An Exploration into Fern Genome Space.
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Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (∼0.4X to 2X) for six fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants.
Repetitive Sequences, Nucleic Acid
Published Version (Please cite this version)10.1093/gbe/evv163
Publication InfoBanks, JA; Der, JP; Gitzendanner, MA; Li, FW; Marchant, DB; Pryer, Kathleen M; ... Wolf, PG (2015). An Exploration into Fern Genome Space. Genome Biol Evol, 7(9). pp. 2533-2544. 10.1093/gbe/evv163. Retrieved from http://hdl.handle.net/10161/10797.
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Professor of Biology
My research focuses on understanding the evolutionary relationships of ancient land plants, especially ferns and horsetails, by integrating evidence from morphology, molecules (DNA sequence data from multiple genes), and the fossil record. I use an explicit phylogenetic framework to examine the morphological evolution of various sporophytic and gametophytic characters within vascular plants, and to gain insight into the evolution of various life history traits and the body plans that typ
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