Astragalean819: An Astragalean clade-specific bait set to resolve phylogenetic relationships in Astragalus

Astragalus (Fabaceae) is the largest genus of flowering plants, with about 3100 species. Most phylogenies of the genus are based on a few nuclear or plastid loci (with one exception that uses ~100 loci) and usually provide poorly resolved trees and even conflicting subgeneric classifications. Target enrichment can greatly improve phylogenetic resolution, even at recently diverged taxonomic units, by generating sequences for hundreds of phylogenetically informative, putative single-copy loci. However, a specific bait set for the Astragalean clade is still lacking.

In this study, we use transcriptome data from 17 species in the Astragalean clade (of which eight are Astragalus) to identify putative single-copy nuclear loci to build a bait set for target enrichment. This resulted in 819 exons from 686 genes across the Astragalean clade. The bait set was validated with a phylogenetic study based on 20 taxa selected across major clades in Astragalus plus three Astragalean species.

We recovered, on average, 739.3 loci covering at least 75% of the corresponding target reference length. The average number of paralog warnings was 76.2, ranging from 12 to 373. Our phylogenetic inference produced full support for all nodes, largely in agreement with the current subgeneric classifications of Astragalus.

Our bait set, Astragalean819, effectively retrieved highly informative loci to build a robust phylogeny that will help to clarify the complex relationships among members of the Astragalean clade and the subgeneric relationships in Astragalus. This study provides a foundation for advancing the understanding of the systematics and evolution of the largest flowering plant genus.