Truly the best of both worlds: Merging lineage-specific and universal probe kits to maximize phylogenomic inference.

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Hybridization capture kits are now commonly used for reduced representation approaches in genomic sequencing, with both universal and clade-specific kits available. Here, we present a probe kit targeting 799 low-copy genes for the plant family Annonaceae. This new version of the kit combines the original 469 genes from the previous Annonaceae kit with 334 genes from the universal Angiosperms353 kit. We also compare the results obtained using the original Angiosperms353 kit with our custom approach using a subset of specimens. Parsimony-informative sites and the results of maximum likelihood phylogenetic inference were assessed for combined matrices using the genera Asimina and Deeringothamnus. The Annonaceae799 genes derived from the Angiosperms353 kit have extremely high recovery rates. Off-target reads were also detected. When evaluating size, the proportion of on- and off-target regions, and the number of parsimony-informative sites, the genes incorporated from the Angiosperms353 panel generally outperformed the genes from the original Annonaceae probe kit. We demonstrated that the new sequences from the Angiosperms353 probe set are variable and relevant for future studies on species-level phylogenomics and within-species studies in the Annonaceae. The integration of kits also establishes a connection between projects and makes new genes available for phylogenetic and population studies.