CoChat
Sign Up
Cited by 117Plant Diversity and EvolutionChromosomal and Genetic VariationsGenomics and Phylogenetic Studies

Whole-genome microsynteny-based phylogeny of angiosperms

Open access
Zhao, Tao, Zwaenepoel, Arthur, Xue, Jia-Yu, Kao, Shu-Min, Li, Zhen, Schranz, M. Eric, Van de Peer, Yves·2021·Nature Communications
DOI 10.1038/s41467-021-23665-0PMC PMC8190143

Published version of a preprint

Open this paper in CoChat — free accountOpen PDF

Abstract

Plant genomes vary greatly in size, organization, and architecture. Such structural differences may be highly relevant for inference of genome evolution dynamics and phylogeny. Indeed, microsynteny—the conservation of local gene content and order—is recognized as a valuable source of phylogenetic information, but its use for the inference of large phylogenies has been limited. Here, by combining synteny network analysis, matrix representation, and maximum likelihood phylogenetic inference, we provide a way to reconstruct phylogenies based on microsynteny information. Both simulations and use of empirical data sets show our method to be accurate, consistent, and widely applicable. As an example, we focus on the analysis of a large-scale whole-genome data set for angiosperms, including more than 120 available high-quality genomes, representing more than 50 different plant families and 30 orders. Our ‘microsynteny-based’ tree is largely congruent with phylogenies proposed based on more traditional sequence alignment-based methods and current phylogenetic classifications but differs for some long-contested and controversial relationships. For instance, our synteny-based tree finds Vitales as early diverging eudicots, Saxifragales within superasterids, and magnoliids as sister to monocots. We discuss how synteny-based phylogenetic inference can complement traditional methods and could provide additional insights into some long-standing controversial phylogenetic relationships.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41467-021-23665-0

Cites

6 of 6 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Locus entanglement, and more broadly genomic topology, can be viewed as a multi-scale unification of existing techniques that infer phylogenies from single genomic scales.

    “In this sense, locus entanglement, and more broadly genomic topology, can be viewed as a multi-scale unification of existing techniques that infer phylogenies from single genomic scales, like locus adjacencies (202), microsyntenic clusters (203), macrosyntenic similarity (202), or irreversible FWM events (97).”

    From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [203]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 114

