Whole mitochondrial and chloroplast genome sequencing of Tunisian date palm cultivars: diversity and evolutionary relationships

Background Date palm (Phoenix dactylifera L.) is the most widespread crop in arid and semi-arid regions and hasgreat traditional and socioeconomic importance, with its fruit well-known for its high nutritional and health value.However, the genetic variation of date palm cultivars is often neglected. The advent of high-throughput sequencinghas made possible the resequencing of whole organelle (mitochondria and chloroplast) genomes to explore thegenetic diversity and phylogenetic relationships of cultivated plants with unprecedented detail.Results Whole organelle genomes of 171 Tunisian accessions (135 females and 36 males) were sequenced. Targetedbioinformatics pipelines were used to identify date palm haplotypes and genome variants, aiming to provide variantannotation and investigate patterns of evolutionary relationship. Our results revealed the existence of uniquehaplotypes, identified by 45 chloroplastic and 156 mitochondrial SNPs. Estimation of the effect of these SNPs ongenes functions was predicted in silico.Conclusions The results of this study have important implications, in the light of ongoing environmental changes,for the conservation and sustainable use of the genetic resources of date palm cultivars in Tunisia, where monoculturethreatens biodiversity leading to genetic erosion. These data will be useful for breeding and genetic improvementprograms of the date palm through selective cross-breeding.