Professional Education


  • Doctor of Philosophy, University of Florida (2018)

All Publications


  • Evolution of rapid blue-light response linked to explosive diversification of ferns in Angiosperm forests. The New phytologist Cai, S., Huang, Y., Chen, F., Zhang, X., Sessa, E., Zhao, C., Marchant, D. B., Xue, D., Chen, G., Dai, F., Leebens-Mack, J. H., Zhang, G., Shabala, S., Christie, J. M., Blatt, M. R., Nevo, E., Soltis, P. S., Soltis, D. E., Franks, P. J., Wu, F., Chen, Z. H. 2020

    Abstract

    Ferns appear in the fossil record some 200 million years before angiosperms. However, as angiosperm-dominated forest canopies emerged in the Cretaceous period there was an explosive diversification of modern (leptosporangiate) ferns, which thrived in low, blue-enhanced light beneath angiosperm canopies. A mechanistic explanation for this transformative event in the diversification of ferns has remained elusive. We used physiological assays, transcriptome analysis and evolutionary bioinformatics to investigate a potential connection between the evolution of enhanced stomatal sensitivity to blue-light in modern ferns and the rise of angiosperm-dominated forests in the geologic record. We demonstrate that members of the largest subclade of leptosporangiate ferns, Polypodiales, have significantly faster stomatal response to blue-light than more ancient fern lineages and a representative angiosperm. We link this higher sensitivity to levels of differentially expressed genes in blue-light signaling, particularly in the cryptochrome (CRY) signaling pathway. Moreover, CRYs of the Polypodiales examined show gene duplication events between 212.9-196.9 and 164.4-151.8 million years ago, when angiosperms were emerging, that are lacking in other major clades of extant land plants. These findings suggest that evolution of stomatal blue-light sensitivity helped modern ferns to exploit the shady habitat beneath angiosperm forest canopies, fueling their Cretaceous hyper-diversification.

    View details for DOI 10.1111/nph.17135

    View details for PubMedID 33280113

  • The C-Fern (Ceratopteris richardii) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly. Scientific reports Marchant, D. B., Sessa, E. B., Wolf, P. G., Heo, K., Barbazuk, W. B., Soltis, P. S., Soltis, D. E. 2019; 9 (1): 18181

    Abstract

    Ferns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of ferns are unclear, largely due to the absence of a sequenced homosporous fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous ferns, but also impeded synthesis of genome evolution across land plants. Here, we used the model fern species Ceratopteris richardii to address the processes (e.g., polyploidy, spread of repeat elements) by which the large genomes and high chromosome numbers typical of homosporous ferns may have evolved and have been maintained. We directly compared repeat compositions in species spanning the green plant tree of life and a diversity of genome sizes, as well as both short- and long-read-based assemblies of Ceratopteris. We found evidence consistent with a single ancient polyploidy event in the evolutionary history of Ceratopteris based on both genomic and cytogenetic data, and on repeat proportions similar to those found in large flowering plant genomes. This study provides a major stepping-stone in the understanding of land plant evolutionary genomics by providing the first homosporous fern reference genome, as well as insights into the processes underlying the formation of these massive genomes.

    View details for DOI 10.1038/s41598-019-53968-8

    View details for PubMedID 31796775