  1. [1]Van de Peer Y Computational approaches to unveiling ancient genome duplications Nat. Rev. Genet. 2004 5 752 763 10.1038/nrg1449 15510166 · DOI
  2. [2]Bowers JE Chapman BA Rong J Paterson AH Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events Nature 2003 422 433 438 10.1038/nature01521 12660784 · DOI
  3. [3]Pevzner P Tesler G Genome rearrangements in mammalian evolution: lessons from human and mouse genomes Genome Res. 2003 13 37 45 10.1101/gr.757503 12529304 PMC430962 · DOI · Paper page
  4. [4]Dewey CN Positional orthology: putting genomic evolutionary relationships into context Brief. Bioinform 2011 12 401 412 10.1093/bib/bbr040 21705766 PMC3178058 · DOI
  5. [5]Koonin EV Orthologs, paralogs, and evolutionary genomics Annu Rev. Genet. 2005 39 309 338 10.1146/annurev.genet.39.073003.114725 16285863 · DOI · Paper page
  6. [6]Van Bel M Dissecting plant genomes with the PLAZA comparative genomics platform Plant Physiol. 2012 158 590 600 10.1104/pp.111.189514 22198273 PMC3271752 · DOI
  7. [7]Zhao T Phylogenomic synteny network analysis of MADS-box transcription factor genes reveals lineage-specific transpositions, ancient tandem duplications, and deep positional conservation Plant Cell 2017 29 1278 1292 10.1105/tpc.17.00312 28584165 PMC5502458 · DOI
  8. [8]Sampedro J Lee Y Carey RE Depamphilis CW Cosgrove DJ Use of genomic history to improve phylogeny and understanding of births and deaths in a gene family Plant J. 2005 44 409 419 10.1111/j.1365-313X.2005.02540.x 16236151 · DOI
  9. [9]Watterson GA Ewens WJ Hall TE Morgan A The chromosome inversion problem J. Theor. Biol. 1982 99 1 7 10.1016/0022-5193(82)90384-8 · DOI
  10. [10]Blanchette M Bourque G Sankoff D Breakpoint phylogenies Genome Inform. 1997 8 25 34 11072302
  11. [11]Fertin, G., Labarre, A., Rusu, I., Vialette, S. & Tannier, E. Combinatorics of genome rearrangements, (MIT press, 2009).
  12. [12]Yancopoulos S Attie O Friedberg R Efficient sorting of genomic permutations by translocation, inversion and block interchange Bioinformatics 2005 21 3340 3346 10.1093/bioinformatics/bti535 15951307 · DOI
  13. [13]Cosner, M. E. et al. An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae. Comparative Genomics 99–121 (Springer, 2000).
  14. [14]Darling AE Miklós I Ragan MA Dynamics of genome rearrangement in bacterial populations PLoS Genet. 2008 4 e1000128 10.1371/journal.pgen.1000128 18650965 PMC2483231 · DOI
  15. [15]Luo H Shi J Arndt W Tang J Friedman R Gene order phylogeny of the genus Prochlorococcus PLoS ONE 2008 3 e3837 e3837 10.1371/journal.pone.0003837 19050756 PMC2585141 · DOI
  16. [16]Drillon, G., Champeimont, R., Oteri, F., Fischer, G. & Carbone, A. Phylogenetic reconstruction based on synteny block and gene adjacencies. Mol. Biol. Evol. (2020). PMC7475045 32384156
  17. [17]Lin, Y., Hu, F., Tang, J. & Moret, B. M. Maximum likelihood phylogenetic reconstruction from high-resolution whole-genome data and a tree of 68 eukaryotes. in Biocomputing 2013 285–296 (World Scientific, 2013). PMC3712796 23424133
  18. [18]Hu F Lin Y Tang J MLGO: phylogeny reconstruction and ancestral inference from gene-order data BMC Bioinf. 2014 15 1 6 PMC4236499 25376663
  19. [19]Zhou L Lin Y Feng B Zhao J Tang J Phylogeny analysis from gene-order data with massive duplications BMC Genomics 2017 18 13 20 10.1186/s12864-016-3415-6 29513196 PMC5657036 · DOI
  20. [21]Sankoff, D. & Zheng, C. Fractionation, rearrangement, consolidation, reconstruction. Models and Algorithms for Genome Evolution 247-260 (Springer, 2013).
  21. [22]Murat F Peer YVD Salse J Decoding plant and animal genome plasticity from differential paleo-evolutionary patterns and processes Genome Biol. Evol. 2012 4 917 928 10.1093/gbe/evs066 22833223 PMC3516226 · DOI
  22. [23]Zhao T Schranz ME Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes Proc. Natl Acad. Sci. USA 2019 116 2165 2174 10.1073/pnas.1801757116 30674676 PMC6369804 · DOI
  23. [24]Van de Peer Y Mizrachi E Marchal K The evolutionary significance of polyploidy Nat. Rev. Genet. 2017 18 411 10.1038/nrg.2017.26 28502977 · DOI
