Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, et al. Phylotranscriptomic analysis of the origin and early diversification of landplants. Proc Natl Acad Sci USA. 2014;111:e4859–68.
Zeng LP, Zhang N, Zhang Q, Endress PK, Huang J, Ma H. Resolution of deep eudicot phylogeny and their Temporal diversification using nuclear genes from transcriptomic and genomic datasets. New Phytol. 2017;214:1338–54.
Zeng LP, Zhang Q, Sun RR, Kong HZ, Zhang N, Ma H. Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times. Nat Commun. 2014;5:4956.
Ran H, Liu Y, Wu C, Cao YN. Phylogenetic and comparative analyses of complete chloroplast genomes of Chinese Viburnum and Sambucus (Adoxaceae). Plants (Basel). 2020;9(9):1143.
Wang YH, Jiang WM, Ye W, Fu CX, Gitzendanner MA, Soltis PS, et al. Evolutionary insights from comparative transcriptome and transcriptome-wide coalescence analyses in Tetrastigma Hemsleyanum. BMC Plant Biol. 2018;18(1):208.
He J, Lyu R, Luo Y, Xiao JM, Xie L, Wen J, et al. A phylotranscriptome study using silica gel-dried leaf tissues produces an updated robust phylogeny of Ranunculaceae. Mol Phylogenet Evol. 2022;174:107545.
Guo P, Huang ZQ, Li XK, Zhao W, Wang YH. Transcriptome sequencing of Broussonetia papyrifera leaves reveals key genes involved in flavonoids biosynthesis. Plants. 2023;12(3):563.
Song N, Zhang H. A comprehensive analysis of higher-level phylogenetic relationships of hemiptera based on transcriptome data. J Syst Evol. 2023;61:572–86.
Wang XX, Huang CH, Morales-Briones DF, Wang XY, Hu Y, Zhang N, et al. Phylotranscriptomics reveals the phylogeny of asparagales and the evolution of allium flavor biosynthesis. Nat Commun. 2024;15(1):9663.
One Thousand Plant Transcriptomes Initiative. One thousand plant transcriptomes and the phylogenomics of green plants. Nature. 2019;574(7780):679–85.
Li Y, Zhao H, Xia HX, Huang J, Ma N, Guo P, et al. Multiomics analyses provide insights into the genomic basis of differentiation among four sweet osmanthus groups. Plant Physiol. 2024;195(4):2815–28.
Zhang C, Rabiee M, Sayyari E, Mirarab S. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics. 2018;19:15–30.
Zhang C, Mirarab S. ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees. Bioinformatics. 2022;38(21):4949–50.
Morales-Briones DF, Lin N, Huang EY, Grossenbacher DL, Sobel JM, Gilmore C, et al. Phylogenomic analyses in phrymaceae reveal extensive gene tree discordance in relationships among major clades. Am J Bot. 2022;109(6):1035–46.
Phipps J. Rosaceae. Flora of North America editorial committeeed. Flora of North America North of Mexico magnoliophyta: Pic-ramniaceae to rosaceae. New York and Oxford: Oxford University Press; 2014.
Tatum TC, Stepanovic S, Biradar DP, Rayburn AL, Korban SS. Variation in nuclear DNA content in Malus species and cultivated apples. Genome. 2005;48(5):924–30.
Liu DD, Wang DR, Yang XY, Zhao CH, Li SH, Sha GL, et al. Apomictic Malus plants exhibit abnormal pollen development. Front Plant Sci. 2023;14:1065032.
Zhang L, Morales-Briones DF, Li YJ, Zhang GJ, Zhang TK, Huang CH, et al. Phylogenomics insights into gene evolution, rapid species diversification, and morphological innovation of the Apple tribe (Maleae, Rosaceae). New Phytol. 2023;240(5):2102–20.
Li MW, Li D, Lu M, Mo S, Ding S, Chen Y, et al. A new species of cotoneaster (Rosaceae) from Western sichuan, China. PhytoKeys. 2023;236:39–52.
Li PP, Lou G, Cai XR, Zhang B, Cheng YX, Wang HW. Comparison of the complete plastomes and the phylogenetic analysis of Paulownia species. Sci Rep. 2020;10(1):2225.
