Comparative Analysis of Date Palm (Phoenix dactylifera L.) Mitochondrial Genomics

Date palm (Phoenix dactylifera L.) is a major fruit crop of arid regions, domesticated ~7000 years ago in the Near and Middle East. With the advancement of next-generation sequencing technology, genomic data of date palm have increased rapidly and yielded new insights into this species and its origins. Four P. dactylifera mitochondrial genome assemblies are available in the National Center for Biotechnology Information (NCBI). These mitochondrial genomes are circular double-stranded DNA molecules ranging in size from 585,493 bp (P. dactylifera; MG257490) to 715,120 bp (in cv. Khanezi; MH176159) and their guanine-cytosine (GC) content range is 44.8–45.1%. Their protein-coding sequences are composed of 4.6–5.35% gene content. Repeat analysis of the P. dactylifera mt genomes revealed 20–24 palindromic repeats, about 26–30 forward repeats and 35–49 tandem repeats, respectively. Similarly, a total of 233, 271, 242 and 271 simple sequence repeats (SSRs) were identified in P. dactylifera (unverified cultivars) and cvs. Khanezi, Khalas and Naghal, respectively. Pairwise mt genomic alignment among different P. dactylifera cultivar genomes showed a high degree of synteny. Phylogenetic analysis revealed that the mt genome of P. dactylifera forms one monophyletic clade. Evolutionary analysis based on the mitochondrial genome will help to understand the evolutionary changes of the various date palm cultivars.