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An Exploration into Fern Genome Space.

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Date
2015-08-26
Authors
Wolf, PG
Sessa, EB
Marchant, DB
Li, F
Rothfels, CJ
Sigel, EM
Gitzendanner, MA
Visger, CJ
Banks, JA
Soltis, DE
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Abstract
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.
Type
Journal article
Subject
chloroplast
comparative genomics
mitochondria
plastome
repeat content
transposons
DNA, Plant
Ferns
Genome Size
Genome, Chloroplast
Genome, Mitochondrial
Genome, Plant
Genomics
Plant Proteins
Repetitive Sequences, Nucleic Acid
Permalink
https://hdl.handle.net/10161/10797
Published Version (Please cite this version)
10.1093/gbe/evv163
Publication Info
Wolf, PG; Sessa, EB; Marchant, DB; Li, F; Rothfels, CJ; Sigel, EM; ... Soltis, DE (2015). An Exploration into Fern Genome Space. Genome Biol Evol, 7(9). pp. 2533-2544. 10.1093/gbe/evv163. Retrieved from https://hdl.handle.net/10161/10797.
This is constructed from limited available data and may be imprecise. To cite this article, please review & use the official citation provided by the journal.
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