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Genome Biol Evol. 2015 Aug 26;7(9):2533-44. doi: 10.1093/gbe/evv163.

An Exploration into Fern Genome Space.

Author information

1
Ecology Center and Department of Biology, Utah State University paul.wolf@usu.edu.
2
Department of Biology, University of Florida Genetics Institute, University of Florida.
3
Department of Biology, University of Florida Genetics Institute, University of Florida Florida Museum of Natural History, University of Florida.
4
Department of Biology, Duke University.
5
University Herbarium and Department of Integrative Biology, University of California, Berkeley.
6
Department of Biology, Duke University Present address: Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia.
7
Department of Botany and Plant Pathology, Purdue University.
8
Genetics Institute, University of Florida Florida Museum of Natural History, University of Florida.
9
Department of Biological Science, California State University, Fullerton.

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.

KEYWORDS:

chloroplast; comparative genomics; mitochondria; plastome; repeat content; transposons

PMID:
26311176
PMCID:
PMC4607520
DOI:
10.1093/gbe/evv163
[Indexed for MEDLINE]
Free PMC Article

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