{
  "abstract": "Premise:: Conifers comprise one-sixth of global forests and landscape genomic studies are urgently needed to understand their biology, yet relatively few conifer species have reference genomes. Targeted exon-capture is a practical alternative to whole-genome sequencing, but selecting loci without a reference genome remains a barrier. We developed a multi-tissue reference transcriptome for pi non pine (Pinus edulis) to ask how multi-tissue sampling improves probe design, and what is lost under a conventional single-tissue approach. Methods: We assembled a reference transcriptome from four diploid tissues (needle, phloem, root, vegetative bud) and one haploid tissue (megagametophyte), using the latter as a pseudo-guide. We designed a target-capture probe-set by prioritizing highly expressed P. edulis transcripts and transcripts matching a conifer exon database. Results: We recovered 76% of conserved plant genes with few duplicated transcripts. Filtering yielded 15,664 transcripts totaling 31.4 Mb, ~0.1% of the genome. Tissue-specific expression was substantial: 27.4% of transcripts occurred exclusively in non-needle tissues. Functional annotation confirmed complementary contributions, including seed-desiccation and germination genes from megagametophytes, and defense- and stress-associated genes from roots and phloem. Discussion: We built a transcriptome and efficient probe set using a roadmap suitable for other non-model plants with large genomes; keys to success were prioritizing complementary tissues and using expression-based filtering.",
  "abstract_shown": true,
  "affiliations": [
    "University of California, Berkeley"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "D. S. Macias"
    },
    {
      "name": "E. F. Gyllenhaal"
    },
    {
      "name": "J. A. Kleinkopf"
    },
    {
      "name": "W. T. Pockman"
    },
    {
      "name": "H. E. Marx"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/69ya5c3evrza2.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.05.756810",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.05.756810v1.full",
  "id": "69ya5c3evrza2",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.05.756810v1",
  "language": null,
  "licence": "CC-BY-NC",
  "licence_label": "CC BY-NC",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "genomics"
    ],
    [
      "openalex",
      "1312|Genomics and Phylogenetic Studies"
    ]
  ],
  "openalex": "W7221472477",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.05.756810v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-05",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/69ya5c3evrza2.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:27:10Z",
      "native_id": "10.64898/2026.10.05.756810",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.05.756810v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:genomics",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "A multi-tissue transcriptome strategy for genomic resource development in Pinus edulis",
  "title_text": "A multi-tissue transcriptome strategy for genomic resource development in Pinus edulis",
  "type": "preprint",
  "updated_at": "2026-10-30T12:27:10Z",
  "url": "https://research.draconitic.com/paper/69ya5c3evrza2",
  "venue": "bioRxiv",
  "versions": []
}