  24. [25]Leebens-Mack JH One thousand plant transcriptomes and the phylogenomics of green plants Nature 2019 574 679 685 10.1038/s41586-019-1693-2 31645766 PMC6872490 · DOI
  25. [26]Payseur BA Rieseberg LH A genomic perspective on hybridization and speciation Mol. Ecol. 2016 25 2337 2360 10.1111/mec.13557 26836441 PMC4915564 · DOI
  26. [27]Fedoroff N Transposons and genome evolution in plants Proc. Natl Acad. Sci. USA 2000 97 7002 7007 10.1073/pnas.97.13.7002 10860963 PMC34376 · DOI
  27. [28]Freeling M Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition Annu Rev. Plant Biol. 2009 60 433 453 10.1146/annurev.arplant.043008.092122 19575588 · DOI
  28. [29]Bowles AM Bechtold U Paps J The origin of land plants is rooted in two bursts of genomic novelty Curr. Biol. 2020 30 530 536.e2 10.1016/j.cub.2019.11.090 31956023 · DOI
  29. [30]Nguyen N Mirarab S Warnow T MRL and SuperFine+MRL: new supertree methods Algorithms Mol. Biol. 2012 7 3 10.1186/1748-7188-7-3 22280525 PMC3308190 · DOI
  30. [31]Mirarab S Bayzid MS Warnow T Evaluating summary methods for multilocus species tree estimation in the presence of incomplete lineage sorting Syst. Biol. 2016 65 366 380 10.1093/sysbio/syu063 25164915 · DOI
  31. [32]Robinson DF Foulds LR Comparison of phylogenetic trees Math. Biosci. 1981 53 131 147 10.1016/0025-5564(81)90043-2 · DOI
  32. [33]Morris JL The timescale of early land plant evolution Proc. Natl Acad. Sci. USA 2018 115 E2274 E2283 10.1073/pnas.1719588115 29463716 PMC5877938 · DOI
  33. [34]Byrne KP Wolfe KH The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species Genome Res. 2005 15 1456 1461 10.1101/gr.3672305 16169922 PMC1240090 · DOI · Paper page
  34. [35]Consortium DG Evolution of genes and genomes on the Drosophila phylogeny Nature 2007 450 203 10.1038/nature06341 17994087 · DOI · Paper page
  35. [36]Wang Y MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity Nucleic Acids Res. 2012 40 e49 e49 10.1093/nar/gkr1293 22217600 PMC3326336 · DOI
  36. [37]Gabaldón T Comparative genomics of emerging pathogens in the Candida glabrata clade BMC Genomics 2013 14 1 16 10.1186/1471-2164-14-623 24034898 PMC3847288 · DOI · Paper page
  37. [38]Kurtzman, C. P. & Fell, J. W. Yeast systematics and phylogeny—implications of molecular identification methods for studies in ecology. Biodiversity and Ecophysiology of Yeasts 11–30 (Springer, 2006).
  38. [39]Ahmad KM Genome structure and dynamics of the yeast pathogen Candida glabrata FEMS Yeast Res 2014 14 529 535 10.1111/1567-1364.12145 24528571 PMC4320752 · DOI · Paper page
  39. [40]Pollard DA Iyer VN Moses AM Eisen MB Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting PLoS Genet 2006 2 e173 10.1371/journal.pgen.0020173 17132051 PMC1626107 · DOI
  40. [41]Alekseyev MA Pevzner PA Breakpoint graphs and ancestral genome reconstructions Genome Res 2009 19 943 957 10.1101/gr.082784.108 19218533 PMC2675983 · DOI
  41. [42]Luo H Phylogenetic analysis of genome rearrangements among five mammalian orders Mol. Phylogen Evol. 2012 65 871 882 10.1016/j.ympev.2012.08.008 PMC4425404 22929217 · DOI
  42. [43]Reyes A Gissi C Pesole G Catzeflis FM Saccone C Where do rodents fit? Evidence from the complete mitochondrial genome of Sciurus vulgaris Mol. Biol. Evol. 2000 17 979 983 10.1093/oxfordjournals.molbev.a026379 10833205 · DOI
  43. [44]Cannarozzi G Schneider A Gonnet G A phylogenomic study of human, dog, and mouse PLoS Comput. Biol. 2007 3 e2 10.1371/journal.pcbi.0030002 17206860 PMC1761043 · DOI
  44. [45]Wang H Xu Z Gao L Hao B A fungal phylogeny based on 82 complete genomes using the composition vector method BMC Evol. Biol. 2009 9 1 13 10.1186/1471-2148-9-1 19664262 PMC3087519 · DOI
  45. [46]Kurtzman CP Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora FEMS Yeast Res. 2003 4 233 245 10.1016/S1567-1356(03)00175-2 14654427 · DOI
  46. [47]Suh S-O Blackwell M Kurtzman CP Lachance M-A Phylogenetics of Saccharomycetales, the ascomycete yeasts Mycologia 2006 98 1006 1017 10.1080/15572536.2006.11832629 17486976 · DOI
