Title

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

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.

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

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

Files

README.txt (1 kB)
MD5 67a7118744bbd216f139c3d69404117f

Bait_info.zip (989 kB)
MD5 16283166588cf7ec2eb6c46c532be8cd

genus_code.csv (1 kB)
MD5 ff52cfea9a9a7807abfaebc87937a770

WF_namelist.txt (1 kB)
MD5 04e791930e1a1fa2928f98d5b2d699e0

MYcroarray_raw_reads_Jan2017.zip (6530595 kB)
MD5 610a7e06d1270e8e9a23bfadb033f510

supercontigs.zip (337 kB)
MD5 30eecbeaf0041ed1c22254b8bfbbc485

Target_files.zip (796 kB)
MD5 a16b798326cfad6aae7bfa31e7955382

Fern_SeqCap_Alignments.zip (1595 kB)
MD5 9ba45b1ed8ad5a72a5836fa8f33dee78

misc_scripts.zip (3 kB)
MD5 4d1b64f0a2f2b91586d3f66d008d0172

Trim_and_HybCommands.txt (1 kB)
MD5 90ff997d3278fd5e6c9b51b54ca98ff7

MYbaits-manual-v3.pdf (900 kB)
MD5 7daa2f051170c39e48e85761c9b5c40d

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