Repository for Asparagaceae1726: a lineage-specific probe set of 1,726 low-copy loci for Hyb-Seq and phylogenomics in the monocot family Asparagaceae

Asparagaceae1726_probes_38581.fa

• Fasta file with 90 nt sequences used to design RNA probes for targeted DNA hybridization/capture
• Contains 38,581 total probes with 2x tiling

Angiosperms353_orthologs_Asparagaceae1726.csv

• List of Asparagaceae1726 targets shared with Angiosperms353

ortholog_target_files

• Directory containing target CDS assemblies for orthologs from Asparagaceae subfamilies Agavoideae, Asparagoideae, Brodiaeoideae, Lomandroideae, Nolinoideae, and Scilloideae
  
  

Asparagaceae1726_DNA_targets_NO_orthologs.fa

• Fasta file containing nucleotide sequences from 1 ortholog for all target loci (reference sequences from Asparagus officinalis or Asparagus setaceus)

Asparagaceae1726_DNA_targets_w_orthologs.fa

• Fasta file containing nucleotide sequences from 1-3 orthologs for all target loci (reference sequences from Asparagus officinalis, Asparagus setaceus, and Yucca aloifolia)

Asparagaceae1726_AA_targets_w_orthologs.fa

• Fasta file containing amino acid sequences from 1-3 orthologs for all target loci (reference sequences from Asparagus officinalis, Asparagus setaceus, and Yucca aloifolia)

Asparagaceae1726 baits can be ordered from Daicel Arbor Biosciences as a "myBaits Predesigned Custom Community Panel" in the "Plants and Fungi" category (Design ID: D10063Aspar): https://arborbiosci.com/products/targeted-ngs/mybaits-predesigned-kits/mybaits-custom-community-panels/plants-and-fungi/#toggle-id-2

Bentz, P.C. and J. Leebens-Mack. (in press). Developing Asparagaceae1726: an Asparagaceae-specific probe set targeting 1,726 loci for Hyb-Seq and phylogenomics in the family. Applications in Plant Sciences.

1. Angiosperms353: https://doi.org/10.1093/sysbio/syy086
2. HybPiper: https://github.com/mossmatters/HybPiper
3. Asparagus officinalis reference sequences: https://doi.org/10.1038/s41467-017-01064-8
4. Asparagus setaceus reference sequences: https://doi.org/10.1038/s41438-020-0271-y
5. Yucca aloifolia reference sequences: https://phytozome-next.jgi.doe.gov/info/YaloifoliaYa24Inoko_v2_1