  47. [48]Chase MW An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV Bot. J. Linn. Soc. 2016 181 1 20 10.1111/boj.12385 · DOI
  48. [49]Zeng L Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets N. Phytol. 2017 214 1338 1354 10.1111/nph.14503 28294342 · DOI
  49. [50]Moore MJ Soltis PS Bell CD Burleigh JG Soltis DE Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots Proc. Natl Acad. Sci. USA 2010 107 4623 10.1073/pnas.0907801107 20176954 PMC2842043 · DOI
  50. [51]Worberg A Phylogeny of basal eudicots: Insights from non-coding and rapidly evolving DNA Org. Divers Evol. 2007 7 55 77 10.1016/j.ode.2006.08.001 · DOI
  51. [52]Soltis DE Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences Bot. J. Linn. Soc. 2000 133 381 461 10.1006/bojl.2000.0380 · DOI
  52. [53]Soltis DE Soltis PS Nuclear genomes of two magnoliids Nat. Plants 2019 5 6 10.1038/s41477-018-0344-1 30626927 · DOI
  53. [54]Chaw SM Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution Nat. Plants 2019 5 63 73 10.1038/s41477-018-0337-0 30626928 PMC6784883 · DOI
  54. [55]Chen J Liriodendron genome sheds light on angiosperm phylogeny and species–pair differentiation Nat. Plants 2019 5 18 10.1038/s41477-018-0323-6 30559417 PMC6784881 · DOI
  55. [56]Rendón-Anaya M The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation Proc. Natl Acad. Sci. USA 2019 116 17081 17089 10.1073/pnas.1822129116 31387975 PMC6708331 · DOI
  56. [57]Shimodaira H An approximately unbiased test of phylogenetic tree selection Syst. Biol. 2002 51 492 508 10.1080/10635150290069913 12079646 · DOI · Paper page
  57. [58]Forsythe ES Nelson AD Beilstein MA Biased gene retention in the face of introgression obscures species relationships Genome Biol. Evol. 2020 12 1646 1663 10.1093/gbe/evaa149 33011798 PMC7533067 · DOI
  58. [59]Fontaine MC Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics Science 2015 347 1258524 10.1126/science.1258524 25431491 PMC4380269 · DOI
  59. [60]Enright AJ Van Dongen S Ouzounis CA An efficient algorithm for large-scale detection of protein families Nucleic Acids Res. 2002 30 1575 1584 10.1093/nar/30.7.1575 11917018 PMC101833 · DOI
  60. [61]Rosvall M Bergstrom CT Maps of random walks on complex networks reveal community structure Proc. Natl Acad. Sci. USA 2008 105 1118 1123 10.1073/pnas.0706851105 18216267 PMC2234100 · DOI · Paper page
  61. [62]Nikolov LA Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity N. Phytol. 2019 222 1638 1651 10.1111/nph.15732 30735246 · DOI
  62. [63]Hohmann N Wolf EM Lysak MA Koch MA A time-calibrated road map of Brassicaceae species radiation and evolutionary history Plant Cell 2015 27 2770 2784 26410304 PMC4682323
  63. [64]Walden N Nguyen T-P Mandáková T Lysak MA Schranz ME Genomic blocks in Aethionema arabicum support Arabideae as next diverging clade in Brassicaceae Front Plant Sci. 2020 11 719 10.3389/fpls.2020.00719 32582250 PMC7286309 · DOI
  64. [65]Grass Phylogeny Working Group II. New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins N. Phytol. 2012 193 304 312 10.1111/j.1469-8137.2011.03972.x 22115274 · DOI
  65. [66]International Wheat Genome Sequencing C Shifting the limits in wheat research and breeding using a fully annotated reference genome Science 2018 361 6403 30115783
  66. [67]Sage RF Sage TL Kocacinar F Photorespiration and the evolution of C4 photosynthesis Annu Rev. Plant Biol. 2012 63 19 47 10.1146/annurev-arplant-042811-105511 22404472 · DOI
  67. [68]Boore JL The use of genome-level characters for phylogenetic reconstruction Trends Ecol. Evol. 2006 21 439 446 10.1016/j.tree.2006.05.009 16762445 · DOI
  68. [69]Rokas A Holland PW Rare genomic changes as a tool for phylogenetics Trends Ecol. Evol. 2000 15 454 459 10.1016/S0169-5347(00)01967-4 11050348 · DOI
  69. [70]Nadeau JH Taylor BA Lengths of chromosomal segments conserved since divergence of man and mouse Proc. Natl Acad. Sci. USA 1984 81 814 818 10.1073/pnas.81.3.814 6583681 PMC344928 · DOI
  70. [71]Sankoff D Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome Proc. Natl Acad. Sci. USA 1992 89 6575 6579 10.1073/pnas.89.14.6575 1631158 PMC49544 · DOI
