Haplotype-resolved genome of Citrus × sinensis ‘Pera IAC’, the most widely cultivated sweet orange in Brazil

A chromosome-scale, haplotype-resolved genome assembly is reported for Citrus × sinensis 'Pera IAC', the most widely cultivated sweet orange in Brazil and a major contributor to global orange juice production. Leveraging PacBio Revio HiFi and Arima Hi-C sequencing, both parental haplotypes were reconstructed into nine chromosome-scale assemblies each (2n = 18), with telomeric repeats detected at multiple chromosome ends, capturing contributions of its ancestral progenitors, C. maxima (pummelo) and C. reticulata (mandarin). The assembly spans ~620 Mb, with 99.9% BUSCO completeness, and provides comprehensive structural and functional annotation (58,171 predicted gene models and 67,796 CDS including isoforms; ~51% transposable elements). Complete chloroplast and mitochondrial circular genomes were also assembled, expanding the genomic resources for citrus. Technical validation included BUSCO, LTR Assembly Index, Inspector, and Merqury analyses, all supporting the accuracy and completeness of the assembly. Synteny analyses and genetic map anchoring further confirmed the structural integrity and chromosome phasing. All datasets are publicly available, providing a robust reference for allele-aware analyses, comparative genomics, and the development of improved sweet orange cultivars.