WGS resequencing data reveal the Asian and Oceanian citrus diversity

The Citrus genus, under its new definition, encompass numerous Asian and Oceanian true species and a lot of admixed horticultural groups resulting from a complex reticulate evolution. The development of NGS has opened the way for genetic diversity studies based on whole genome information. We performed a wide analysis of citrus germplasm based on WGS resequencing data. 190 accessions representatives of 10 ancestral Asian species, 8 Oceanian species and admixed genotypes were pair-end sequenced (2 x 150 bps) while 21 additional accessions were submitted to TellSeq sequencing. Paired reads of the TellSeq data were joined to the new WGS pair-end data as well as available pair-end data on NCBI. Genotype calling was performed on two chromosome scale genome assemblies (Australian finger lime and Cleopatra mandarin). For Asian citrus, phylogenetic analysis at nuclear and cytoplasmic revealed seven main clades, four of them associating wild and cultivated species. Nine main clades were identified for the Oceanian species. SNP diagnostic of the different ancestral species were identified and allowed to decipher the origin and phylogenomic structure of all admixed accessions. The data reveal high levels of interspecific heterozygosity and strong population structure within the genus, reflecting their complex evolutionary history and hybridization patterns, offering essential tools for downstream applications in citrus breeding, conservation, and evolutionary genomics. The resources generated lay the groundwork for future association studies and the targeted introgression of beneficial traits into cultivated citrus.