  71. [72]Sankoff D Nadeau JH Chromosome rearrangements in evolution: from gene order to genome sequence and back Proc. Natl Acad. Sci. USA 2003 100 11188 11189 10.1073/pnas.2035002100 14506293 PMC208729 · DOI
  72. [73]Lewis PO A likelihood approach to estimating phylogeny from discrete morphological character data Syst. Biol. 2001 50 913 925 10.1080/106351501753462876 12116640 · DOI · Paper page
  73. [76]Carmel, L., Wolf, Y. I., Rogozin, I. B. & Koonin, E. V. EREM: parameter estimation and ancestral reconstruction by expectation-maximization algorithm for a probabilistic model of genomic binary characters evolution. Adv Bioinf.2010, 167408 (2010). PMC2866244 20467467
  74. [77]Simakov O Insights into bilaterian evolution from three spiralian genomes Nature 2013 493 526 531 10.1038/nature11696 23254933 PMC4085046 · DOI · Paper page
  75. [78]Hibbett DS Trends in morphological evolution in homobasidiomycetes inferred using maximum likelihood: a comparison of binary and multistate approaches Syst. Biol. 2004 53 889 903 10.1080/10635150490522610 15764558 · DOI
  76. [79]Nagy LG The evolution of autodigestion in the mushroom family Psathyrellaceae (Agaricales) inferred from Maximum Likelihood and Bayesian methods Mol. Phylogen Evol. 2010 57 1037 1048 10.1016/j.ympev.2010.08.022 20801224 · DOI
  77. [80]Kim T Hao W DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood BMC Bioinforma. 2014 15 1 6 PMC4261585 25260628
  78. [81]Yang Y Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution Nat. Plants 2020 6 215 222 10.1038/s41477-020-0594-6 32094642 PMC8075997 · DOI
  79. [82]Hu L The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis Nat. Commun. 2019 10 1 11 10.1038/s41467-018-07882-8 31619678 PMC6795880 · DOI · Paper page
  80. [83]Soltis PS Soltis DE Chase MW Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology Nature 1999 402 402 404 10.1038/46528 10586878 · DOI
  81. [84]Sun G Archaefructaceae, a new basal angiosperm family Science 2002 296 899 904 11988572
  82. [85]Endress PK Doyle JA Reconstructing the ancestral angiosperm flower and its initial specializations Am. J. Bot. 2009 96 22 66 10.3732/ajb.0800047 21628175 · DOI
  83. [86]Zhang N Zeng L Shan H Ma H Highly conserved low‐copy nuclear genes as effective markers for phylogenetic analyses in angiosperms N. Phytol. 2012 195 923 937 10.1111/j.1469-8137.2012.04212.x 22783877 · DOI
  84. [87]Sun M Deep phylogenetic incongruence in the angiosperm clade Rosidae Mol. Phylogen Evol. 2015 83 156 166 10.1016/j.ympev.2014.11.003 25463749 · DOI
  85. [88]Qiu YL Angiosperm phylogeny inferred from sequences of four mitochondrial genes J. Syst. Evol. 2010 48 391 425 10.1111/j.1759-6831.2010.00097.x · DOI
  86. [90]Finet C Timme RE Delwiche CF Marlétaz F Multigene phylogeny of the green lineage reveals the origin and diversification of land plants Curr. Biol. 2010 20 2217 2222 10.1016/j.cub.2010.11.035 21145743 · DOI
  87. [92]Zeng L Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times Nat. Commun. 2014 5 4956 10.1038/ncomms5956 25249442 PMC4200517 · DOI
  88. [93]Lyons E Pedersen B Kane J Freeling M The value of nonmodel genomes and an example using SynMap within CoGe to dissect the hexaploidy that predates the rosids Tropl Plant Biol. 2008 1 181 190 10.1007/s12042-008-9017-y · DOI
  89. [94]Jiao Y A genome triplication associated with early diversification of the core eudicots Genome Biol. 2012 13 1 14 10.1186/gb-2012-13-1-r3 PMC3334584 22280555 · DOI
  90. [95]Aköz G Nordborg M The Aquilegia genome reveals a hybrid origin of core eudicots Genome Biol. 2019 20 256 10.1186/s13059-019-1888-8 31779695 PMC6883705 · DOI
  91. [96]Ming R Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) Genome Biol. 2013 14 1 11 10.1186/gb-2013-14-5-r41 PMC4053705 23663246 · DOI
  92. [97]Dasmahapatra KK Butterfly genome reveals promiscuous exchange of mimicry adaptations among species Nature 2012 487 94 10.1038/nature11041 22722851 PMC3398145 · DOI
