Chromosome-Level Reference Genome of the Beach False Foxglove, Agalinis fasciculata (Orobanchaceae).

Orobanchaceae is the largest family of parasitic plants, encompassing a full spectrum of parasitic strategies, ranging from autotrophic to holoparasitic. Agalinis is a genus of facultative hemiparasites comprising about 70 species distributed throughout the Americas, including several endemic and rare taxa. Agalinis fasciculata, the beach false foxglove, is a widely distributed species across southeastern North America. Here, we use PacBio HiFi, Omni-C, and RNA-seq data to generate the first high-quality reference genome for the genus. The nuclear genome is 2.29 Gb in size, with most sequences anchored to 14 pseudochromosomes and an N50 of 162 Mb. BUSCO analyses indicate high completeness (98.4%). Structural genome annotation identified 34,133 protein-coding genes and 39,266 transcripts, most of which have at least one functional annotation. We have also assembled the plastid and mitochondrial genomes into complete circular molecules. We further examined genetic diversity and demographic history in A. fasciculata, revealing low genome-wide heterozygosity and evidence of inbreeding. This reference genome is an important resource for understanding the evolutionary history of the genus and the evolutionary patterns of parasitism within Orobanchaceae.