Chromosome-level reference genome of the beach false foxglove, Agalinis fasciculata (Orobanchaceae)

Abstract

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. The plastid and mitochondrial genomes were also assembled. 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. SignificanceThis high-quality genome is the first chromosome-level assembly for Agalinis, a hemiparasitic genus in the plant family Orobanchaceae. It improves the taxon sampling within Orobanchaceae, representing an important resource for investigating patterns of genome evolution in parasitic lineages. Furthermore, Agalinis has served as a focal genus for studies of the anatomy of haustorial development, and genome annotation incorporated RNA from multiple tissues, enabling the identification of genes expressed in different tissues, including roots and haustoria. This genome also serves as a reference for evolutionary studies of other Agalinis species, many of which are endemic and of conservation concern in North and South America. Overall, the beach false foxglove genome will support studies of the evolutionary history of Agalinis and genome evolution across Orobanchaceae.