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

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.