Nuclear phylogenomics of grasses (Poaceae) supports current classification and reveals repeated reticulation

Grass Phylogeny Working Group 3,; Arthan, W.; Baker, W. J.; Barrett, M. D.; Barrett, R. L.; Bennetzen, J.; Besnard, G.; Bianconi, M. E.; Birch, J. L.; Catalan, P.; Chen, W.; Christenhusz, M.; Christin, P.-A.; Clark, L. G.; Couch, C. A.; Columbus, J. T.; Crayn, D. M.; Davidse, G.; Dunning, L. T.; Duvall, M. R.; Dransfield, S.; Ficinski, S. Z.; Fisher, A. E.; Fjellheim, S.; Forest, F.; Gillespie, L. J.; Hackel, J.; Haevermans, T.; Hodkinson, T. R.; Huang, C.-H.; Huang, W.; Humphreys, A. M.; Jobson, R. W.; Kayombo, C. J.; Kellogg, E. A.; Kimeu, J. M.; Larridon, I.; Letsara, R.; Li, D.-Z.; Liu,

doi:10.1101/2024.05.28.596153

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bioRxiv · 10.1101/2024.05.28.596153

Nuclear phylogenomics of grasses (Poaceae) supports current classification and reveals repeated reticulation

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Abstract

O_LIGrasses (Poaceae) comprise around 11,800 species and are central for human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome-scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a new reference species tree of the family. C_LIO_LIWe inferred a comprehensive species tree of grasses by combining new and published sequences for 331 nuclear genes from genome, transcriptome, target enrichment and shotgun data. Our 1,153-tip tree covers 79% of grass genera (including 21 genera sequenced for the first time) and all but two small tribes. We compared it to a 910-tip plastome tree. C_LIO_LIThe nuclear phylogeny matches that of the plastome at most deep branches, with only a few instances of incongruence. Gene tree-species tree reconciliation suggests that reticulation events occurred repeatedly in the history of grasses. C_LIO_LIWe provide a robust framework for the grass tree of life to support research on grass evolution, including modes of reticulation, and genetic diversity for sustainable agriculture. C_LI

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Grass Phylogeny Working Group 3,, Arthan, W., Baker, W. J., Barrett, M. D., Barrett, R. L., Bennetzen, J., Besnard, G., Bianconi, M. E., Birch, J. L., Catalan, P., Chen, W., Christenhusz, M., Christin, P.-A., Clark, L. G., Couch, C. A., Columbus, J. T., Crayn, D. M., Davidse, G., Dunning, L. T., Duvall, M. R., Dransfield, S., Ficinski, S. Z., Fisher, A. E., Fjellheim, S., Forest, F., Gillespie, L. J., Hackel, J., Haevermans, T., Hodkinson, T. R., Huang, C.-H., Huang, W., Humphreys, A. M., Jobson, R. W., Kayombo, C. J., Kellogg, E. A., Kimeu, J. M., Larridon, I., Letsara, R., Li, D.-Z., Liu,. 2024-06-02. Nuclear phylogenomics of grasses (Poaceae) supports current classification and reveals repeated reticulation. https://doi.org/10.1101/2024.05.28.596153

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