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A telomere-to-telomere genome of Manilkara zapota (Chiku) reveals the repeat-mediated genome evolution

Bisht, M. S.; Singh, M.; Puthumana, M. A.; Sharma, S.; Sharma, V. K.

2026-09-04 genomics
10.64898/2026.09.02.748860 bioRxiv
Show 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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