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Peer-reviewedCC BY 4.0The Plant Journal

Telomere‐to‐telomere genome assembly of the endangered Jacktree (Sinojackia xylocarpa Hu) reveals its centromeric landscape and evolutionary dilemma as a small population

  • Si‐Di Liang1,2
  • Si‐Si Zheng1
  • Lei Wu3
  • Ang Liu3
  • Hong‐Hu Meng4
  • Yun Jiang1
  • Zheng‐Wei Wang1
  • Bin‐Jie Ge1
  • Wen‐Li Zou5
  • Qian Wan5
  • Xi‐Ling Dai2
  • Gregor Kozlowski1,6,7
3 more authors
  • Nai‐Wei Li8
  • Xiao‐Ling Yan1
  • Yi‐Gang Song1
8 affiliations
  1. 1Key Laboratory of National Forestry and Grassland Administration on East China Plant Conservation and Utilization Shanghai Chenshan Botanical Garden Shanghai 201602 China
  2. 2College of Life Sciences Shanghai Normal University Shanghai 200234 China
  3. 3College of Forestry Central South University of Forestry and Technology Changsha 410004 China
  4. 4Applied Research Center for Tropical Plant Conservation & Southeast Asia Biodiversity Research Institute, Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Mengla 656303 China
  5. 5Administration Bureau of Longgan Lake National Nature Reserve Huangmei 435500 Hubei Province China
  6. 6Department of Biology and Botanic Garden University of Fribourg Fribourg Switzerland
  7. 7Natural History Museum Fribourg Fribourg Switzerland
  8. 8Institute of Botany Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat‐Sen) Nanjing 210014 China
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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.

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Cite

BibTeXRIS
BibTeX
@article{liang2026telomeretotelomere,
  title = {{Telomere‐to‐telomere genome assembly of the endangered Jacktree (Sinojackia xylocarpa Hu) reveals its centromeric landscape and evolutionary dilemma as a small population}},
  author = {Si‐Di Liang and Si‐Si Zheng and Lei Wu and Ang Liu and Hong‐Hu Meng and Yun Jiang and Zheng‐Wei Wang and Bin‐Jie Ge and Wen‐Li Zou and Qian Wan and Xi‐Ling Dai and Gregor Kozlowski and Nai‐Wei Li and Xiao‐Ling Yan and Yi‐Gang Song},
  journal = {The Plant Journal},
  year = {2026},
  month = nov,
  doi = {10.1111/tpj.71186},
  url = {https://doi.org/10.1111/tpj.71186},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Telomere‐to‐telomere genome assembly of the endangered Jacktree (Sinojackia xylocarpa Hu) reveals its centromeric landscape and evolutionary dilemma as a small population
AU  - Si‐Di Liang
AU  - Si‐Si Zheng
AU  - Lei Wu
AU  - Ang Liu
AU  - Hong‐Hu Meng
AU  - Yun Jiang
AU  - Zheng‐Wei Wang
AU  - Bin‐Jie Ge
AU  - Wen‐Li Zou
AU  - Qian Wan
AU  - Xi‐Ling Dai
AU  - Gregor Kozlowski
AU  - Nai‐Wei Li
AU  - Xiao‐Ling Yan
AU  - Yi‐Gang Song
PY  - 2026
DA  - 2026/11/04
JO  - The Plant Journal
DO  - 10.1111/tpj.71186
UR  - https://doi.org/10.1111/tpj.71186
AB  - 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.
SN  - 0960-7412
SN  - 1365-313X
ER  -