Data from: Target Sequence Capture of Nuclear-Encoded Genes for Phylogenetic Analysis in Ferns

Creators

Paul G. Wolf, Utah State UniversityFollow
Tanner A. Robison, Utah State UniversityFollow
Matthew G. Johnson, Texas Tech UniversityFollow
Michael A. Sundue, University of VermontFollow
Weston L. Testo, University of VermontFollow
Carl J. Rothfels, University of California, BerkeleyFollow

Description

Premise of the study: Until recently, most phylogenetic studies of ferns were based on chloroplast genes. Evolutionary inferences based on these data can be incomplete because the characters are from a single linkage group and are uniparentally inherited. These limitations are particularly acute in studies of hybridization, which is prevalent in ferns; fern hybrids are common and ferns are able to hybridize across highly diverged lineages, up to 60 million years since divergence in one documented case. However, it not yet clear what effect such hybridization has on fern evolution, in part due to a paucity of available biparentally inherited (nuclear-encoded) markers.

Methods: We designed oligonucleotide baits to capture 25 targeted, low-copy nuclear markers from a sample of 24 species spanning extant fern diversity.

Results: Most loci were successfully sequenced from most accessions. Although the baits were designed from exon (transcript) data, we successfully captured intron sequences that should be useful for more focused phylogenetic studies. We present phylogenetic analyses of the new target sequence capture data and integrate these into a previous transcript-based dataset.

Discussion: We make our bait sequences available to the community as a resource for further studies of fern phylogeny.

Author ORCID Identifier

Paul G. Wolf https://orcid.org/ 0000-0002-4317-6976

Tanner A. Robison https://orcid.org/ 0000-0002-1629-9786

Matthew G. Johnson https://orcid.org/ 0000-0002-1958-6334

Michael A. Sundue https://orcid.org/ 0000-0003-1568-150X

Weston L. Testo https://orcid.org/ 0000-0003-3194-5763

Carl J. Rothfels https://orcid.org/ 0000-0002-6605-1770

OCLC

1078403652

Document Type

Dataset

DCMI Type

Dataset

File Format

.fastq, .nexus, .fasta, .txt, .pdf

Viewing Instructions

see README

Publication Date

12-15-2017

Publisher

Utah State Universtiy

Methodology

Details in paper in Applications in Plant Science (https://doi.org/10.1002/aps3.1148)

Referenced by

Wolf, P. G., T. A. Robison, M. G. Johnson, M. A. Sundue, W. L. Testo, and C. J. Rothfels. 2018. Target sequence capture of nuclear‐encoded genes for phylogenetic analysis in ferns. Applications in Plant Sciences 6(5): e1148. https://doi.org/10.1002/aps3.1148

Language

eng

Disciplines

Biology | Genetics and Genomics

License

This work is licensed under a Creative Commons Attribution 4.0 License.

Recommended Citation

Wolf, P. G., Robinson, T. A., Johnson, M. G., Sundue, M. A., Testo, W. L., & Rothfels, C. J. (2017). Data from: Target Sequence Capture of Nuclear-Encoded Genes for Phylogenetic Analysis in Ferns. Utah State University. https://doi.org/10.15142/T3MG95

Checksum

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