An Exploration into Fern Genome Space.

Journal Article

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.

Full Text

Duke Authors

Cited Authors

  • Wolf, PG; Sessa, EB; Marchant, DB; Li, F-W; Rothfels, CJ; Sigel, EM; Gitzendanner, MA; Visger, CJ; Banks, JA; Soltis, DE; Soltis, PS; Pryer, KM; Der, JP

Published Date

  • September 2015

Published In

Volume / Issue

  • 7 / 9

Start / End Page

  • 2533 - 2544

PubMed ID

  • 26311176

Electronic International Standard Serial Number (EISSN)

  • 1759-6653

International Standard Serial Number (ISSN)

  • 1759-6653

Digital Object Identifier (DOI)

  • 10.1093/gbe/evv163

Language

  • eng