Intraspecific herbarium genomics of Taraxacum apomictic clonal lineages: universal kits capture considerable intraspecific variation
A customised target capture sequencing study was conducted on herbarium and fresh material of several apomictic clonal lineages of dandelions. The purpose of this study was the critical comparison of genotyping accuracy below the species level between loci from universal target capture kits (Angiosperms-353, Compositae-1061) and customised target capture kits (capture of GBS loci; custom selected genes under diversifying selection). The study revealed that customised approaches generate considerably more intraspecific variation than universal approaches, and therefore achieved higher resolution in intraspecific genotyping. However, exons universal kits still capture sufficient intraspecific variation to distinguish closely related genotypes of the same apomictic clonal lineages and can thus be used in high-resolution intraspecific genotyping. Considering the amount of money and time saved when deploying universal kits, this approach is recommended for upscaling in intraspecific herbarium genomics. The raw sequence read data provided in this project was used to conduct this study.
A customised target capture sequencing study was conducted on herbarium and fresh material of several apomictic clonal lineages of dandelions. The purpose of this study was the critical comparison of genotyping accuracy below the species level between loci from universal target capture kits (Angiosperms-353, Compositae-1061) and customised target capture kits (capture of GBS loci; custom selected genes under diversifying selection). The study revealed that customised approaches generate considerably more intraspecific variation than universal approaches, and therefore achieved higher resolution in intraspecific genotyping. However, exons universal kits still capture sufficient intraspecific variation to distinguish closely related genotypes of the same apomictic clonal lineages and can thus be used in high-resolution intraspecific genotyping. Considering the amount of money and time saved when deploying universal kits, this approach is recommended for upscaling in intraspecific herbarium genomics. The raw sequence read data provided in this project was used to conduct this study.