Abstract Detail


Pelosi, Jessie [1], Kim, Emily [2], Barbazuk, W. Brad [3], Sessa, Emily [1].

Here we go again (and again): repeated rounds of polyploidy and biased gene retention in ferns.

Ferns are the second largest clade of vascular plants with over 10,000 species, yet the generation of genomic resources for the group has lagged behind other major clades of plants. Transcriptomic data have proven to be a powerful tool to assess phylogenetic relationships, using thousands of markers that are largely conserved across the genome, and without the need to sequence entire genomes. We assembled the largest nuclear phylogenetic dataset for ferns to date, including 2884 single-copy nuclear loci from 244 transcriptomes (239 ferns, 5 outgroups), and investigated phylogenetic relationships across the fern tree, the placement of whole genome duplications (WGDs), and gene retention patterns following WGDs. We generated a well-supported phylogeny of ferns and identified several regions of the fern phylogeny that demonstrate high levels of gene treeā€“species tree conflict, which largely correspond to areas of the phylogeny that have been difficult to resolve. Using a combination of approaches, we identified 28 WGDs across the phylogeny, including 19 large-scale events (involving more than one sampled taxon) and 9 small-scale events (involving only one sampled taxon). Most inferred WGDs occur within single lineages (e.g., orders, families) rather than on the backbone of the phylogeny, although two events are shared by leptosporangiate ferns (excluding Osmundales) and Polypodiales (excluding Lindsaeineae and Saccolmatineae), clades which correspond to the majority of fern diversity. We further examined how retained duplicates following WGDs compared across independent events and found that functions of retained genes were largely convergent, with processes involved in binding, responses to stimuli, and certain organelles over-represented in paralogs while processes involved in transport, organelles derived from endosymbiotic events, and signaling were under-represented. To date, our study is the most comprehensive investigation of the nuclear fern phylogeny, though several avenues for future research remain unexplored.

1 - University Of Florida, Biology, 521 Bartram Hall PO Box 118525, Gainesville, FL, 32611, United States
2 - University of Florida , Department of Microbiology and Cell Science, 1355 Museum Dr, Gainesville, FL, 32603, USA
3 - University of Florida, Department of Biology and Genetics Institute, 220 Bartram Hall, Gainesville, FL, 32611, USA

whole genome duplication
biased gene retentionĀ .

Presentation Type: Oral Paper
Number: PTR1005
Abstract ID:49
Candidate for Awards:Edgar T. Wherry award

Copyright © 2000-2022, Botanical Society of America. All rights reserved