Haplotype-resolved assembly and multi-omics reveal allelic regulation in a Citrus intergeneric hybrid

We generated a haplotype-resolved genome assembly of a Citrus F1 hybrid (C. reticulata × C. australasica) using Nanopore long reads and TellSeq short reads, enabling high-contiguity reconstruction of both parental subgenomes through a trio-binning approach. This assembly supported a multi-omics analysis—combining RNA-seq, whole-genome bisulfite sequencing, and small RNA-seq—at haplotype resolution. Our work provides valuable resources and novel insights into the regulatory architecture of intergeneric hybrids, with direct applications in citrus breeding. The data presented here correspond to the TellSeq reads from the parental genotypes.