Although revisiting the discoveries and implications of genetic variations using phased genomics is critical, such efforts are still lacking. Somatic mutations represent a crucial source of genetic diversity for breeding and are especially remarkable in heterozygous perennial and asexual crops. In this study, we focused on a diploid sweet orange (Citrus sinensis) and constructed a haplotype-resolved genome using high fidelity (HiFi) reads, which revealed 10.6% new sequences. Based on the phased genome, we elucidate significant genetic admixtures and haplotype differences. We developed a somatic detection strategy that reveals hidden somatic mutations overlooked in a single reference genome. We generated a phased somatic variation map by combining high-depth whole-genome sequencing (WGS) data from 87 sweet orange somatic varieties. Notably, we found twice as many somatic mutations relative to a single reference genome. Using these hidden somatic mutations, we separated sweet oranges into seven major clades and provide insight into unprecedented genetic mosaicism and strong positive selection. Furthermore, these phased genomics data indicate that genomic heterozygous variations contribute to allele-specific expression during fruit development. By integrating allelic expression differences and somatic mutations, we identified a somatic mutation that induces increases in fruit size. Applications of phased genomics will lead to powerful approaches for discovering genetic variations and uncovering their effects in highly heterozygous plants. Our data provide insight into the hidden somatic mutation landscape in the sweet orange genome, which will facilitate citrus breeding.

The citrus cultivar ‘Local Juhong’, which has historically been used as a traditional Chinese medicinal material, originated in Yuanjiang County, Hunan Province.Its parental type and genetic background are indistinct as of yet. Morphological observation shows that ‘Local Juhong’ has a slight oblateness in fruit shape, a relatively smooth pericarp, a fine and slightly raised oil vacuole, and an inward concave at the blossom end. The tree form and fruit and leaf morphology of ‘Local Juhong’ are similar to those of ‘Huangpi’ sour orange. To reveal the genetic background of ‘Local Juhong’, 21 citrus accessions were evaluated using nuclear and chloroplast SSR markers and whole-genome SNP information. ‘Local Juhong’ was grouped with mandarins and sub-grouped with ‘Miyagawa Wase’ and ‘Yanxi Wanlu’ in a nuclear SSR analysis, which indicated that its pollen parent might be mandarins. It was closely clustered with orange and pummelo in the chloroplast SSR analysis. The genomic sequence similarity rate of ‘Local Juhong’ with mandarin and pummelo heterozygosity was 70.88%; the main part was the heterozygosity, except for the unknown (19.66%), mandarin (8.73%), and pummelo (3.9%) parts. Thus, ‘Local Juhong’ may be an F₁ hybrid with pummelo as the female parent and mandarin as the male parent, sharing sisterhood with ‘Huangpi’ sour orange.

Background In bayberry cultivation, low yields and poor fruit quality are often linked to insufficient pollen availability and low compatibility for heterogamous pollination. To overcome these challenges and develop high-quality varieties, identifying a consistent source of high-quality, controllable pollen is essential. Main Body: Previous studies have shown that applying certain chemicals can induce the conversion of female flower buds into male flowers in bayberry. In this study, we applied various chemicals to the new shoots of YS bayberry plants to identify compounds that effectively promote male flower formation in female trees. We employed high-throughput techniques, including transcriptomics, to analyze the underlying mechanisms of these agents. Conclusion The results demonstrated that applying uniconazole to the spring shoots of female plants during the critical period of flower bud differentiation (October to November) successfully induced the formation of reproductive male flowers by mid-February of the following year. Transcriptomic analysis revealed that uniconazole reduces gibberellin translocation and levels by regulating the expression of key genes (CJ030_MR4G011967, CJ030_MR4G013737, and CJ030_MR4G006450). This reduction promotes the expression of the MADS-box gene family (CJ030_MR0G004521 and CJ030_MR4G015426), which controls the differentiation of female flower buds into male buds. The male flowers induced by uniconazole produced abundant, high-quality pollen, addressing the issue of heterogamous pollination. This study provides a novel strategy for improving bayberry quality and advancing the breeding of new varieties.