Whole-genome sequences confirm Castilleja lassenensis (Orobanchaceae) as a distinct species from Castilleja lemmonii.

Castilleja lassenensis, a species of root-parasitic plants endemic to the Mt. Lassen region in northern California, has been subject to taxonomic debate since its first description in 1940. While morphological and ecological distinctions from its close relative Castilleja lemmonii have been documented, many regional floras do not list C. lassenensis or treat it as a synonym of C. lemmonii. We sequenced the nuclear genomes of C. lassenensis and C. lemmonii and performed comparative genomic analyses including gene content, functional enrichment, and phylogenetic placement. The genome of C. lassenensis, although slightly smaller than that of C. lemmonii, shows higher gene content, with different patterns of gene duplication. Functional genomic analysis revealed distinct enrichment patterns in the two species, with metabolic and transport functions enriched in C. lassenensis versus cellular organization in C. lemmonii. The taxa also show divergence in peptidase and CAZyme distributions, as well as in KAI2d proteins involved in strigolactone perception. Population-level validation using diagnostic gene markers across multiple individuals from geographically separate populations confirmed stable genomic differences. Our results support the recognition of C. lassenensis as a distinct species and underscore the need for measures to ensure its conservation.