

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
[12]

Huang X, Chen S, Peng X, Bae EK, Dai X, et al. 2021. An improved draft genome sequence of hybrid Populus alba × Populus glandulosa. Journal of Forestry Research 32:1663−72

doi: 10.1007/s11676-020-01235-2
[13]

Bai S, Wu H, Zhang J, Pan Z, Zhao W, et al. 2021. Genome assembly of Salicaceae Populus deltoides (Eastern Cottonwood) I-69 based on nanopore sequencing and Hi-C technologies. Journal of Heredity 112:303−10

doi: 10.1093/jhered/esab010
[14]

Li Y, Wang D, Wang W, Yang W, Gao J, et al. 2023. A chromosome-level Populus qiongdaoensis genome assembly provides insights into tropical adaptation and a cryptic turnover of sex determination. Molecular Ecology 32:1366−80

doi: 10.1111/mec.16566
[15]

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 20:781−94

doi: 10.1111/1755-0998.13142
[16]

An X, Gao K, Chen Z, Li J, Yang X, et al. 2022. High quality haplotype-resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species widespread in Asia. Molecular Ecology Resources 22:786−802

doi: 10.1111/1755-0998.13507
[17]

Chen S, Yu Y, Wang X, Wang S, Zhang T, et al. 2023. Chromosome-level genome assembly of a triploid poplar Populus alba 'Berolinensis'. Molecular Ecology Resources 23:1092−107

doi: 10.1111/1755-0998.13770
[18]

Ma J, Wan D, Duan B, Bai X, Bai Q, et al. 2019. Genome sequence and genetic transformation of a widely distributed and cultivated poplar. Plant Biotechnology Journal 17:451−60

doi: 10.1111/pbi.12989
[19]

Liu Y, Wang X, Zeng Q. 2019. De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China. Science China Life Sciences 62:609−18

doi: 10.1007/s11427-018-9455-2
[20]

Bae EK, Kang MJ, Lee SJ, Park EJ, Kim KT. 2023. Chromosome-level genome assembly of the Asian aspen Populus davidiana Dode. Scientific Data 10:431

doi: 10.1038/s41597-023-02350-5
[21]

Yang W, Wang K, Zhang J, Ma J, Liu J, et al. 2017. The draft genome sequence of a desert tree Populus pruinosa. GigaScience 6:gix075

doi: 10.1093/gigascience/gix075
[22]

Chen Z, Ai F, Zhang J, Ma X, Yang W, et al. 2020. Survival in the Tropics despite isolation, inbreeding and asexual reproduction: insights from the genome of the world's southernmost poplar (Populus ilicifolia). The Plant Journal 103:430−42

doi: 10.1111/tpj.14744
[23]

Zhou R, Jenkins JW, Zeng Y, Shu S, Jang H, et al. 2023. Haplotype-resolved genome assembly of Populus tremula × P. alba reveals aspen-specific megabase satellite DNA. The Plant Journal 116:1003−17

doi: 10.1111/tpj.16454
[24]

Wu H, Yao D, Chen Y, Yang W, Zhao W, et al. 2020. De novo genome assembly of Populus simonii further supports that Populus simonii and Populus trichocarpa belong to different sections. G3 Genes|Genomes|Genetics 10:455−66

doi: 10.1534/g3.119.400913
[25]

Shen L, Ding C, Zhang W, Zhang T, Li Z, et al. 2023. The Populus koreana genome provides insights into the biosynthesis of plant aroma. Industrial Crops and Products 197:116453

doi: 10.1016/j.indcrop.2023.116453
[26]

Zhang Y, Tian Y, Ding S, Lv Y, Samjhana W, et al. 2020. Growth, carbon storage, and optimal rotation in poplar plantations: a case study on clone and planting spacing effects. Forests 11:842

doi: 10.3390/f11080842
[27]

