ArticleNature communications2021
Whole-genome microsynteny-based phylogeny of angiosperms.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
- Genome-Wide Characterization and Salt-Responsive Expression Divergence of Chromosome Group 2 and Group 6Plants (Basel, Switzerland) · 2026Article
- Chromosomal evolution and speciation inferred from chromosome-scale genome assemblies in three Cupressaceae species.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Genomic Distortion of Jawed Vertebrate Phylogeny.bioRxiv : the preprint server for biology · 2026Article
- Structural genomics sheds light on protein functions and remote homologs across the insect tree of life.Cell research · 2026Article
- Near chromosome-level genome assembly of Neomusotima conspurcatalis gives insights into the evolution of moth genome architecture and fern-insect interactions.G3 (Bethesda, Md.) · 2026Article
- Searching for α-solenoid proteins involved in organellar gene expression.BMC genomics · 2026Article
- PGDD 2.0: Plant Genome Duplication Database with updated content and tools.Nucleic acids research · 2026Article
- Integrative characterization of the heat shock transcription factors inFrontiers in plant science · 2026Article
- Integrative genomic and machine learning approaches reveal evolutionary signatures in the winged bean mitochondrial genome.BMC plant biology · 2025Article
- Phylogenomic discordance is driven mainly by pervasive ancient hybridization and incomplete lineage sorting during the early divergence of major angiosperm lineages.Plant communications · 2025Article
- Interpretation of RNA Universe and Coding Potential Using IntRNA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Catalytically active inclusion bodies of cold-adapted lipase: production and its industrial potential.AMB Express · 2025Article
- AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids.Plant methods · 2025Article
- Characterization and Phylogenetic Analysis of MADS-Box Gene Family in Magnoliids: Insights into the Evolution of Floral Morphogenesis in Angiosperms.Plants (Basel, Switzerland) · 2025Article
- Chromosome-scale genome assembly of Sauvagesia rhodoleuca (Ochnaceae) provides insights into its genome evolution and demographic history.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- A near-gapless genome assembly of Pseudocydonia sinensis uncovers unique phenylpropanoid pathways.Plant biotechnology journal · 2025Article
- Targeted deletions of large syntenic regions inProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Teasing apart the sources of phylogenetic tree discordance across three genomes in the oak family (Fagaceae).BMC plant biology · 2025Article
- Article
- Uncertainty in the timing of diversification of flowering plants rests with equivocal interpretation of their fossil record.Royal Society open science · 2025Article
6 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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