On the universality of target‐enrichment baits for phylogenomic research

Abstract

Capturing conserved genomic elements to shed light on deep evolutionary history is becoming the new gold standard for phylogenomic research. Ultraconserved elements are shared among distantly related organisms, allowing the capture of unpreceded amounts of genomic data of non‐model taxa. An underappreciated consequence of hybrid enrichment methods is the potential of introducing undetected DNA sequences from organisms outside the lineage of interest, facilitated through the high degree of conservation of the target regions. In this in silico study, we quantify ultraconserved loci using a data set of 400 published genomes. We utilized six newly designed UCE bait sets, tailored to various arthropod groups, and screened for shared conserved elements in all 242 currently published arthropod genomes. Additionally, we included a diverse set of other potential contaminating organisms, such as various species of fungi and bacteria. Our results show that specific UCE bait sets can capture genomic elements from vastly divergent lineages, including human DNA. Nonetheless, our in silico modeling demonstrates that sufficiently strict bioinformatic processing parameters effectively filter out unintentionally targeted DNA from taxa other than the focus group. Lastly, we characterize all the 100 most widely shared UCE loci as highly conserved exonic regions. We give practical recommendations to address contamination in data sets generated through targeted‐enrichment.

Sequence capture phylogenomics of historical ethanol‐preserved museum specimens: Unlocking the rest of the vault

“…Bossert and Danforth () demonstrated that some UCE loci are shared across all arthropod UCE probe sets designed to date and correspond to genes with known function. Similarly, the vast majority (>98%) of arachnid UCEs were shown to be exonic in origin and annotated to genes with known functions (Hedin et al, ), making sequence capture of UCEs in arachnids essentially exon capture with the potential sequencing of adjacent intronic regions.…”

“…Other considerations may certainly help locus recovery, including adjustments to the hybridization protocol (Li, Hofreiter, Straube, Corrigan, & Naylor, 2013;Paijmans, Fickel, Courtiol, Hofreiter, & Förster, 2016) and deeper sequencing, particularly for extremely important specimens (e.g., type or rare specimens). Bossert and Danforth (2018) demonstrated that some UCE loci are shared across all arthropod UCE probe sets designed to date and correspond to genes with known function. Similarly, the vast majority (>98%) of arachnid UCEs were shown to be exonic in origin and annotated to genes with known functions , making sequence capture of UCEs in arachnids essentially exon capture with the potential sequencing of adjacent intronic regions.…”

Phylogenomic analysis of the beetle suborder Adephaga with comparison of tailored and generalized ultraconserved element probe performance

“…Cleaned and trimmed reads were inspected for quality using fastqc (Andrews, 2010), then assembled into contigs with spades 3.7.1 (Bankevich et al, 2012). Using phyluce, the Adephaga 2.9Kv1 UCE probes were matched to the assembled contigs with a minimum identity of 82% so as to avoid off-target contaminating sequences (Bossert & Danforth, 2018) and the UCE loci were extracted. Using phyluce, UCE loci were then aligned with mafft 7.215 (Katoh & Standley, 2013) and internally trimmed with gblocks 0.91 (Castresana, 2000;Talavera & Castresana, 2007).…”

Transcriptome‐based target‐enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia)

“…Capitalizing on recent technological advancements, the hybrid capture approach has been steadily gaining traction over the last decade (Bossert & Danforth, 2018; Bragg, Potter, Bi, & Moritz, 2016; Faircloth et al, 2012; Lemmon, Emme, & Lemmon, 2012). Principally, DNA or RNA probes are designed based on conserved sequences within the genome and used to hybridize to these targeted loci in a DNA library that are subsequently enriched and sequenced.…”