ArticleNature communications2023
Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 50 citations in OpenAlex.
- Chromosome-Level Genome and Organ-Specific Transcriptome of Alnus glutinosa Uncover Lineage-Specific Innovations in Root Nodule Symbiosis.Plant, cell & environment · 2026Article
- Resolving sampling and population-size biases in domestication genomics supports a South Asian origin of walnuts.Genome biology · 2026Article
- Distinct haplotypes and reversed dominance at a single-gene balanced polymorphism controlling heterodichogamy in two genera of wingnuts.Current biology : CB · 2025Article
- Genome duplications, genomic conflict, and rapid phenotypic evolution characterize the Cretaceous radiation of Fagales.Journal of integrative plant biology · 2025Article
- Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss.Genome biology and evolution · 2025Article
- Genome analyses provide insights intoPlant diversity · 2025Article
- Reticulate allopolyploidy and subsequent dysploidy drive evolution and diversification in the cotton family.Nature communications · 2025Article
- Ancient allopolyploidy and specific subgenomic evolution drove the radiation of poplars and willows.Nature communications · 2025Article
- Genetic Mechanisms and Adaptive Benefits of Anthocyanin Red Stigmas in a Wind-Pollinated Tree.Molecular biology and evolution · 2025Article
- Genome Assembly and Winged Fruit Gene Regulation of Chinese Wingnut: Insights from Genomic and Transcriptomic Analyses.Genomics, proteomics & bioinformatics · 2025Article
- Genomic insights into ecological adaptation of oaks revealed by phylogenomic analysis of multiple species.Plant diversity · 2025Article
- Phylotranscriptomic analyses reveal the evolutionary complexity of Paris L. (Melanthiaceae), a morphologically distinctive genus with significant pharmaceutical importance.Annals of botany · 2024Article
- Uncovering ghost introgression through genomic analysis of a distinct eastern Asian hickory species.The Plant journal : for cell and molecular biology · 2024Article
- Plastome evolution of Engelhardia facilitates phylogeny of Juglandaceae.BMC plant biology · 2024Article
- Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information.Systematic biology · 2024Article
- Multi-omics analyses provide insights into the evolutionary history and the synthesis of medicinal components of the Chinese wingnut.Plant diversity · 2024Article
- The promise and pitfalls of synteny in phylogenomics.PLoS biology · 2024Article
- Subgenome-aware analyses reveal the genomic consequences of ancient allopolyploid hybridizations throughout the cotton family.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- A haplotype-resolved genome provides insight into allele-specific expression in wild walnut (Juglans regia L.).Scientific data · 2024Article
- Distinct ancient structural polymorphisms control heterodichogamy in walnuts and hickories.bioRxiv : the preprint server for biology · 2024Article
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7 authors at 2 institutions in 2 countries.
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Abstract
In lineages of allopolyploid origin, sets of homoeologous chromosomes may coexist that differ in gene content and syntenic structure. Presence or absence of genes and microsynteny along chromosomal blocks can serve to differentiate subgenomes and to infer phylogenies. We here apply genome-structural data to infer relationships in an ancient allopolyploid lineage, the walnut family (Juglandaceae), by using seven chromosome-level genomes, two of them newly assembled. Microsynteny and gene-content analyses yield identical topologies that place Platycarya with Engelhardia as did a 1980s morphological-cladistic study. DNA-alignment-based topologies here and in numerous earlier studies instead group Platycarya with Carya and Juglans, perhaps misled by past hybridization. All available data support a hybrid origin of Juglandaceae from extinct or unsampled progenitors nested within, or sister to, Myricaceae. Rhoiptelea chiliantha, sister to all other Juglandaceae, contains proportionally more DNA repair genes and appears to evolve at a rate 2.6- to 3.5-times slower than the remaining species.
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