A pangenome for cultivated citrus reveals evolutive features during the allopatric phase of their reticulate evolution.
Most modern citrus varieties have arisen from reticulate evolution involving four ancestral taxa: C. medica, C. reticulata, C. micrantha and C. maxima that evolved in allopatry before admixing. The modern varieties representatives of these four species and the horticultural groups resulting from admixing, such as sweet and sour oranges, grapefruits, limes and lemons, constitute fundamental genetic resources to breed new citrus varieties. In such context of reticulate evolution, both genome diversity studies, GWAS analysis and transcriptomic studies should be strongly improved through pangenome approaches.  For the first time we report in this paper de novo assembly in pseudochromosome for C. medica, C. reticulata and C. micrantha. A pangenome for cultivated citrus was implemented from these three genomes and a previously published C.  maxima chromosome scale assembly, integrating the PAV information from resequencing data of 43 accessions representative of the four ancestral species. The four genome assemblies were annotated de novo with Eugene including RNASeq data of the four ancestors as evidences. The comparative analysis of the assembled genomes and the pangenome reveals evolutive features during the allopatric step of the reticulate evolution of cultivated Citrus.