Conifers are vital for both ecological and economic reasons, offering valuable insights into land plant evolution. Molecular phylogenetics plays a significant role in studying evolution, but research on conifers using large-scale data from multiple nuclear genes has been limited. Target enrichment sequencing has emerged as a crucial method in phylogenomic studies. However, a specific bait set for conifers is missing. The REMcon probe set targets around 100 single-copy nuclear loci for family- and species-level phylogenetic studies of conifers. High target recovery and read coverage were observed for the REMcon when tested on 69 species, including conifers and other gymnosperm taxa. Phylogenetic analysis based on the DNA sequences generated from REMcon recovered the existing understanding of conifer relationships. The REMcon bait set will be beneficial in generating large-scale nuclear data consistently for any conifer lineage.

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