title: Association between Chloroplast and Mitochondrial DNA sequences in Chinese Prunus genotypes (Prunus persica, Prunus domestica, and Prunus avium).
abstract: BACKGROUND
  The nuclear DNA is conventionally used to assess the diversity and relatedness among different species, but variations at the DNA genome level has also been used to study the relationship among different organisms. In most species, mitochondrial and chloroplast genomes are inherited maternally; therefore it is anticipated that organelle DNA remains completely associated. Many research studies were conducted simultaneously on organelle genome. The objectives of this study was to analyze the genetic relationship between chloroplast and mitochondrial DNA in three Chinese Prunus genotypes viz., Prunus persica, Prunus domestica, and Prunus avium.
  
  
  RESULTS
  We investigated the genetic diversity of Prunus genotypes using simple sequence repeat (SSR) markers relevant to the chloroplast and mitochondria. Most of the genotypes were genetically similar as revealed by phylogenetic analysis. The Y2 Wu Xing (Cherry) and L2 Hong Xin Li (Plum) genotypes have a high similarity index (0.89), followed by Zi Ye Li (0.85), whereas; L1 Tai Yang Li (plum) has the lowest genetic similarity (0.35). In case of cpSSR, Hong Tao (Peach) and L1 Tai Yang Li (Plum) genotypes demonstrated similarity index of 0.85 and Huang Tao has the lowest similarity index of 0.50. The mtSSR nucleotide sequence analysis revealed that each genotype has similar amplicon length (509 bp) except M5Y1 i.e., 505 bp with CCB256 primer; while in case of NAD6 primer, all genotypes showed different sizes. The MEHO (Peach), MEY1 (Cherry), MEL2 (Plum) and MEL1 (Plum) have 586 bps; while MEY2 (Cherry), MEZI (Plum) and MEHU (Peach) have 585, 584 and 566 bp, respectively. The CCB256 primer showed highly conserved sequences and minute single polymorphic nucleotides with no deletion or mutation. The cpSSR (ARCP511) microsatellites showed the harmonious amplicon length. The CZI (Plum), CHO (Peach) and CL1 (Plum) showed 182 bp; whileCHU (Peach), CY2 (Cherry), CL2 (Plum) and CY1 (Cherry) showed 181 bp amplicon lengths.
  
  
  CONCLUSIONS
  These results demonstrated high conservation in chloroplast and mitochondrial genome among Prunus species during the evolutionary process. These findings are valuable to study the organelle DNA diversity in different species and genotypes of Prunus to provide in depth insight in to the mitochondrial and chloroplast genomes.
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P R China. tariq_bac@yahoo.com.
authors.forename: Tariq
authors.initials: T
authors.lastname: Pervaiz
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P R China. 2012204004@njau.edu.cn.
authors.forename: Xin
authors.initials: X
authors.lastname: Sun
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P R China. 35049635@qq.com.
authors.forename: Yanyi
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P R China. 514467939@qq.com.
authors.forename: Ran
authors.initials: R
authors.lastname: Tao
authors.affiliation: Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Science, Beijing, 100093, P R China. zhung_junhuan@163.com.
authors.forename: Junhuan
authors.initials: J
authors.lastname: Zhang
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P R China. fanggg@njau.edu.cn.
authors.forename: Jinggui
authors.initials: J
authors.lastname: Fang
mesh_terms: D000483:Alleles; D001483:Base Sequence; D018742:DNA, Chloroplast / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics*; D005819:Genetic Markers; D005838:Genotype; D018895:Microsatellite Repeats / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D011110:Polymorphism, Genetic; D027861:Prunus / Q000235:genetics*; D000068220:Prunus avium / Q000235:genetics; D000068242:Prunus domestica / Q000235:genetics; D000068239:Prunus persica / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D018742:DNA, Chloroplast; D004272:DNA, Mitochondrial; D005819:Genetic Markers