Zhang Y, Yang X, Cao P, Xiao Z, Zhan C, et al. 2020. The bZIP53–IAA4 module inhibits adventitious root development in Populus. Journal of Experimental Botany 71:3485−98

doi: 10.1093/jxb/eraa096
[28]

Luo J, Nvsvrot T, Wang N. 2021. Comparative transcriptomic analysis uncovers conserved pathways involved in adventitious root formation in poplar. Physiology and Molecular Biology of Plants 27:1903−18

doi: 10.1007/s12298-021-01054-7
[29]

Cai G, Zhang Y, Huang L, Wang N. 2023. Uncovering the role of PdePrx12 peroxidase in enhancing disease resistance in poplar trees. Journal of Fungi 9:410

doi: 10.3390/jof9040410
[30]

Yang X, Zhang K, Nvsvrot T, Zhang Y, Cai G, et al. 2022. Phosphate (Pi) stress-responsive transcription factors PdeWRKY6 and PdeWRKY65 regulate the expression of PdePHT1;9 to modulate tissue Pi concentration in poplar. The Plant Journal 111:1753−67

doi: 10.1111/tpj.15922
[31]

Luo J, Xia W, Cao P, Xiao Z, Zhang Y, et al. 2019. Integrated transcriptome analysis reveals plant hormones jasmonic acid and salicylic acid coordinate growth and defense responses upon fungal infection in poplar. Biomolecules 9:12

doi: 10.3390/biom9010012
[32]

Gui J, Luo L, Zhong Y, Sun J, Umezawa T, et al. 2019. Phosphorylation of LTF1, an MYB transcription factor in Populus, acts as a sensory switch regulating lignin biosynthesis in wood cells. Molecular Plant 12:1325−37

doi: 10.1016/j.molp.2019.05.008
[33]

Li R, Wang Z, Wang J, Li L. 2023. Combining single-cell RNA sequencing with spatial transcriptome analysis reveals dynamic molecular maps of cambium differentiation in the primary and secondary growth of trees. Plant Communications 4:100665

doi: 10.1016/j.xplc.2023.100665
[34]

Zhang Y, Cai G, Zhang K, Sun H, Huang L, et al. 2024. PdeERF114 recruits PdeWRKY75 to regulate callus formation in poplar by modulating the accumulation of H2O2 and the relaxation of cell walls. New Phytologist 241:732−46

doi: 10.1111/nph.19349
[35]

Zhang Y, Xiao Z, Zhan C, Liu M, Xia W, et al. 2019. Comprehensive analysis of dynamic gene expression and investigation of the roles of hydrogen peroxide during adventitious rooting in poplar. BMC Plant Biology 19:99

doi: 10.1186/s12870-019-1700-7
[36]

Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114−20

doi: 10.1093/bioinformatics/btu170
[37]

Wang Y, Huang J, Li E, Xu S, Zhan Z, et al. 2022. Phylogenomics and biogeography of Populus based on comprehensive sampling reveal deep-level relationships and multiple intercontinental dispersals. Frontiers in Plant Science 13:813177

doi: 10.3389/fpls.2022.813177
[38]

Liu B, Shi Y, Yuan J, Hu X, Zhang H, et al. 2013. Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. arXiv 35:62−67

doi: 10.48550/arXiv.1308.2012
[39]

Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, et al. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research 27:722−36

doi: 10.1101/gr.215087.116
[40]

Cheng HY, Concepcion GT, Feng XW, Zhang HW, Li H. 2021. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nature Methods 18:170−75

doi: 10.1038/s41592-020-01056-5
[41]

Xiao C, Chen Y, Xie S, Chen K, Wang Y, et al. 2017. MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads. Nature Methods 14:1072−74

doi: 10.1038/nmeth.4432
[42]

Ruan J, Li H. 2020. Fast and accurate long-read assembly with wtdbg2. Nature Methods 17:155−58

doi: 10.1038/s41592-019-0669-3
[43]