Wang RZ, Xue YS, Fan J, Yao JL, Qin M, Lin T, et al. A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of Pear fruit. Genome Biol. 2021;22:313.
Hu HJ, Pan LQ, Sun Ke, Tu SC, Ye S, Wei YY, Tu K. Differentiation of deciduous-calyx and persistent-calyx Pears using hyperspectral reflectance imaging and multivariate analysis. Comput Electron Agric. 2017;137:150–6.
Li DF, Yu Y, Yang HJ, Yan XC. Persistent Calyces increase floral longevity and female fitness in Salvia miltiorrhiza (Lamiaceae). AoB Plants. 2022;14(2):plac004.
Qian GZ, Liu LF, Tang GG. A new section in Malus (Rosaceae) from China. Ann Botanici Fennici. 2006;43:68–73.
Rehder A. New species, varieties and combinations from the herbarium andthe collections of the Arnold arboretum. J Arnold Arboretum. 1926;7:22–37.
Rehder A. Manual of cultivated trees and shrubs hardy in North america, exclusive of the subtropical and warmer temperate regions. New York: Macmillan; 1940.
Liu BB, Ren C, Kwak M, Hodel RGJ, Xu C, He J, et al. Phylogenomic conflict analyses in the Apple genus Malus s.l. Reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern hemisphere. J Integr Plant Biol. 2022;64:1020–43.
Li W, Chu C, Zhang TK, Sun H, Wang S, Liu Z, et al. Pan-genome analysis reveals the evolution and diversity of Malus. Nat Genet. 2025. https://doi.org/10.1038/s41588-025-02166-6. Advance online publication.
Evans RC, Campbell CS. The origin of the Apple subfamily (Maloideae; Rosaceae) is clarified by DNA sequence data from duplicated GBSSI genes. Am J Bot. 2002;89:1478–84.
Wang L, Li ZC, Wang DJ, Tian W, Sun SM, Wang GY, et al. Genetic diversity and geographic distribution patterns of Malus landraces from 5 cultivated species under climate change in China. Sci Hort. 2024;336:113389.
Huckins CA. A revision of the sections of the genus Malus miller. New York: Cornell University; 1972.
Dickson EE. Systematic studies of Malus sect. Chloromeles. Ph.D. dissertation. Cornell University 1995.
Song L, Florea L. Rcorrector: efficient and accurate error correction for illumina RNA-seq reads. Gigascience. 2015;4:48.
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics. 2014;30(15):2114–20.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644–52.
Smith-Unna R, Boursnell C, Patro R, Hibberd JM, Kelly S. Transrate: reference-free quality assessment of de Novo transcriptome assemblies. Genome Res. 2016;26:1134–44.
Daccord N, Celton JM, Linsmith G, Becker C, Choisne N, Schijlen E, van de Geest H, et al. High-quality de Novo assembly of the Apple genome and methylome dynamics of early fruit development. Nat Genet. 2017;49:1099–106.
Fu LM, Niu BF, Zhu ZW, Wu ST, Li WZ. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28:3150–2.
Yang Y, Smith SA. Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics. Mol Biol Evol. 2014;31:3081–92.
Morales-Briones DF, Kadereit G, Tefarikis DT, Moore MJ, Smith SA, Brockington SF, et al. Disentangling sources of gene tree discordance in phylogenomic data sets: testing ancient hybridizations in amaranthaceae s.l. Syst Biol. 2021;70:219–35.
van Dongen S, Abreu-Goodger C. Using MCL to extract clusters from networks. Methods Mol Biol. 2012;804:281–95.
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.
Smith SA, Dunn CW. Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics. 2008;24:715–6.
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.
Mai U, Mirarab S. TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees. BMC Genomics. 2018;19:272.
Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020;37:1530–4.
Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol Biol Evol. 2017;34(3):772–3.
Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh. LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol. 2018;35(2):518–22.
Salichos L, Stamatakis A, Rokas A. Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Mol Biol Evol. 2014;31(5):1261–71.
Smith SA, Moore MJ, Brown JW, Yang Y. Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants. BMC Ecol Evol. 2015;15:150.