  93. [98]Edelman NB Genomic architecture and introgression shape a butterfly radiation Science 2019 366 594 599 10.1126/science.aaw2090 31672890 PMC7197882 · DOI
  94. [99]Browning SR Browning BL Zhou Y Tucci S Akey JM Analysis of human sequence data reveals two pulses of archaic Denisovan admixture Cell 2018 173 53 61. e9 10.1016/j.cell.2018.02.031 29551270 PMC5866234 · DOI · Paper page
  95. [100]Huerta-Sánchez E Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA Nature 2014 512 194 197 10.1038/nature13408 25043035 PMC4134395 · DOI · Paper page
  96. [101]Shan X Mobilization of the active MITE transposons mPing and Pong in rice by introgression from wild rice (Zizania latifolia Griseb.) Mol. Biol. Evol. 2005 22 976 990 10.1093/molbev/msi082 15647520 · DOI
  97. [102]Wang N Transpositional reactivation of the Dart transposon family in rice lines derived from introgressive hybridization with Zizania latifolia BMC Plant Biol. 2010 10 190 10.1186/1471-2229-10-190 20796287 PMC2956540 · DOI
  98. [103]Serrato-Capuchina A Matute DR The role of transposable elements in speciation Genes 2018 9 254 10.3390/genes9050254 29762547 PMC5977194 · DOI
  99. [104]Folk RA Soltis PS Soltis DE Guralnick R New prospects in the detection and comparative analysis of hybridization in the tree of life Am. J. Bot. 2018 105 364 375 10.1002/ajb2.1018 29683488 · DOI
  100. [105]Hedges SB Dudley J Kumar S TimeTree: a public knowledge-base of divergence times among organisms Bioinformatics 2006 22 2971 2972 10.1093/bioinformatics/btl505 17021158 · DOI · Paper page
  101. [107]Zwaenepoel, A. & Van de Peer, Y. Model-based detection of whole-genome duplications in a phylogeny. BioRxiv (2020). PMC7116244 32359154
  102. [108]Nguyen L-T Schmidt HA von Haeseler A Minh BQ IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies Mol. Biol. Evol. 2014 32 268 274 10.1093/molbev/msu300 25371430 PMC4271533 · DOI · Paper page
  103. [109]Buchfink B Xie C Huson DH Fast and sensitive protein alignment using DIAMOND Nat. Methods 2015 12 59 60 10.1038/nmeth.3176 25402007 · DOI · Paper page
  104. [110]Yang Z A space-time process model for the evolution of DNA sequences Genetics 1995 139 993 1005 10.1093/genetics/139.2.993 7713447 PMC1206396 · DOI
  105. [111]Soubrier J The influence of rate heterogeneity among sites on the time dependence of molecular rates Mol. Biol. Evol. 2012 29 3345 3358 10.1093/molbev/mss140 22617951 · DOI
  106. [112]Shimodaira H Hasegawa M Multiple comparisons of log-likelihoods with applications to phylogenetic inference Mol. Biol. Evol. 1999 16 1114 1114 10.1093/oxfordjournals.molbev.a026201 · DOI · Paper page
  107. [113]Hoang DT Chernomor O Von Haeseler A Minh BQ Vinh LS UFBoot2: improving the ultrafast bootstrap approximation Mol. Biol. Evol. 2017 35 518 522 10.1093/molbev/msx281 29077904 PMC5850222 · DOI · Paper page
  108. [114]Simão FA Waterhouse RM Ioannidis P Kriventseva EV Zdobnov EM BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Bioinformatics 2015 31 3210 3212 10.1093/bioinformatics/btv351 26059717 · DOI · Paper page
  109. [115]Katoh K Standley DM MAFFT multiple sequence alignment software version 7: improvements in performance and usability Mol. Biol. Evol. 2013 30 772 780 10.1093/molbev/mst010 23329690 PMC3603318 · DOI · Paper page
  110. [116]Capella-Gutiérrez S Silla-Martínez JM Gabaldón T trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses Bioinformatics 2009 25 1972 1973 10.1093/bioinformatics/btp348 19505945 PMC2712344 · DOI
  111. [117]Zhang, C., Scornavacca, C., Molloy, E. K. & Mirarab, S. ASTRAL-Pro: quartet-based species-tree inference despite paralogy. Mol. Biol. Evol. 37, 3292–3307 (2020). PMC7751180 32886770
  112. [118]Baum BR Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees Taxon 1992 41 3 10 10.2307/1222480 · DOI
  113. [119]Kagale S The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure Nat. Commun. 2014 5 1 11 10.1038/ncomms4706 PMC4015329 24759634 · DOI
  114. [120]Zhao, T. et al. Whole-genome microsynteny-based phylogeny of angiosperms. Harvard Dataverse, 10.7910/DVN/7ZZWIH (2021). PMC8190143 34108452 · DOI

