Phylogenetic analysis of Prunus genus using nuclear and chloroplast gene markers as a bioorganic structure profiling

Abstract

Prunus species are known as model species for the family Rosaceae and other woody plants with their small genome size and relatively small life cycle as woody plants. Also Prunus species are economically important plants in the subfamily Amygdaloideae of the Rosaceae have a controversial taxonomic history due to the lack of a phylogenetic framework. Therefore, mapping, classification, determination the genetic structure and characterization of genes as a spesific chemical and fuctional units of nucleic acids and making phylogenetic analysis in these species have important implications. The aim of this study to find any gene markers as a bioorganic – chemical structure profiling to determine genetic diversity of different Prunus species from Iraq by using nuclear and chloroplast DNA markers to evaluate the phylogeny of Prunus. A total of 12 species Prunus subgenus amygdalus were collected from Iraq. Ten gene region markers on both nuclear DNA and chloroplast DNA have been tested to evaluate the genetic variation at their molecular levels by using multiplex PCR with 10 gene region primers and sequence analysis for matK. The name of the gene regions using in this study are ITS (ITS1+ITS2+5.8S coding region), rbcL, matK, rpl16, trnL-trnF, atpB-rbcL, rp136-infA-rps8, trnK-rps16, pbsM-trnD, psbA-trnH. As a result, five different phylogenetic trees were obtained from the gene sequences of the samples and the base sequences were close to each other. The estimated value of the shape parameter for the discrete Gamma Distribution is 0.05. The nucleotide frequencies are A = 29.41%, T/U = 37.37%, C = 17.52%, and G = 15.67%. The nucleotide diversity of the sequence was low with the 0.004113 value. There were 14 different informative base site between the samples. The polymorphism observed was less in agreement with higher level of conservation of the gene regions. The Prunus species from Iraq region were grouped on two closed clusters on the phylogenetic trees.