CAPITULUM: The International Compositae Alliance Newsletter

What’s all the hype about HybSeq? A brief history and introduction to target enrichment in Compositae

Jennifer Mandel

https://orcid.org/0000-0003-3539-2991

Keywords: Target enrichment, high-throughput sequencing, phylogenomics, phylogenetics

Abstract

HybSeq (target enrichment/sequence capture) has rapidly transformed phylogenetic and phylogenomic inference in Compositae by enabling scalable recovery of hundreds to thousands of nuclear loci from many samples, including challenging tissues such as silica-dried, frozen, and herbarium material. This contribution provides a concise, step-by-step introduction to the HybSeq workflow for systematists new to high-throughput sequencing, placing its adoption in Compositae in historical context and outlining key practical concepts underlying the method. The “Seq” component is summarized from DNA extraction through library preparation, indexing (barcoding) to permit multiplexing, quality control, and short-read sequencing, with emphasis on Illumina platforms and the logic of producing large numbers of reads from fragmented templates. The “Hyb” component is explained as locus-specific enrichment of prepared libraries using biotinylated RNA baits (custom or kit-based) coupled to streptavidin-coated magnetic beads, followed by stringent washes to remove non-target fragments and PCR amplification of the enriched fraction prior to sequencing. Examples from Compositae probe resources (including lineage-specific panels and universal angiosperm kits) illustrate how target capture generates reduced-representation datasets appropriate for resolving relationships across taxonomic scales. By demystifying the laboratory mechanics and conceptual basis of target enrichment, this overview aims to facilitate broader and more effective application of HybSeq in Compositae systematics and comparative evolutionary studies.