Target Sequence Capture of Nuclear-Encoded Genes for Phylogenetic Analysis in Ferns
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.
.fastq, .nexus, .fasta, .txt, .pdf
Utah State Universtiy
Details in paper in Applications in Plant Science (https://doi.org/10.1002/aps3.1148)
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
Biology | Genetics and Genomics
This work is licensed under a Creative Commons Attribution 4.0 License.
Wolf, Paul G.; Robison, Tanner A.; Johnson, Matthew G.; Sundue, Michael A.; Testo, Weston L.; and Rothfels, Carl J., "Target Sequence Capture of Nuclear-Encoded Genes for Phylogenetic Analysis in Ferns" (2017). Browse all Datasets. Paper 34.
FilesREADME.txt (1 kB)
Bait_info.zip (989 kB)
genus_code.csv (1 kB)
WF_namelist.txt (1 kB)
MYcroarray_raw_reads_Jan2017.zip (6530595 kB)
supercontigs.zip (337 kB)
Target_files.zip (796 kB)
Fern_SeqCap_Alignments.zip (1595 kB)
misc_scripts.zip (3 kB)
Trim_and_HybCommands.txt (1 kB)
MYbaits-manual-v3.pdf (900 kB)