This web page was created programmatically, to learn the article in its unique location you possibly can go to the hyperlink bellow:
https://www.nature.com/articles/s41477-026-02281-0
and if you wish to take away this text from our website please contact us
Amborella Genome, P. The Amborella genome and the evolution of flowering crops. Science 342, 1241089 (2013).
Soltis, P. S. & Soltis, D. E. The position of hybridization in plant speciation. Annu. Rev. Plant Biol. 60, 561–588 (2009).
Theissen, G. Development of floral organ id: tales from the MADS home. Curr. Opin. Plant Biol. 4, 75–85 (2001).
Wu, Q. et al. Transcriptome sequencing and metabolite evaluation for revealing the blue flower formation in waterlily. BMC Genomics 17, 897 (2016).
Zhang, L. et al. The water lily genome and the early evolution of flowering crops. Nature 577, 79–84 (2020).
Borsch, T., Löhne, C., Mbaye, M. & Wiersema, J. Towards an entire species tree of Nymphaea: shedding additional mild on subg. Brachyceras and its relationships to the Australian water-lilies. Telopea 13, 193–217 (2011).
Pellicer, J., Kelly, L. J., Magdalena, C. & Leitch, I. J. Insights into the dynamics of genome dimension and chromosome evolution within the early diverging angiosperm lineage Nymphaeales (water lilies). Genome 56, 437–449 (2013).
Borsch, T. et al. Phylogeny of Nymphaea (Nymphaeaceae): proof from substitutions and microstructural adjustments within the chloroplast trnT-trnF area. Int. J. Plant Sci. 168, 639–671 (2007).
Yuan, J. et al. Rapid drift of the Tethyan Himalaya terrane earlier than two-stage India-Asia collision. Natl. Sci. Rev. 8, nwaa173 (2021).
Jiang, X. et al. Chromosome fusions formed karyotype evolution and evolutionary relationships within the mannequin household Brassicaceae. Nat. Commun. 16, 4631 (2025).
Sun, P. et al. Subgenome-aware analyses reveal the genomic penalties of historical allopolyploid hybridizations all through the cotton household. Proc. Natl Acad. Sci. USA 121, e2313921121 (2024).
Li, S. X., Liu, Y., Zhang, Y. M., Chen, J. Q. & Shao, Z. Q. Convergent discount of immune receptor repertoires throughout plant adaptation to various particular life and habitats. Nat. Plants 11, 248–262 (2025).
Hierarchical discount in plant immune receptor repertoires throughout adaptation to particular life and habitats. Nat. Plants 11, 163–164 (2025).
Liu, Y. et al. An angiosperm NLR Atlas reveals that NLR gene discount is related to ecological specialization and sign transduction element deletion. Mol. Plant 14, 2015–2031 (2021).
Araguirang, G. E. & Richter, A. S. Activation of anthocyanin biosynthesis in excessive mild – what’s the preliminary sign? New Phytol. 236, 2037–2043 (2022).
Lam, Ok. C., Ibrahim, R. Ok., Behdad, B. & Dayanandan, S. Structure, perform, and evolution of plant O-methyltransferases. Genome 50, 1001–1013 (2007).
Beilstein, M. A., Nagalingum, N. S., Clements, M. D., Manchester, S. R. & Mathews, S. Dated molecular phylogenies point out a Miocene origin for Arabidopsis thaliana. Proc. Natl Acad. Sci. USA 107, 18724–18728 (2010).
Zhang, D. et al. Diverse roles of MYB transcription elements in crops. J. Integr. Plant Biol. 67, 539–562 (2025).
Gonzalez, A., Zhao, M., Leavitt, J. M. & Lloyd, A. M. Regulation of the anthocyanin biosynthetic pathway by the TTG1/bHLH/Myb transcriptional advanced in Arabidopsis seedlings. Plant J. 53, 814–827 (2008).
Li, S. et al. MYB75 phosphorylation by MPK4 is required for light-induced anthocyanin accumulation in Arabidopsis. Plant Cell 28, 2866–2883 (2016).
Li, W. et al. A key R2R3-MYB transcription issue prompts anthocyanin biosynthesis and results in leaf reddening in poplar mutants. Plant Cell Environ. 48, 2067–2082 (2025).
Naing, A. H. & Kim, C. Ok. Roles of R2R3-MYB transcription elements in transcriptional regulation of anthocyanin biosynthesis in horticultural crops. Plant Mol. Biol. 98, 1–18 (2018).
Liu, G. et al. Diverse O-methyltransferases catalyze the biosynthesis of floral benzenoids that repel aphids from the flowers of waterlily Nymphaea prolifera. Hortic. Res. 10, uhad237 (2023).
Carta, A., Bedini, G. & Peruzzi, L. A deep dive into the ancestral chromosome quantity and genome dimension of flowering crops. New Phytol. 228, 1097–1106 (2020).
Murat, F., Armero, A., Pont, C., Klopp, C. & Salse, J. Reconstructing the genome of the newest widespread ancestor of flowering crops. Nat. Genet. 49, 490–496 (2017).
