{
  "abstract": "SUMMARY: The endangered status of many plant species is often attributed to a decline in fitness, which drives a sustained decrease in population size under natural conditions. However, the role of highly repetitive genomic regions in the decline of endangered plants remains poorly understood. Here, we present the gap‐free telomere‐to‐telomere (T2T) reference genome for the endangered Jacktree (Sinojackia xylocarpa Hu). It has a genome size of 961.94 Mb, an N50 of 78.05 Mb, and 36 446 predicted protein‐coding genes. Using CENH3 chromatin immunoprecipitation sequencing (ChIP‐seq), we identified centromeric regions across all 12 chromosomes and revealed that S. xylocarpa centromeres are composed of diverse transposable element (TE) families, with long terminal repeat (LTR) retrotransposons and LINE elements as major components. Notably, the right arm of chromosome 1 exhibited ectopic CENH3 enrichment and a TE accumulation similar to that of centromeric regions, suggesting the formation of a centromere‐like chromatin domain. In addition, we detected inversion polymorphisms and inversion heterozygotes in natural populations, predominantly concentrated on the same chromosomal arm. These features may be associated with meiotic abnormalities. Using a high‐quality T2T genome assembly, we identified a pattern of genomic erosion facing these small populations characterized by local suppression of recombination linked LTR proliferation and by the accumulation of deleterious mutations in DNA repair genes. This genomic erosion creates an evolutionary dilemma that impairs the purging of deleterious alleles, ultimately threatening long‐term adaptability and survival. This study highlights the utility of T2T genome assembly for the conservation of endangered plants.",
  "abstract_shown": true,
  "affiliations": [
    "Key Laboratory of National Forestry and Grassland Administration on East China Plant Conservation and Utilization Shanghai Chenshan Botanical Garden Shanghai 201602 China",
    "College of Life Sciences Shanghai Normal University Shanghai 200234 China",
    "College of Forestry Central South University of Forestry and Technology Changsha 410004 China",
    "Applied Research Center for Tropical Plant Conservation & Southeast Asia Biodiversity Research Institute, Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Mengla 656303 China",
    "Administration Bureau of Longgan Lake National Nature Reserve Huangmei 435500 Hubei Province China",
    "Department of Biology and Botanic Garden University of Fribourg Fribourg Switzerland",
    "Natural History Museum Fribourg Fribourg Switzerland",
    "Institute of Botany Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat‐Sen) Nanjing 210014 China"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 15,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Si‐Di Liang",
      "orcid": "0009-0001-8012-9159"
    },
    {
      "affs": [
        0
      ],
      "name": "Si‐Si Zheng"
    },
    {
      "affs": [
        2
      ],
      "name": "Lei Wu",
      "orcid": "0000-0003-1451-7855"
    },
    {
      "affs": [
        2
      ],
      "name": "Ang Liu",
      "orcid": "0000-0001-6281-7145"
    },
    {
      "affs": [
        3
      ],
      "name": "Hong‐Hu Meng",
      "orcid": "0000-0002-4504-0001"
    },
    {
      "affs": [
        0
      ],
      "name": "Yun Jiang"
    },
    {
      "affs": [
        0
      ],
      "name": "Zheng‐Wei Wang",
      "orcid": "0000-0002-0124-5849"
    },
    {
      "affs": [
        0
      ],
      "name": "Bin‐Jie Ge"
    },
    {
      "affs": [
        4
      ],
      "name": "Wen‐Li Zou"
    },
    {
      "affs": [
        4
      ],
      "name": "Qian Wan"
    },
    {
      "affs": [
        1
      ],
      "name": "Xi‐Ling Dai"
    },
    {
      "affs": [
        0,
        5,
        6
      ],
      "name": "Gregor Kozlowski",
      "orcid": "0000-0003-4856-2005"
    },
    {
      "affs": [
        7
      ],
      "name": "Nai‐Wei Li",
      "orcid": "0009-0004-6262-2646"
    },
    {
      "affs": [
        0
      ],
      "name": "Xiao‐Ling Yan",
      "orcid": "0000-0002-7344-4097"
    },
    {
      "affs": [
        0
      ],
      "name": "Yi‐Gang Song",
      "orcid": "0000-0003-2584-2338"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/9108jewr3nk0q.bib",
  "cited_by": 0,
  "doi": "10.1111/tpj.71186",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13732550/",
  "id": "9108jewr3nk0q",
  "issns": [
    "0960-7412",
    "1365-313X"
  ],
  "landing_url": "https://doi.org/10.1111/tpj.71186",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Original Article"
    ],
    [
      "openalex",
      "1311|Chromosomal and Genetic Variations"
    ]
  ],
  "openalex": "W7225242723",
  "pdf_url": "https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/tpj.71186",
  "pmcid": "PMC13732550",
  "pmid": "42979777",
  "published": "2026-11-04",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/9108jewr3nk0q.ris",
  "sources": [
    {
      "first_seen": "2026-11-08T12:22:31Z",
      "native_id": "PMC13732550",
      "source": "pmc",
      "url": "https://doi.org/10.1111/tpj.71186"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:1311|Chromosomal and Genetic Variations",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Telomere‐to‐telomere genome assembly of the endangered Jacktree (Sinojackia xylocarpa Hu) reveals its centromeric landscape and evolutionary dilemma as a small population",
  "title_text": "Telomere‐to‐telomere genome assembly of the endangered Jacktree (Sinojackia xylocarpa Hu) reveals its centromeric landscape and evolutionary dilemma as a small population",
  "type": "peer-reviewed",
  "updated_at": "2026-11-08T12:22:31Z",
  "url": "https://research.draconitic.com/paper/9108jewr3nk0q",
  "venue": "The Plant Journal",
  "versions": []
}