Phased genomics reveals hidden somatic mutations and provides insight into fruit development in sweet orange

Abstract

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.

Acknowledgements

This project was supported by the National Key Research and Development Program of China (2022YFF1003100, 2019YFD1001400), the Agricultural Science and Technology Innovation Funds Project of Hunan Province (2022CX127, 2023CX71), and the Natural Science Foundation of Hunan Province (2021JJ40308). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Author contributions

Q.X., N.W., Y.Z. and P.C. conceived and designed the project. N.W. performed the bioinformatics analyses of the genome assembly, somatic mutant, prepared the figures, and coordinated teamwork. P.C. generated genome sequencing data and provided analysis tools. Y.X. collected samples and measured morphological traits, and generated expression data. Y.Z. and Q.X. supervised the bioinformatics analyses. N.W. and Q.X. wrote the manuscript with contributions from H.Y., L.G., X.L., R.M.L., and X.D.

Data availability statement

Data supporting the findings of this work are available within the paper and its supplementary information files. Whole genome sequencing and RNA-seq data are accessible through NCBI under the BioProject ID PRJNA967756. Genome sequences, gene annotations, and somatic mutation maps were uploaded to https://zenodo.org/record/8016647.

Conflict of interest

All authors have declared that no competing interests exist.

Supplementary information

Supplementary data is available at Horticulture Research online.

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