Pease JB, Brown JW, Walker JF, Hinchliff CE, Smith SA. Quartet sampling distinguishes lack of support from conflicting support in the green plant tree of life. Am J Bot. 2018;105(3):385–403.
Yang ZH. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24:1586–91.
Revell LJ. Phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol Evol. 2012;3:217–23.
Yao L, Yuan Y. A unified method for detecting phylogenetic signals in continuous, discrete, and multiple trait combinations. Ecol Evol. 2025;15(3):e71106.
Guo J, Xu WB, Hu Y, Huang J, Zhao YY, Zhang L, et al. Phylotranscriptomics in cucurbitaceae reveal multiple whole-genome duplications and key morphological and molecular innovations. Mol Plant. 2020;13:1117–33.
Huang WC, Zhang L, Columbus JT, Hu Y, Zhao YY, Tang L, et al. A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C4 photosynthesis. Mol Plant. 2022;15:755–77.
Song N, Wang M, Tang H, Dang Z. A phylogenetic analysis of scale insects (Hemiptera, Coccoidea) based on genomic and transcriptomic data. J Syst Evol. 2025;63:693–707.
Koenen EJM, Kidner C, de Souza ER, Simon MF, Iganci JR, Nicholls JA, et al. Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large Pantropical radiation. Am J Bot. 2020;107:1710–35.
Cai LM, Xi ZX, Lemmon EM, Lemmon AR, Mast A, Buddenhagen CE, Liu L, et al. The perfect storm: gene tree Estimation error, incomplete lineage sorting, and ancient gene flow explain the most recalcitrant ancient angiosperm clade, malpighiales. Syst Biol. 2021;70:491–507.
Shen XX, Steenwyk JL, Rokas A. Dissecting incongruence between concatenation- and quartet-based approaches in phylogenomic data. Syst Biol. 2021;70(5):997–1014.
Springer MS, Gatesy J. The gene tree delusion. Mol Phylogenet Evol. 2016;94:1–33.
Blom MPK, Bragg JG, Potter S, Moritz C. Accounting for uncertainty in gene tree estimation: summary-coalescent species tree inference in a challenging radiation of Australian lizards. Syst Biol. 2017;66(3):352–66.
Simmons MP, Kessenich J. Divergence and support among slightly suboptimal likelihood gene trees. Cladistics. 2020;36(3):322–40.
Korban SS. Interspecific hybridization in Malus. HortScience. 1986;21:41–8.
Harris SA, Robinson JP, Juniper BE. Genetic clues to the origin of the Apple. Trends Genet. 2002;18(8):426–30.
Konopelko A. P 2020 Peculiarities of the reproductive biology of the genus Malus mill. J Native Alien Plant Stud 16 96–111.
Aguiar B, Vieira J, Cunha AE, Fonseca NA, Iezzoni A, van Nocker S, et al. Convergent evolution at the gametophytic self-incompatibility system in Malus and Prunus. PLoS ONE. 2015;10(5):e0126138.
Vieira J, Pimenta J, Gomes A, Laia J, Rocha S, Heitzler P, et al. The identification of the Rosa S-locus and implications on the evolution of the rosaceae gametophytic self-incompatibility systems. Sci Rep. 2021;11(1):3710.
Xiang YZ, Huang CH, Hu Y, Wen J, Li SS, Yi TS, et al. Evolution of rosaceae fruit types based on nuclear phylogeny in the context of geological times and genome duplication. Mol Biol Evol. 2017;34:262–81.
Zhang TG, Qiao Q, Du X, Zhang X, Hou YL, Wei X, et al. Cultivated Hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe). J Integr Plant Biol. 2022;64:1487–501.
Axelrod DI. The eocene thunder mountain flora of central idaho. Berkeley: University of Califonia Press . 1998.
Budantsev LY. Early palaeogene flora of Western Kamchatka. Trudy Bot Inst Ross Akad Nauk. 2006;22:113.
Duan NB, Bai Y, Sun HH, Wang N, Ma YM, Li MJ, et al. Genome re-sequencing reveals the history of Apple and supports a two-stage model for fruit enlargement. Nat Genet. 2017;8:249.