Formenti, G. et al. The period of reference genomes in conservation genomics. Trends Ecol. Evol. 37, 197–202 (2022).
Soltis, P. S., Marchant, D. B., Van de Peer, Y. & Soltis, D. E. Polyploidy and genome evolution in crops. Curr. Opin. Genet. Dev. 35, 119–125 (2015).
Huang, X., Huang, S., Han, B. & Li, J. The built-in genomics of crop domestication and breeding. Cell 185, 2828–2839 (2022).
Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo meeting utilizing phased meeting graphs with hifiasm. Nat. Methods 18, 170–175 (2021).
Camacho, C. et al. BLAST+: structure and purposes. BMC Bioinformatics 10, 421 (2009).
Zeng, X. et al. Chromosome-level scaffolding of haplotype-resolved assemblies utilizing Hi-C information with out reference genomes. Nat. Plants 10, 1184–1200 (2024).
Durand, N. C. et al. Juicebox supplies a visualization system for Hi-C contact maps with limitless zoom. Cell Syst. 3, 99–101 (2016).
Xu, M. et al. TGS-GapCloser: a quick and correct hole nearer for giant genomes with low protection of error-prone lengthy reads. Gigascience 9, giaa094 (2020).
Lin, Y. et al. quarTeT: a telomere-to-telomere toolkit for gap-free genome meeting and centromeric repeat identification. Hortic. Res. 10, uhad127 (2023).
Goel, M., Sun, H., Jiao, W. B. & Schneeberger, Ok. SyRI: discovering genomic rearrangements and native sequence variations from whole-genome assemblies. Genome Biol. 20, 277 (2019).
Goel, M. & Schneeberger, Ok. plotsr: visualizing structural similarities and rearrangements between a number of genomes. Bioinformatics 38, 2922–2926 (2022).
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Manni, M., Berkeley, M. R., Seppey, M., Simao, F. A. & Zdobnov, E. M. BUSCO replace: novel and streamlined workflows together with broader and deeper phylogenetic protection for scoring of eukaryotic, prokaryotic, and viral genomes. Mol. Biol. Evol. 38, 4647–4654 (2021).
Sun, P. et al. WGDI: a user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes. Mol. Plant 15, 1841–1851 (2022).
Ou, S. et al. Benchmarking transposable component annotation strategies for creation of a streamlined, complete pipeline. Genome Biol. 20, 275 (2019).
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a quick spliced aligner with low reminiscence necessities. Nat. Methods 12, 357–360 (2015).
Goodstein, D. M. et al. Phytozome: a comparative platform for inexperienced plant genomics. Nucleic Acids Res. 40, D1178–D1186 (2012).
UniProt, C. UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Res. 51, D523–D531 (2023).
Gabriel, L. et al. BRAKER3: totally automated genome annotation utilizing RNA-seq and protein proof with GeneMark-ETP, AUGUSTUS, and TSEBRA. Genome Res. 34, 769–777 (2024).
Gabriel, L., Hoff, Ok. J., Bruna, T., Borodovsky, M. & Stanke, M. TSEBRA: transcript selector for BRAKER. BMC Bioinformatics 22, 566 (2021).
Kovaka, S. et al. Transcriptome meeting from long-read RNA-seq alignments with StringTie2. Genome Biol. 20, 278 (2019).
Bruna, T., Lomsadze, A. & Borodovsky, M. A brand new gene discovering instrument GeneMark-ETP considerably improves the accuracy of computerized annotation of huge eukaryotic genomes. Preprint at bioRxiv (2024).
Stanke, M., Diekhans, M., Baertsch, R. & Haussler, D. Using native and syntenically mapped cDNA alignments to enhance de novo gene discovering. Bioinformatics 24, 637–644 (2008).
Chen, C. et al. TBtools-II: a ‘one for all, all for one’ bioinformatics platform for organic big-data mining. Mol. Plant 16, 1733–1742 (2023).
Cantalapiedra, C. P., Hernandez-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: useful annotation, orthology assignments, and area prediction on the metagenomic scale. Mol. Biol. Evol. 38, 5825–5829 (2021).
Huerta-Cepas, J. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology useful resource based mostly on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47, D309–D314 (2019).
Jin, J. J. et al. GetOrganelle: a quick and versatile toolkit for correct de novo meeting of organelle genomes. Genome Biol. 21, 241 (2020).
Tillich, M. et al. GeSeq – versatile and correct annotation of organelle genomes. Nucleic Acids Res. 45, W6–W11 (2017).
Zhang, D. et al. PhyloSuite: an built-in and scalable desktop platform for streamlined molecular sequence information administration and evolutionary phylogenetics research. Mol. Ecol. Resour. 20, 348–355 (2020).
Grabherr, M. G. et al. Full-length transcriptome meeting from RNA-seq information and not using a reference genome. Nat. Biotechnol. 29, 644–652 (2011).
Li, W. & Godzik, A. Cd-hit: a quick program for clustering and evaluating massive units of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).
