An Exploration into Fern Genome Space.
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 articleSubject
chloroplastcomparative genomics
mitochondria
plastome
repeat content
transposons
DNA, Plant
Ferns
Genome Size
Genome, Chloroplast
Genome, Mitochondrial
Genome, Plant
Genomics
Plant Proteins
Repetitive Sequences, Nucleic Acid
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https://hdl.handle.net/10161/10797Published Version (Please cite this version)
10.1093/gbe/evv163Publication 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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