2023
DOI: 10.1038/s41467-023-36247-z
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Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes

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 … Show more

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Cited by 26 publications
(29 citation statements)
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“…An alternative approach may involve utilizing genome-structure information, such as gene order or content, which is more resistant to the effects of gene flow. Incorporating these features into the inference of species tree topologies could provide a promising avenue for overcoming this challenge (Zhao et al 2021;Ding et al 2023).…”
Section: The Promise Of Full-likelihood Methods In Detecting Ghost In...mentioning
confidence: 99%
“…An alternative approach may involve utilizing genome-structure information, such as gene order or content, which is more resistant to the effects of gene flow. Incorporating these features into the inference of species tree topologies could provide a promising avenue for overcoming this challenge (Zhao et al 2021;Ding et al 2023).…”
Section: The Promise Of Full-likelihood Methods In Detecting Ghost In...mentioning
confidence: 99%
“…We find that the divergence between G-locus haplotypes is comparable to the divergence between Juglans and Carya , indicating deep divergence of Juglans G-locus haplotypes, potentially occurring close in time to the split between Juglans and Carya ( ∼ 70 Myr). We used a molecular clock approach with substitution rates estimated from nonsynonymous coding regions in Juglans (Ding et al . 2023; Zhu et al .…”
Section: Methodsmentioning
confidence: 99%
“…We then calculated the divergence time as T = D XY / (2 µ ). Using two reported estimates of the substitution rate ( µ = 1.5 × 10 − 9 per bp per year (Ding et al . 2023), and 2.5 × 10 − 9 per bp per year (Zhu et al .…”
Section: Methodsmentioning
confidence: 99%
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