Haplotype-resolved genome assembly provides insights into genomic variation and CpSVP-associated peduncle elongation in papaya

Carica papaya L. is a trioecious species with a sex chromosome system and diverse floral morphology, but the genomic basis linking peduncle elongation and sex remains unclear. We assembled a haplotype-resolved, chromosome-scale genome for the elite cultivar 'Zhongbai', with only 2-3 gaps per haplotype. Based on gene density and Hi-C data, we annotated centromeres and telomeres and resolved centromeric repeat composition. A multi-tool variant discovery pipeline partitioned variants into tissue culture-associated and transgene integration-associated sets. Comparative genomics revealed a recurrent instability hotspot at the centromeric region of chromosome 5 in transgenic lines, but not in empty-vector controls, implicating transposon-mediated rearrangements during transformation. Overexpression of the papaya SHORT VEGETATIVE PHASE homolog promoted peduncle elongation without altering floral sex. Transcriptomic analysis of long-peduncle transgenic lines showed activation of auxin transport and sensitivity, early auxin response, cell wall remodeling, and light signaling pathways. These findings provide a high-quality reference genome, uncover transformation-induced genomic instability, and establish a mechanistic framework in which CpSVP regulates peduncle growth through the integration of hormone and light signaling--highlighting key targets for molecular breeding in papaya.