{
  "abstract": "Castilleja (Orobanchaceae) is a diverse, facultatively hemiparasitic plant genus characterized by a complex evolutionary history of reticulate evolution and significant taxonomic ambiguity. High-quality genomic resources have historically been limited, hindering robust macro-evolutionary and macro-ecological inquiries. Here, we present the first high-quality, phased, chromosome-level reference genome for the diploid species Castilleja foliolosa. Utilizing a hybrid assembly strategy, we integrated long-read PacBio HiFi sequencing with Omni-C proximity ligation data to generate a highly contiguous nuclear assembly, complemented by reconstructed mitochondrial and chloroplastic genomes. The primary nuclear haplotype spans approximately 510 Mbp, containing 39,417 predicted genes and a substantial repetitive landscape covering ~66% of the genome. Our organellar assemblies reveal notable structural complexity: the chloroplast maintains heteroplasmy via two primary structural haplotypes, while the 611 kbp mitogenome adopts a circular master topology existing in two isomeric forms. Comparative genomic analyses demonstrate a largely conserved chromosomal architecture relative to the closely related Pedicularis cranolopha, punctuated by the presence of lineage-specific genes. Functional enrichment of Castilleja-specific orthogroups identifies a consistent association with telomere maintenance, DNA integration, and zinc ion binding, likely stemming from the substantial repeat content. This reference genome provides a robust framework for dissecting the genomic drivers of taxonomic diversification and adaptation within the Orobanchaceae family. This resource significantly enhances our capacity to untangle reticulate evolutionary patterns, offering a definitive foundation for future comparative studies of genome evolution in the Orobanchaceae lineage of parasitic plants.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Botany, California Academy of Sciences, San Francisco, USA"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "name": "R. N. Hamm"
    },
    {
      "name": "J. Leung"
    },
    {
      "name": "M. S. Lo"
    },
    {
      "name": "A. I. Hernandez"
    },
    {
      "affs": [
        0
      ],
      "name": "S. J. Jacobs"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/3s9x43x0j0sgn.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.21.753328",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.21.753328v1.full",
  "id": "3s9x43x0j0sgn",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.21.753328v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "plant biology"
    ],
    [
      "openalex",
      "1110|Chromosomal and Genetic Variations"
    ]
  ],
  "openalex": "W7214032670",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.21.753328v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-21",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/3s9x43x0j0sgn.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:23:57Z",
      "native_id": "10.64898/2026.09.21.753328",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.21.753328v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:plant biology",
      "subfield": "plant-biology"
    }
  ],
  "title": "Phased Chromosome-level Genome and Organellar Assemblies of Castilleja foliolosa Provide Vital Resource for Orobanchaceae Genomics",
  "title_text": "Phased Chromosome-level Genome and Organellar Assemblies of Castilleja foliolosa Provide Vital Resource for Orobanchaceae Genomics",
  "type": "preprint",
  "updated_at": "2026-10-30T12:23:57Z",
  "url": "https://research.draconitic.com/paper/3s9x43x0j0sgn",
  "venue": "bioRxiv",
  "versions": []
}