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The Amborella Genome and the Evolution of Flowering Plants (2013)

Amborella Genome Project.  2013.  The Amborella Genome and the Evolution of Flowering Plants.   Science 342: DOI: 10.1126/science.1241089

Monocot Systematics and Evolution

(See Google ScholarResearchGate or PubMed for expanded and likely more current publication list)

Selected Publications

Phylogenomic Investigations of Green Plant (Viridiplantae) Diversification

Bratzel, F., Paule, J., Leebens-Mack, J., Leme, E. M. C., Forzza, R. C. C., Koch, M. A. A., Zizka, G. 2023. Target-enrichment sequencing reveals for the first time a well-resolved phylogeny of the core Bromelioideae (family Bromeliaceae). Taxon 72(1): 47-63.

Timilsena, P. R., Wafula, E. K., Barrett, C. F., Ayyampalayam, S., McNeal, J. R., Rentsch, J. D., . . . Leebens-Mack, J., dePamphilis, C. W. 2022. Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes. Frontiers in Plant Science 13: 18 pages.

Thomas, S.K. X. Liu, Z-Y. Du, Y. Dong, A. Cummings, L. Pokorny, Q-Y. Xiang, J.H. Leebens-Mack. 2021. Comprehending the Cornales: Phylogenetic reconstruction of the order using the Angiosperms353 probe set. American Journal of Botany 108(7):1112–1121.

One Thousand Plant Transcriptomes Initiative (194 co-authors including leads Leebens-Mack, J.H., Barker, M. S., Carpenter, E. J., Deyholos, M. K., Gitzendanner, M. A., Graham, S. W, Grosse, I., Li, Z., Melkonian, M., Mirarab, S., Porsch, M., Quint, M., Rensing, S. A., Soltis, D. E., Soltis P.S., Stevenson D. W., Ullrich, K. K., Wickett, N.J., , Wong, G. K.-S.) 2019. One Thousand Plant Transcriptomes Elucidate Green Plant Phylogenomics.  Nature 574:679–685 DOI: 10.1038/s41586-019-1693-2.

Heyduk, K., M.R. McKain, F. Lalani, J. Leebens-Mack. 2016.  Evolution of a CAM anatomy predates the origins of Crassulacean acid metabolism in the Agavoideae (Asparagaceae).  Mol Phylogenet Evol. 105:102-13. doi: 10.1016/j.ympev.2016.08.018.

Origin and Early Diversification of Flowering Plants

Qin, L., Y. Hu, J. Wang, R. Zhao, H. Shan, K. Li, P. Xu, H. Wu, X. Yan, L. Liu, X. Yi, S. Wanke, J. E. Bowers, J. H. Leebens-Mack, C. W. dePamphilis, P. S. Soltis, D. E. Soltis, H. Kong, Y. Jiao 2021. Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome. Nat. Plants 7:1239-1253. DOI: 10.1038/s41477-021-00990-2

Amborella Genome Project.  2013.  The Amborella Genome and the Evolution of Flowering Plants.  Science 342: DOI: 10.1126/science.1241089


Jiao, Y., J. Leebens-Mack, S, Ayyampalayam, J. E. Bowers, M. R McKain, J. McNeal, M. Rolf, D. R Ruzicka, E. Wafula, N. J Wickett, X. Wu, Y. Zhang, J. Wang, Y. Zhang, E. Carpenter, M. K Deyholos, T. M Kutchan, A. S. Chanderbali, P. S. Soltis, D. W. Stevenson, R. McCombie, J. C. Pires, G. Ka-Shu Wong, D. E. Soltis and C. W. dePamphilis. 2012. A genome triplication associated with early diversification of the core eudicots. Genome Biology 13(1):R3. DOI:10.1186/gb-2012-13-1-r3.

Monocot Systematics and Evolution

Timilsena, P. R., Barrett, C. F., Nelson, A. P., Wafula, E. K., Ayyampalayam, S., McNeal, J. R., . . . Leebens-Mack, J, dePamphilis, C. W. 2023. Phylotranscriptomic analyses of mycoheterotrophic monocots show a continuum of convergent evolutionary changes in expressed nuclear genes from three independent nonphotosynthetic lineages. Genome Biol Evol. 15(1)

McKain, M.R., Tang, J.R., Ayyampalayam, S., Davis, J.I., dePamphilis, C.W., Givnish, T.J., Pires, J.C., Stevenson, D.W., Leebens-Mack, J.H. 2016.  A phylogenomic assessment of ancient polyploidy and genome evolution across the poales.  Genome Biology and Evolution. 8 (4): 1150–1164.

Givnish, T.J., Zuluaga, A., Spalink, D., Soto Gomez, M,, Lam, V.K.Y., Saarela, J.M., Sass, C., Iles, W.J.D., de Sousa, D.J.L., Leebens-Mack, J., Pires, J.C., Zomlefer, W.B., Gandolfo, M.A., Davis, J.I., Stevenson, D.W., dePamphilis, C., Specht, C.D., Graham S.W., Barrett, C.F., Ané, C. 2018.  Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots.  American Journal of Botany 105(11):1888-1910

Evolution of Dioecy and Sex Determination in Flowering Plants

Carey S.B., J.T. Lovell, J. Jenkins, J.H. Leebens-Mack, J. Schmutz, M.A. Wilson, A. Harkess. 2022. Representing sex chromosomes in genome assemblies. Cell Genomics 2 (5): 100132, doi: 10.1016/j.xgen.2022.100132.