Sun XP, Jiao C, Schwaninger H, Chao CT, Ma Y, Duan N, et al. Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of Apple domestication. Nat Genet. 2020;52:1423–32.
Rohrer JR, Robertson KR, Phipps JB. Floral morphology of maloideae (Rosaceae) and its systematic relevance. Am J Bot. 1994;81:574–81.
Robinson JP, Harris SA, Juniper BE. Taxonomy of the genus Malus mill. (Rosaceae) with emphasis on the cultivated apple, Malus domestica Borkh. Plant Syst Evol. 2001;226:35–58.
Jiang N. A preliminary research on the original centre of genus Malus miller. J Southwest Agricultural Univ. 1986;1:94–7.
Forté AV, Ignatov AN, Ponomarenko VV, Dorokhov DB, Savel’ev NI. Phylogeny of the Malus (apple tree) species, inferred from its morphological traits and molecular DNA analysis. Genetika. 2002;38(10):1357–69.
Li Y. An investigation of the genetic centre of M. pumila and Malus in the world. Acta Hortic Sinica. 1989;16:101–8.
Endress PK. Flower structure and trends of evolution in eudicots and their major subclades. Ann Mo Bot Gard. 2010;97:541–83.
Stull GW, Schori M, Soltis DE, Soltis PS. Character evolution and missing (morphological) data across Asteridae. Am J Bot. 2018;105:470–9.
Liu JX, Guo C, Ma PF, Zhou MY, Luo YH, Zhu GF, et al. The origin and morphological character evolution of the Paleotropical Woody bamboos. J Integr Plant Biol. 2024;66(10):2242–61.
Reich Peter B. The world-wide‘fast-slow’plant economics spectrum: a traits manifesto. J Ecol. 2014;102:275–301.
Cao YN, Wang MH, Ran H, Tian B, Liu LX, Wu QN, et al. Phylogenetic and molecular dating analyses of Chinese endemic genus Dipelta (Caprifoliaceae) based on nuclear RAD-Seq and Chloroplast genome data. J Syst Evol. 2025;63:170–82.
Han M, Zhang J, Li D, Sun S, Zhang C, Zhang C, et al. Phylogeographical pattern and population evolution history of Indigenous Elymus sibiricus L. on Qinghai-Tibetan plateau. Front Plant Sci. 2022;13:882601.
Yang J, Miao CY, Mao RL, Li Y. Landscape population genomics of Forsythia (Forsythia suspensa) reveal that ecological habitats determine the adaptive evolution of species. Front Plant Sci. 2017;8:481.
Moles AT, Westoby M, Eriksson O. Seed size and plant strategy across the whole life cycle. Oikos. 2006;113:91–105.
Zanne AE, Tank DC, Cornwell WK, Eastman JM, Smith SA, FitzJohn RG, et al. On the origin of giant seeds: the macroevolution of the double coconut (Lodoicea maldivica) and its relatives (Borasseae, Arecaceae). New Phytol. 2020;228:1134–48.
Zhang JX, Chen MH, Gan L, Zhang CJ, Shen Y, Qian J, et al. Diversity patterns of Bermuda grass along latitudinal gradients at different temperatures in southeastern China. Plants (Basel). 2020;9(12):1778.
Xia Z, Li CC, Wen J, Wang YZ. Rehmannieae or rehmanniaceae?? Evidence from plastome sequences and floral morphology. Bot J Linn Soc. 2021;196:10.
Shao YZ, Chen Y, Zhang XC, Xiang QP. Species delimitation and phylogeography of Abies Delavayi complex: inferred from morphological, molecular, and Climatic data. J Syst Evol. 2020;58:234–46.
Wang L, Sun J, Wang C, Shangguan Z. Leaf photosynthetic function duration during yield formation of large-spike wheat in rainfed cropping systems. PeerJ. 2018;6:e5532.
Vogel S. Leaves in the lowest and highest winds: temperature, force and shape: Tansley review. New Phytol. 2009;183:13–26.
Liu WJ, Shao YZ, Guo SQ, Liu FQ, Tian XY, Chen Y, et al. Latitudinal gradient patterns and driving factors of Woody plant fruit types based on multiple forest dynamic monitoring plots. J Plant Ecol. 2025;18(2):rtaf018.