Chloroplast DNA analysis in Tunisian date-palm cultivars (Phoenix dactylifera L.): Sequence variations and molecular evolution of trnL (UAA) intron and trnL (UAA) trnF (GAA) intergenic spacer

Abstract

Sequences of trnL intron and trnL–trnF spacer of chloroplast DNA of date palm (Phoenix dactylifera L.) were analyzed to detect polymorphism and elucidate molecular evolution. The size of these non-coding regions ranged from 364 to 397 for the intergenic spacer, from 545 to 591 for the intron and from 897 to 981 base pairs for the combined sequences. The averages of GC-contents were 33.3%, 35.9% and 34.8% in the spacer, the intron and the combined data, respectively. The overall ration of transition/transversion R was of 2.19 for the intergenic spacer, indicating that transitions are more frequent than transversions. Haplotypic and nucleotide diversities showed high level of variation of chloroplast non-coding regions. Phylogenetic trees generated using neighbor joining and maximum parsimony analyses showed two groups. The structure of which is independent of the geographic origin or sex of trees. The observed mismatch distribution of pairwise nucleotide differences for cpDNA differed from the one predicted under a model of expansion, as the shapes of the functions was not unimodal. This deviation was also supported by tests of neutrality, which showed that Tajima's D and Fu's Fs values were mostly negative but always insignificant. These results rejected the hypothesis that there has been recent demographic population growth in this species. We may conclude that date palm chloroplast genome provides a new efficient opportunity to evaluate the genetic diversity and to examine the phylogenetic relationships in this crop.