Käfer, J., A. Bewick, A. Andres-Robin, G. Lapetoule, A. Harkess, J. Caïus, B. Fogliani, G. Gâteblé, P. Ralph, C. W. dePamphilis, F. Picard, C. P. Scutt, G.A.B. Marais, J.H. Leebens-Mack. 2022. A derived ZW chromosome system in Amborella trichopoda, the sister species to all other extant flowering plants. New Phytologist 233(4): 1636-1642.

Harkess, A. K.Huang, R. van der Hulst, B. Tissen, J. L. Caplan, A. Koppula, M. Batish, B.C. Meyers, J. Leebens-Mack. 2020. Sex chromosome evolution via two genes. Plant Cell 32: 1790–1796.

Harkess, A., Zhou, J., Xu, C., Bowers, JE., Hulst, R., Ayyampalayam, S., Mercati, F., Riccardi, P., McKain, MR., Kakrana, A., Tang, H., Ray, J., Groenendijk J., Arikit, S., Mathioni, SM., Nakano, M., Shan, H., Telgmann-Rauber, A., Kanno, A., Yue, Z., Chen, H., Li, Y., Chen, Y., Xu, X., Zhang, Y., Luo, S., Chen, H., Gao, J., Mao, Z., Pires, JC., Luo, M., Kudrna, D., Wing, RA., Meyers, BC., Yi, K., Kong, H., Lavrijsen, P., Sunseri, F., Falavigna, A., Ye, Y., Leebens-Mack, JH., Chen, G.  2017. The asparagus genome sheds light on the origin and evolution of a young Y chromosome. Nature Communications. 8(1):1279. doi:10.1038/s41467-017-01064-8

Harkess, A., Mercati, F., Shan, H.-Y., Sunseri, F., Falavigna, A., Leebens-Mack, J. 2015. Sex-biased gene expression in dioecious garden asparagus (Asparagus officinalis). New Phytologist. 207:883–892.

Plant-Pollinator Coevolution

Mckain, M.R., Mcneal, J.R., Kellar, P.R., Eguiarte, L.E., Pires, J.C., Leebens-Mack, J. 2016. Timing of rapid diversification and convergent origins of active pollination within Agavoideae (Asparagaceae). American Journal of Botany. 103:1717–1729.

Rentsch, J.D., and J. Leebens-Mack. 2014.  Yucca aloifolia (Asparagaceae) opts out of an obligate pollination mutualism. American Journal of Botany. 101(12):2062-2067.

Crassulecean Acid Metabolism and its Impact on Biodiversity

Heyduk, K., McAssey, E.V, Field, R., Leebens-Mack, J.H.. 2023. The Agavoideae: an emergent model clade system for CAM evolutionary biology. Annals of Botany, Advance Access

Heyduk K., McAssey E.V., Leebens-Mack J.H. 2022.  Timing of gene expression and recruitment in independent origins of CAM in the Agavoideae (Asparagaceae). New Phytologist 235(5), 2111-2126 -

Heyduk, K., Ray, J.N., Ayyampalayam, S., Leebens-Mack, J. 2018. Shifts in gene expression profiles are associated with weak and strong Crassulacean acid metabolism. American Journal of Botany. 105, 587–601.

Heyduk, K., Mckain, M.R., Lalani, F., Leebens-Mack, J. 2016. Evolution of a CAM anatomy predates the origins of Crassulacean acid metabolism in the Agavoideae (Asparagaceae). Molecular Phylogenetics and Evolution. 105:102–113.

Ming, R., Vanburen, R., Wai, C.M., Tang, H., Schatz, M.C., Bowers, J.E., Lyons, E., Wang, M.-L., Chen, J., Biggers, E., Zhang, J., Huang, L., Zhang, L., Miao, W., Zhang, J., Ye, Z., Miao, C., Lin, Z., Wang, H., Zhou, H., Yim, W.C., Priest, H.D., Zheng, C., Woodhouse, M., Edger, P.P., Guyot, R., Guo, H.-B., Guo, H., Zheng, G., Singh, R., Sharma, A., Min, X., Zheng, Y., Lee, H., Gurtowski, J., Sedlazeck, F.J., Harkess, A., Mckain, M.R., Liao, Z., Fang, J., Liu, J., Zhang, X., Zhang, Q., Hu, W., Qin, Y., Wang, K., Chen, L.-Y., Shirley, N., Lin, Y.-R., Liu, L.-Y., Hernandez, A.G., Wright, C.L., Bulone, V., Tuskan, G.A., Heath, K., Zee, F., Moore, P.H., Sunkar, R., Leebens-Mack, J.H., Mockler, T., Bennetzen, J.L., Freeling, M., Sankoff, D., Paterson, A.H., Zhu, X., Yang, X., Smith, J.A.C., Cushman, J.C., Paull, R.E., Yu, Q. 2015. The pineapple genome and the evolution of CAM photosynthesis. Nature Genetics. 47, 1435–1442. doi: 10.1038/ng.3435

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