Molecular diversity and phylogeny of Tunisian Prunus armeniaca L. by evaluating three candidate barcodes of the chloroplast genome

Abstract Three intergenic spacers ( atp B- rbc L, trn L- trn F and rps 16- trn Q) of chloroplast DNA (cpDNA) considered as candidate DNA barcode markers were used on a total of 42 Tunisian apricot accessions to assess the genetic diversity and phylogenetic structure. A total of 702 variable sites, including 208 singleton variable sites and 492 parsimony informative sites were obtained from the combined cpDNA sequences (2333 bp). Forty-two haplotypes were identified based on the combined fragments. The values of nucleotide diversity ( P i ), and haplotype diversity ( H d ) were 0.049 and 1, respectively. No statistical significance was detected in Tajima’s D and Fu and Li’s tests. The accession 1 F (‘Bedri’) from Kairouan was considered as one of the ancient haplotypes. Four genetic groups were identified in a neighbour-joining tree that are independent from the geographic origin and the mode of propagation of the studied accessions. Overall, the analysis of data sequence revealed that rps 16- trn Q region was the most suitable candidate barcode and gave an overall variation at the interspecies level. This study provides required information to develop strategies of conservation.