Cited by

Sorted by citations

Authors
Zhao, T., Zwaenepoel, A., Xue, J.-Y., Kao, S.-M., Li, Z., Schranz, M. E., & Van de Peer, Y.
Affiliations
  • Ghent University (BE)
  • Nanjing Agricultural University (CN)
  • Wageningen University & Research (NL)
Corresponding author
Zhao, Tao
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2021-06-09
Volume
12
Issue
1
Pages
3498-3498
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-021-23665-0
PMC
PMC8190143
OpenAlex
W3111377105
Cited by
117
References
6
Citations by year
2026: 19 · 2025: 22 · 2024: 27 · 2023: 25 · 2022: 16 · 2021: 6 · 2020: 2
FWCI
15.01
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • Research Square (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Socio-Environmental Systems Modeling (acceptedVersion, public-domain)
  • Ghent University Academic Bibliography (Ghent University) (submittedVersion, cc-by)
  • UpSpace Institutional Repository (University of Pretoria) (submittedVersion, public-domain)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Socio-Environmental Systems Modeling (submittedVersion)
  • Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
  • Data Archiving and Networked Services (DANS) (submittedVersion, cc-by)
Funders
  • European Commission (HORIZON2020, 833522)
  • Fonds Wetenschappelijk Onderzoek
  • Universiteit Gent (BOF.MET.2021.0005.01, BOFPDO2018001701)
  • Vlaamse regering
  • Bijzonder Onderzoeksfonds UGent (BOF.MET.2021.0005.01)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
microsynteny, angiosperm phylogeny, genome evolution, Vitales, Saxifragales, Magnoliidae, monocotyledons, eudicots, phylogenetic incongruence, matrix representation
MeSH terms
Multigene Family, Models, Genetic, Phylogeny, Genes, Plant, Genome, Plant, Evolution, Molecular, Magnoliopsida, Synteny

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review