Emms, D. M. & Kelly, S. OrthoFinder: fixing basic biases in entire genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 16, 157 (2015).
Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238 (2019).
Edgar, R. C. MUSCLE: a number of sequence alignment with excessive accuracy and excessive throughput. Nucleic Acids Res. 32, 1792–1797 (2004).
Capella-Gutierrez, S., Silla-Martinez, J. M. & Gabaldon, T. trimAl: a instrument for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. Ok. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: quick mannequin choice for correct phylogenetic estimates. Nat. Methods 14, 587–589 (2017).
Minh, B. Q. et al. IQ-TREE 2: new fashions and environment friendly strategies for phylogenetic inference within the genomic period. Mol. Biol. Evol. 37, 1530–1534 (2020).
Yang, Z. PAML 4: phylogenetic evaluation by most chance. Mol. Biol. Evol. 24, 1586–1591 (2007).
Letunic, I. & Bork, P. Interactive Tree of Life (iTOL) v6: current updates to the phylogenetic tree show and annotation instrument. Nucleic Acids Res. 52, W78–W82 (2024).
Yu, Y., Harris, A. J., Blair, C. & He, X. RASP (Reconstruct Ancestral State in Phylogenies): a instrument for historic biogeography. Mol. Phylogenet. Evol. 87, 46–49 (2015).
Mendes, F. Ok., Vanderpool, D., Fulton, B. & Hahn, M. W. CAFE 5 fashions variation in evolutionary charges amongst gene households. Bioinformatics 36, 5516–5518 (2021).
He, S. et al. DataColor: unveiling organic information relationships via distinctive coloration mapping. Hortic. Res. 11, uhad273 (2024).
Mistry, J. et al. Pfam: the protein households database in 2021. Nucleic Acids Res. 49, D412–D419 (2021).
Eddy, S. R. Accelerated profile HMM pearches. PLoS Comput. Biol. 7, e1002195 (2011).
Chen, T., Zhang, H., Liu, Y., Liu, Y. X. & Huang, L. EVenn: simple to create repeatable and editable Venn diagrams and Venn networks on-line. J. Genet. Genomics 48, 863–866 (2021).
Shen, W., Sipos, B. & Zhao, L. SeqKit2: a Swiss military knife for sequence and alignment processing. Imeta 3, e191 (2024).
Liao, Y., Smyth, G. Ok. & Shi, W. featureCounts: an environment friendly basic objective program for assigning sequence reads to genomic options. Bioinformatics 30, 923–930 (2014).
Chen, Y., Chen, L., Lun, A. T. L., Baldoni, P. L. & Smyth, G. Ok. edgeR v4: highly effective differential evaluation of sequencing information with expanded performance and improved assist for small counts and bigger datasets. Nucleic Acids Res. 53, gkaf018 (2025).
Abramson, J. et al. Accurate construction prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024).
Bailey, T. L. et al. MEME SUITE: instruments for motif discovery and looking out. Nucleic Acids Res. 37, W202–W208 (2009).
Wang, J. et al. The conserved area database in 2023. Nucleic Acids Res. 51, D384–D388 (2023).
Gu, Z., Eils, R. & Schlesner, M. Complex heatmaps reveal patterns and correlations in multidimensional genomic information. Bioinformatics 32, 2847–2849 (2016).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq information with DESeq2. Genome Biol. 15, 550 (2014).
Langfelder, P. & Horvath, S. WGCNA: an R package deal for weighted correlation community evaluation. BMC Bioinformatics 9, 559 (2008).
Langfelder, P. & Horvath, S. Fast R features for sturdy correlations and hierarchical clustering. J. Stat. Softw. 46, i11 (2012).
Xu, Y. et al. Gibberellin signaling regulates pectin biosynthesis in Arabidopsis. Nat. Commun. 16, 4065 (2025).
Clough, S. J. & Bent, A. F. Floral dip: a simplified technique for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735–743 (1998).
Deikman, J. & Hammer, P. E. Induction of anthocyanin accumulation by cytokinins in Arabidopsis thaliana. Plant Physiol. 108, 47–57 (1995).
Song, Z. et al. BBX28/BBX29, HY5 and BBX30/31 type a suggestions loop to fine-tune photomorphogenic growth. Plant J. 104, 377–390 (2020).
Liu, G., Yang, M., Yang, X., Ma, X. & Fu, J. Five TPSs are chargeable for risky terpenoid biosynthesis in Albizia julibrissin. J. Plant Physiol. 258-259, 153358 (2021).
This web page was created programmatically, to learn the article in its unique location you possibly can go to the hyperlink bellow:
https://www.nature.com/articles/s41477-026-02281-0
and if you wish to take away this text from our website please contact us
This web page was created programmatically, to learn the article in its unique location you'll…
This web page was created programmatically, to learn the article in its authentic location you…
This web page was created programmatically, to learn the article in its unique location you'll…
This web page was created programmatically, to learn the article in its unique location you…
This web page was created programmatically, to learn the article in its authentic location you'll…
This web page was created programmatically, to learn the article in its unique location you…