DOI: 10.5061/dryad.s3h9r6j
title: Data from: A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering

description: Sequencing of target-enriched libraries is an efficient and cost-effective
 method for obtaining DNA sequence data from hundreds of nuclear loci for
 phylogeny reconstruction. Much of the cost of developing targeted
 sequencing approaches is associated with the generation of preliminary
 data needed for the identification of orthologous loci for probe design.
 In plants, identifying orthologous loci has proven difficult due to a
 large number of whole-genome duplication events, especially in the
 angiosperms (flowering plants). We used multiple sequence alignments from
 over 600 angiosperms for 353 putatively single-copy protein-coding genes
 identified by the One Thousand Plant Transcriptomes Initiative to design a
 set of targeted sequencing probes for phylogenetic studies of any
 angiosperm group. To maximize the phylogenetic potential of the probes
 while minimizing the cost of production, we introduce a k-medoids
 clustering approach to identify the minimum number of sequences necessary
 to represent each coding sequence in the final probe set. Using this
 method, five to 15 representative sequences were selected per orthologous
 locus, representing the sequence diversity of angiosperms more efficiently
 than if probes were designed using available sequenced genomes alone. To
 test our approximately 80,000 probes, we hybridized libraries from 42
 species spanning all higher-order groups of angiosperms, with a focus on
 taxa not present in the sequence alignments used to design the probes. Out
 of a possible 353 coding sequences, we recovered an average of 283 per
 species and at least 100 in all species. Differences among taxa in
 sequence recovery could not be explained by relatedness to the
 representative taxa selected for probe design, suggesting that there is no
 phylogenetic bias in the probe set. Our probe set, which targeted 260 kbp
 of coding sequence, achieved a median recovery of 137 kbp per taxon in
 coding regions, a maximum recovery of 250 kbp, and an additional median of
 212 kbp per taxon in flanking non-coding regions across all species. These
 results suggest that the Angiosperms353 probe set described here is
 effective for any group of flowering plants and would be useful for
 phylogenetic studies from the species level to higher-order groups,
 including the entire angiosperm clade itself.
description: Supplemental Table 1:
 Variable Sites in Selected GeneraVariable sites in
 Angiosperms353 genes within the genera Oenothera, Linum, Neurachne, and
 PortulacaVariableSites.xlsxVoucher_tableVoucher table for samples used to test Angiosperm353 dataset.onekp_only_angios_degappedMultiple sequence alignments for genes used in Angiosperms353 probe design (FASTA format). Original alignments contained up to 1400 sequences, which have been reduced to remove non-angiosperms. All gap-only sites have been removed.onekp_only_angios_pdistancePairwise matrices of sequence dissimilarity for angiosperm sequences used to design the Angiosperms353 probe set.Angiosperms353_extracted_seqeuences.tarSequences extracted from Angiosperms353 via HybPiper for 42 species of angiosperms. Includes: coding sequences ("exon"), non-coding ("intron") sequences and concatenated coding/non-coding ("supercontig") sequences.SuppFig1_RecoveryVSGenomeSizeSupplemental figure showing the relationship between genome size and gene recovery rate using the Angiosperms353 target capture set on 42 angiosperm species.Angiosperms353 Gene AnnotationsAll genes in the Angiosperms353 target capture set annotated using Arabidopsis orthologs.Supplementary_File_1.tar.gz