Characterizing the structural variations in the genome of the mandarin variety, IrM2, induced by gamma irradiation

Fruits with few or no seeds are favoured by consumers because they provide an improved eating experience alongside other important quality traits such as taste and shelf-life. Gamma irradiation has been widely used to induce favourable trait changes in plants, including a reduction in seediness. For this reason, it has been extremely important in the development of new commercial citrus cultivars. The variety IrM2 is a mutant derived from the mandarin variety, Murcott, by gamma irradiation. IrM2 has improved consumer and economic appeal due to its earlier fruit maturity time, low number of seeds and improved external skin colour compared with its progenitor. Here, we developed high-quality, haplotype-resolved genomes for Murcott and IrM2, using PacBio HiFi and Hi-C sequencing. The assemblies ranged from 329 to 344 Mb, with N50s of more than 30 Mb, and more than 98% assembly and annotation completeness for the four haplotypes. Duplications, inversions, translocations and INDELs were the predominant types of mutations found in IrM2. Two large heterozygous inversions (3.1 Mb in Chr3 and 8.6 Mb in Chr6) and one large heterozygous, non-reciprocal translocation (between Chr3 and Chr6) were prominent in IrM2 and may be the causes of the reduced seeds. Variations such as insertions and deletions were also found, resulting in additions and loss of genes in IrM2. The genes lost in IrM2 were associated with many processes, including hormone signalling, flowering, DNA transcription, reproduction, gene expression and transmembrane transport. These high-quality genomes contribute to a deeper understanding of how irradiation affects plant genomes.