Developing Asparagaceae1726: An Asparagaceae‐specific probe set targeting 1726 loci for Hyb‐Seq and phylogenomics in the family

• Published in: Applications in plant sciences Vol. 12; no. 5; pp. e11597 - n/a
• Main Authors: Bentz, Philip C., Leebens‐Mack, Jim
• Format: Journal Article
• Language: English
• Published: United States John Wiley & Sons, Inc 01.09.2024; Botanical Society of America; John Wiley and Sons Inc; Wiley
• Subjects: Application; Asparagaceae; Bycatch; Conserved sequence; cost effectiveness; Datasets; Design; DNA probes; family; Gene loci; Genomes; genomics; Hyb‐Seq; lineage‐specific target sequence capture probe set; Nucleotide sequence; Phylogenetics; phylogenomics; Plant Sciences; Radiation; RNA; RNA probes; Taxonomy; topology; Vegetables; Asparagaceae; Hyb‐Seq; phylogenomics; lineage‐specific target sequence capture probe set
• ISSN: 2168-0450; 2168-0450
• DOI: 10.1002/aps3.11597

Premise Target sequence capture (Hyb‐Seq) is a cost‐effective sequencing strategy that employs RNA probes to enrich for specific genomic sequences. By targeting conserved low‐copy orthologs, Hyb‐Seq enables efficient phylogenomic investigations. Here, we present Asparagaceae1726—a Hyb‐Seq probe set targeting 1726 low‐copy nuclear genes for phylogenomics in the angiosperm family Asparagaceae—which will aid the often‐challenging delineation and resolution of evolutionary relationships within Asparagaceae. Methods Here we describe and validate the Asparagaceae1726 probe set (https://github.com/bentzpc/Asparagaceae1726) in six of the seven subfamilies of Asparagaceae. We perform phylogenomic analyses with these 1726 loci and evaluate how inclusion of paralogs and bycatch plastome sequences can enhance phylogenomic inference with target‐enriched data sets. Results We recovered at least 82% of target orthologs from all sampled taxa, and phylogenomic analyses resulted in strong support for all subfamilial relationships. Additionally, topology and branch support were congruent between analyses with and without inclusion of target paralogs, suggesting that paralogs had limited effect on phylogenomic inference. Discussion Asparagaceae1726 is effective across the family and enables the generation of robust data sets for phylogenomics of any Asparagaceae taxon. Asparagaceae1726 establishes a standardized set of loci for phylogenomic analysis in Asparagaceae, which we hope will be widely used for extensible and reproducible investigations of diversification in the family.