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Journal of Integrative Plant Biology >

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DOI: https://doi.org/10.1111/jipb.13972

Research Article

Nuclear phylogenomics provide evidence to clarify key morphological evolution and whole-genome duplication across rosids

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  • 1. State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Key Laboratory of Herbage & Endemic CropBiology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010000, China

    2. State Key Laboratory of Genetics and Development of Complex Phenotypes, State Key Laboratory of Wetland Conservation andRestoration, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education KeyLaboratory of Biodiversity Sciences and Ecological Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, Schoolof Life Sciences, Fudan University, Shanghai 200438, China

    3. Department of Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, PA 16802, USA

    4. Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China

    5. Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA6. Department of Bioscience, Aarhus University, Aarhus 8000, Denmark

    *Correspondences: Hong Ma (hxm16@psu.edu); Chien‐Hsun Huang (huang_ch@fudan.edu.cn, Dr. Huang is fully responsible for thedistribution of all materials associated with this article)

Received date: 2025-04-28

  Accepted date: 2025-06-21

  Online published: 2025-07-21

Supported by

 This work was sup-ported by funds from the National Natural Science Foundationof China (32270232, 31970224, and 31770242).

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Abstract

Rosids, comprising 90,000–120,000 species, form a large clade of angiosperms, including extensively studied families with many economically and scientifically important plants. They are also ecologically important, dominating many temperate and tropical ecosystems. Great progress in understanding rosid phylogenetic relationships has facilitated evolutionary studies, but phylogenetic uncertainties remain. To construct a more comprehensive nuclear phylogeny with expanded taxon coverage at the familial levels, we generated 203 new transcriptomes and two shotgun genomes. Along with other available data sets, our sample includes 419 eudicots, including 316 rosids, representing 83 families and all 16 rosid orders. Compared to the 1KP study, our highly resolved rosid phylogeny provides strongly supported internal relationships for one additional order and 16 families. We uncovered cytoplasmic-nuclear discordance for several deep rosid relationships with possible evidence of hybridization/gene flow and incomplete lineage sorting. By tracing ancestral states of morphological characters, we revealed putative floral evolutionary trends in some major clades. We detected strong evidence for 27 putative whole-genome duplication (WGD) events distributed across 20 rosid families, including five novel WGDs. Additionally, our expanded taxon sampling allowed for revised phylogenetic positions of several previously reported WGD events. Most of the supported WGDs correspond to origins of families or large subclades and occurred near times of geological and global climate upheavals, including those at the Cretaceous–Paleogene boundary. Our findings support the idea that large-scale genomic changes and key morphological innovations might have contributed to adaptive evolution and increased biodiversity in rosids.

Key words： ancestral character reconstruction; divergence times; nuclear genes; phylogeny; transcriptome sequencing; whole‐genome duplication

Cite this article

Yiyong Zhao, Di Yu, Wenyu Kuo, Jie Huang, Jing Guo, Miao Sun, Yi Hu, Douglas E. Soltis, Pamela S. Soltis, Hong Ma, Chien-Hsun Huang . Nuclear phylogenomics provide evidence to clarify key morphological evolution and whole-genome duplication across rosids[J]. Journal of Integrative Plant Biology, 0 : 1 . DOI: 10.1111/jipb.13972

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