Enrichment Probe Sets Combining Universal and Lineage-Specific Targets Help Resolve Recalcitrant Lineages

Abstract The combination of target capture sequencing (TCS) with low-coverage whole genome sequencing (lcWGS), an approach known as Hyb-Seq, has allowed the integration of natural history collections into the genomics revolution, transforming biodiversity research. To implement Hyb-Seq, a collection of genomic targets, often nuclear orthologs, is needed to design probes for TCS. In flowering plants, the universal Angiosperms353 probe set has been proven resolutive at multiple evolutionary scales, with caveats. Malpighiales is known to be one of the most challenging flowering plant orders to resolve. Within this order, the clusioid clade (∼2.2K species, 94 genera, five families) is no exception. To resolve phylogenetic relationships in this recalcitrant clade, we design a custom probe set, the Clusioids626 kit, composed of 39,936 120-mer probes targeting 626 nuclear orthologs (∼6.6M nucleotides). This probe set includes all Angiosperms353 targets and 273 clusioid-specific ones, carefully chosen taking copy-number, length evenness, and phylo-informativeness into account. We test our probe set on 70 accessions representing all families and tribes in the clusioid clade. On average, 50.4% of TCS reads mapped to our targets, recovering a median of ∼600 orthologs. Relationships for all clusioid families are fully resolved for our nuclear targets. Additionally, 105 plastid coding DNA sequences were retrieved from the lcWGS fraction. A strong cyto-nuclear conflict was detected. The Clusioids626 kit performs better than the universal Angiosperms353 enrichment panel alone. Our kit design workflow can be extended into other lineages for which a universal probe set exists but more resolution is needed.