A telomere-to-telomere genome of Manilkara zapota (Chiku) reveals the repeat-mediated genome evolution
- 1Indian Institute of Science Education and Research Bhopal
Abstract
Manilkara zapota (Chiku) is a tropical fruit tree in the Sapotaceae family. In this study, we assembled the first Telomere-to-telomere (T2T) genome assembly of M. zapota, spanning 1.6 Gb with high contiguity (N50 = 134 Mb). Comparative analysis revealed a very recent divergence and a shared WGD among Sapotaceae members. A newly constructed Ancestral Sapotaceae Karyotype (ASK) suggests a fusion-dominated chromosome structure in the family. The genome exhibits lineage-specific proliferation of transposable elements (TEs) accompanied by a recent burst of LTR-Gypsy elements (~0.09 mya). Genome-wide methylation profiling revealed elevated CpG and CHG methylation levels and age-dependent reinforcement of TE silencing, suggesting strong epigenetic regulation that stabilises the repeat-rich genome while maintaining gene expression. Collectively, these findings advance our understanding of repeat-rich genome evolution in plants and provide a valuable framework for genomic-assisted breeding in M. zapota.
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BibTeX
@misc{bisht2026telomeretotelomere,
title = {{A telomere-to-telomere genome of Manilkara zapota (Chiku) reveals the repeat-mediated genome evolution}},
author = {M. S. Bisht and M. Singh and M. A. Puthumana and S. Sharma and V. K. Sharma},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.02.748860},
url = {https://www.biorxiv.org/content/10.64898/2026.09.02.748860v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - A telomere-to-telomere genome of Manilkara zapota (Chiku) reveals the repeat-mediated genome evolution
AU - M. S. Bisht
AU - M. Singh
AU - M. A. Puthumana
AU - S. Sharma
AU - V. K. Sharma
PY - 2026
DA - 2026/09/02
PB - bioRxiv
DO - 10.64898/2026.09.02.748860
UR - https://www.biorxiv.org/content/10.64898/2026.09.02.748860v1
AB - Manilkara zapota (Chiku) is a tropical fruit tree in the Sapotaceae family. In this study, we assembled the first Telomere-to-telomere (T2T) genome assembly of M. zapota, spanning 1.6 Gb with high contiguity (N50 = 134 Mb). Comparative analysis revealed a very recent divergence and a shared WGD among Sapotaceae members. A newly constructed Ancestral Sapotaceae Karyotype (ASK) suggests a fusion-dominated chromosome structure in the family. The genome exhibits lineage-specific proliferation of transposable elements (TEs) accompanied by a recent burst of LTR-Gypsy elements (~0.09 mya). Genome-wide methylation profiling revealed elevated CpG and CHG methylation levels and age-dependent reinforcement of TE silencing, suggesting strong epigenetic regulation that stabilises the repeat-rich genome while maintaining gene expression. Collectively, these findings advance our understanding of repeat-rich genome evolution in plants and provide a valuable framework for genomic-assisted breeding in M. zapota.
ER -