Image above: Early morning in Loxahatchee Wildlife Refuge.
invasion -omics
Fertile frond of Lygodium microphyllum. Each fertile frond is capable of releasing thousands of spores!
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Ferns are one of the final frontiers in plant genomics; the first fern genome was published in 2018! We are currently sequencing the genome of the invasive fern Lygodium microphyllum, commonly known as the Old World climbing fern. This invasive species has cost the state of Florida millions of dollars and untold ecological damage to vulnerable ecosystems. We are using a combination of approaches to sequence and assemble the genome of L. microphyllum including short and long-read technologies and chromatin confirmation sequencing. We are working with Fay-Wei Li (Boyce-Thompson Institute/Cornell), Li-Yaung Kuo (National Tsing Hua University), and Trevor Krabbenhoft (University at Buffalo) to sequence this genome. I plan to develop L. microphyllum as a model system for understanding invasive fern biology with the hope of generating resources for applied sciences.
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Relevant Publications:
- Pelosi, J.A., B.A. Zumwalde, O. Hornych, K. Wheatly, E.H. Kim, and E.B. Sessa. Lygodium japonicum (Lygodiaceae) is represented by a tetraploid cytotype in Florida. The American Fern Journal 113(1):43-55
Gametophyte Biology: Natural History to -Omics
Colony of Vittaria appalachiana.
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Strap-like gametophyte of Polytaenium cajense.
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Cordate gametophyte of Lygodium polystachyum.
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All plants undergo an alternation of generations between gametophyte (haploid) and sporophyte (diploid) life phases, and yet these morphologically and functionally disparate phases share a single genome. Understanding the complexities of the genome and gene expression profiles that facilitate these different phases and how these impact application-based science are some of of my main research aims. I am using several systems to explore these differences, including developing Lygodium microphyllum, Dryopteris spp., and Vittaria appalachiana.
The Appalachian gametophyte, Vittaria appalachiana, is one example of a handful of ferns that have lost the sporophyte portion of their life cycle. We are investigating the genomic consequences of complete asexual reproduction and how extant populations are related. Using a combination of approaches (transcriptomics, population genomics), we aim to unravel some of the mysteries remaining around obligate asexual reproduction in ferns.
The Appalachian gametophyte, Vittaria appalachiana, is one example of a handful of ferns that have lost the sporophyte portion of their life cycle. We are investigating the genomic consequences of complete asexual reproduction and how extant populations are related. Using a combination of approaches (transcriptomics, population genomics), we aim to unravel some of the mysteries remaining around obligate asexual reproduction in ferns.
Relevant Publications:
- Pelosi, J.A., W.B. Barbazuk, and E.B. Sessa. Life without a sporophyte: the origins and genomic consequences of asexual reproduction in a gametophyte-only fern. In Press at the International Journal of Plant Sciences.
- Pelosi, J.A., E.S. Sorojsrisom, B.A. Zumwalde, and E.B. Sessa. A genome size for the Appalachian gametophyte. In Press at the American Fern Journal..
- Aros-Mualin, D., C. Flores-Galván, S. Páez, J.A. Pelosi, E.S. Sorojsrisom, N. Yawn, and J.E. Watkins. In situ observations of gametophytes of six fern species of Costa Rica. In Press at The American Fern Journal.
Polyploidy: Patterns and processes
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Polyploidy, or whole genome duplication (WGD) is a prominent force in plant evolution, with nearly one-third of speciation events in ferns associated with a change in ploidy. Our recent work has focused on both ancient (paleopolyploidy) and recent/ongoing (neopolyploidy) WGD events and their placement on the phylogeny. Using a combination of data types, such as transcriptomics, target-capture sequencing, chromosome counts, and flow cytometry, I aim to elucidate the patterns and processes behind polyploidy in ferns. We employ bioinformatic and wet-lab approaches to determine ploidy and generate hypotheses of parentage of these putative polyploids. Work has focused on Asplenium, Lygodium, and the cactus genus Cylindropuntia. On a larger scale, we are interested in the processes that shape genome evolution following polyploidy and the patterns of gene retention that arise as a consequence.
Relevant Publications:
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