Haplotype-phased genome assembly for Ficus carica breeding

The availability of the genome sequence is a fundamental prerequisite to applying modern breeding procedures to crops. It is increasingly important to obtain information on the variations between the two haplotypes, which represent a fundamental resource for studying allele-specific expression. Fig (Ficus carica L.) has great potential for commercial expansion due to its valued nutritional and nutraceutical characteristics, along with its ability to adapt well to harsh environmental conditions. In this work, the fig genome was the starting point to identify intergenic and intragenic structural variations better to understand their impact from a functional point of view. A total of 2,700,243 single nucleotide polymorphisms (SNPs), 1,488,669 insertions/deletions (INDELs), and 8,360 structural variations (SVs) were identified. Overall, intragenomic diversity was estimated to be approximately 0.4%. 540 syntenic regions were identified, corresponding to approximately 95% of the fig genome. Among the syntenic regions, 22,120 gene pairs were considered reliable allelic genes. Of these, 15,927 gene pairs showed genetic mutations, including putative high-impact mutations identified in 5,997 gene pairs. Specifically, a total of 230,612 mutations were identified, divided into 121,028 SNPs (52.48%) and 109,584 INDELs (47.52%). Most of these mutations were identified within intronic regions (42.84%), with the remaining ones located downstream of genes (24.99%), upstream of genes (18.31%), in exonic regions (12.73%), and at splice sites (1.13%). Considering mutations in coding regions, 18,047 missense mutations (54.48%), 14,875 synonymous mutations (44.9%), and 204 nonsense mutations (0.62%) were classified. These genomic resources will be the prerequisite for genome-wide association studies (GWAS) to identify genes linked to traits of agronomic interest and environmental adaptation for use in fig genetic improvement.