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
[44]

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
[45]

Dudchenko O, Shamim MS, Batra SS, Durand NC, Musial NT, et al. 2018. The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. bioRxiv

doi: 10.1101/254797
[46]

Seppey M, Manni M, Zdobnov EM. 2019. BUSCO: Assessing genome assembly and annotation completeness. In Gene Prediction, ed. Kollmar M. Volume 1962. New York, NY: Humana. pp. 227–45. https://doi.org/10.1007/978-1-4939-9173-0_14

[47]

Pan L, Liu M, Kang Y, Mei X, Hu G, et al. 2023. Comprehensive genomic analyses of Vigna unguiculata provide insights into population differentiation and the genetic basis of key agricultural traits. Plant Biotechnology Journal 21:1426−39

doi: 10.1111/pbi.14047
[48]

Nie C, Zhang Y, Zhang X, Xia W, Sun H, et al. 2023. Genome assembly, resequencing and genome-wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry. The Plant Journal 114:519−33

doi: 10.1111/tpj.16151
[49]

Luo J, Ren W, Cai G, Huang L, Shen X, et al. 2022. The chromosome-scale genome sequence of Triadica sebifera provides insight into fatty acids and anthocyanin biosynthesis. Communications Biology 5:786

doi: 10.1038/s42003-022-03751-9
[50]

Stanke M, Keller O, Gunduz I, Hayes A, Waack S, et al. 2006. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Research 34:W435−W439

doi: 10.1093/nar/gkl200
[51]

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
[52]

Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, et al. 2003. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Research 31:5654−66

doi: 10.1093/nar/gkg770
[53]

Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. 2019. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnology 37:907−15

doi: 10.1038/s41587-019-0201-4
[54]

Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139−40

doi: 10.1093/bioinformatics/btp616
[55]

McCormick RF, Truong SK, Mullet JE. 2015. RIG: recalibration and interrelation of genomic sequence data with the GATK. G3 Genes|Genomes|Genetics 5:655−65

doi: 10.1534/g3.115.017012
[56]

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
[57]

O'Donnell S, Fischer G. 2020. MUM&Co: accurate detection of all SV types through whole-genome alignment. Bioinformatics 36:3242−43

doi: 10.1093/bioinformatics/btaa115
[58]

Yousaf A, Liu J, Ye S, Chen H. 2021. Current progress in evolutionary comparative genomics of great apes. Frontiers in Genetics 12:657468

doi: 10.3389/fgene.2021.657468
[59]

Gregg C, Zhang J, Butler JE, Haig D, Dulac C. 2010. Sex-specific parent-of-origin allelic expression in the mouse brain. Science 329:682−85

doi: 10.1126/science.1190831
[60]

Zhang J, Zhang W, Ji F, Qiu J, Song X, et al. 2020. A high-quality walnut genome assembly reveals extensive gene expression divergences after whole-genome duplication. Plant Biotechnology Journal 18:1848−50

doi: 10.1111/pbi.13350
[61]

Liu J, Shi C, Shi C, Li W, Zhang Q, et al. 2020. The chromosome-based rubber tree genome provides new insights into spurge genome evolution and rubber biosynthesis. Molecular Plant 13:336−50

doi: 10.1016/j.molp.2019.10.017
[62]

He L, Jia K, Zhang R, Wang Y, Shi T, et al. 2021. Chromosome-scale assembly of the genome of Salix dunnii reveals a male-heterogametic sex determination system on chromosome 7. Molecular Ecology Resources 21:1966−82

doi: 10.1111/1755-0998.13362
[63]

Yang YZ, Cuenca J, Wang N, Liang ZC, Sun HH, et al. 2020. A key 'foxy' aroma gene is regulated by homology-induced promoter indels in the iconic juice grape 'Concord'. Horticulture Research 7:67

doi: 10.1038/s41438-020-0304-6
[64]

