Integrating genomic sequencing resources: an innovative perspective on recycling with universal Angiosperms353 probe sets

Abstract Sequencing strategies have continually advanced, with high-throughput sequencing (HTS) technologies emerging as pivotal tools in plant phylogenomics. As a standard form of target capture sequencing, hybridization target enrichment sequencing (Hyb-seq) is innovative and flexible, and then HTS strategy is widely adopted in phylogenomics. The universal Angiosperms353 probe sets (Angiosperms353) are instrumental in Hyb-seq and have been witnessed increased application in recent years. This review integrates numerous publications and empirical datasets to comprehensively assess the potential applications of Angiosperms353. Through evaluations using 18-taxa and 343-taxa genomic datasets, this review explores potential factors influencing Angiosperms353 gene capture. The RNA-seq strategy yielded the highest number of Angiosperms353 genes, followed by whole-genome sequencing and genome skimming. Increased sequencing depth enhanced gene capture yields, and no evident bias was observed across all tested angiosperm groups. In the genomics era with extensive HTS data, this review provides comprehensive guidelines for the practical application of Angiosperms353, promoting resource recycling and maximizing genomic data sharing and utilization.