Pezzi, P. H. | bioRxiv Science

bioRxiv2026

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. 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.

genomics↗

bioRxiv2025

'Dispersification' of Agalinis (Orobanchaceae) into South America is associated with hummingbird pollination and perennial life history shifts

AimSeveral mechanisms contribute to the plant biodiversity of the Neotropics, with the highlands of South America serving as important hotspots of diversity. In particular, the Brazilian highlands exhibit high biodiversity due to complex diversification dynamics and a mixture of contributions from different biomes. In this study, we reconstruct the timing and potential triggers of diversification of Agalinis, hemiparasitic plants that inhabit open grassland habitats, to investigate their biogeographic history and migration patterns across the Americas. LocationNorth, Central, and South America TaxonAgalinis. MethodsWe reconstructed dated phylogenies of Agalinis using a secondary calibration approach, sampling 73% of the known species, including multiple species from the Andes and Brazilian highlands. We inferred ancestral distributions to understand migration patterns between North and South America and within South America. Additionally, we investigated shifts in diversification rates within the genus and reconstructed ancestral pollination syndrome and life history strategy states. All analyses were performed across a distribution of trees to account for phylogenetic uncertainty. ResultsAgalinis likely originated in southeastern North America during the early Miocene and rapidly diversified, followed by movement into South America in the Late Miocene or Early Pliocene. We propose two possible routes for Agalinis movement into South America: either through the Andes or via the South American lowland grasslands (e.g., Chaco, Pampas, Cerrado, Caatinga, Llanos), using grassland corridors for dispersal within the continent. After its arrival in South American highlands, the clade underwent rapid diversification. State reconstructions indicated that the genus had a bee-pollinated ancestor and that hummingbird pollination evolved only once, with many transitions back to bee pollination. In contrast, the perennial life strategy evolved multiple times within the genus, including at least once in the ancestor of all South American species and twice in the North American species. Main ConclusionsAgalinis likely originated in North America and later migrated to South America, followed by rapid diversification (i.e., dispersification). Thus, Agalinis is a clade that refutes the tropical conservatism hypothesis and the out-of-the-tropics model. Moreover, the dispersal to the Brazilian highlands was from nearby species pools and not from other highland habitats such as the Andes, followed by several in situ speciation events. These high diversification rates were partly associated with Quaternary climatic oscillations, and perennial and hummingbird-pollinated species exhibited higher turnover rates.

plant biology↗