Wu X, Liu Y, Zhang Y, Gu R. 2021. Advances in research on the mechanism of heterosis in plants. Frontiers in Plant Science 12:745726

doi: 10.3389/fpls.2021.745726
[65]

Liu S, Zhang L, Sang Y, Lai Q, Zhang X, et al. 2022. Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome. Molecular Biology and Evolution 39:msac008

doi: 10.1093/molbev/msac008
[66]

Ma T, Wang K, Hu Q, Xi Z, Wan D, et al. 2017. Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex. Proceedings of the National Academy of Sciences of the United States of America 115:E236−E243

doi: 10.1073/pnas.1713288114
[67]

Wang M, Zhang L, Zhang Z, Li M, Wang D, et al. 2020. Phylogenomics of the genus Populus reveals extensive interspecific gene flow and balancing selection. New Phytologist 225:1370−82

doi: 10.1111/nph.16215
[68]

Liu N, Du Y, Warburton ML, Xiao Y, Yan J. 2021. Phenotypic plasticity contributes to maize adaptation and heterosis. Molecular Biology and Evolution 38:1262−75

doi: 10.1093/molbev/msaa283
[69]

Blum A. 2013. Heterosis, stress, and the environment: a possible road map towards the general improvement of crop yield. Journal of Experimental Botany 64:4829−37

doi: 10.1093/jxb/ert289
[70]

López-Maury L, Marguerat S, Bähler J. 2008. Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. Nature Reviews Genetics 9:583−93

doi: 10.1038/nrg2398
[71]

Ho WC, Zhang J. 2019. Genetic gene expression changes during environmental adaptations tend to reverse plastic changes even after the correction for statistical nonindependence. Molecular Biology and Evolution 36:1847−48

doi: 10.1093/molbev/msz073
[72]

Nvsvrot T, Yang X, Zhang Y, Huang L, Cai G, et al. 2023. The PdeWRKY65-UGT75L28 gene module negatively regulates lignin biosynthesis in poplar petioles. Industrial Crops and Products 191:115937

doi: 10.1016/j.indcrop.2022.115937
[73]

Liu M, Huang L, Zhang Y, Yan Z, Wang N. 2022. Overexpression of PdeGATA3 results in a dwarf phenotype in poplar by promoting the expression of PdeSTM and altering the content of gibberellins. Tree Physiology 42:2614−26

doi: 10.1093/treephys/tpac086
[74]

Xiao Z, Zhang Y, Liu M, Zhan C, Yang X, et al. 2020. Coexpression analysis of a large-scale transcriptome identified a calmodulin-like protein regulating the development of adventitious roots in poplar. Tree Physiology 40:1405−19

doi: 10.1093/treephys/tpaa078
[75]

Luo J, Liang Z, Wu M, Mei L. 2019. Genome-wide identification of BOR genes in poplar and their roles in response to various environmental stimuli. Environmental and Experimental Botany 164:101−13

doi: 10.1016/j.envexpbot.2019.04.006
[76]

Xia W, Yu H, Cao P, Luo J, Wang N. 2017. Identification of TIFY family genes and analysis of their expression profiles in response to phytohormone treatments and infection in poplar. Frontiers in Plant Science 8:493

doi: 10.3389/fpls.2017.00493
[77]

Zhang L, Liu M, Qiao G, Jiang J, Jiang Y, et al. 2013. Transgenic poplar "NL895" expressing CpFATB gene shows enhanced tolerance to drought stress. Acta Physiologiae Plantarum 35:603−13

doi: 10.1007/s11738-012-1101-0
[78]

Chen Y, Yuan B, Wei Z, Chen X, Chen Y, et al. 2018. The ion homeostasis and ROS scavenging responses in 'NL895' poplar plantlet organs under in vitro salinity stress. In Vitro Cellular & Developmental Biology-Plant 54:318−31

doi: 10.1007/s11627-018-9896-z