Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Six Almond Species (Prunus spp. L.)

• Published in: Scientific reports 2020-06, Vol.10 (1), p.10137-10137, Article 10137
• Main Authors: Wang, Wei, Yang, Tao, Wang, Hui-Ling, Li, Zhen-Jian, Ni, Jian-Wei, Su, Shang, Xu, Xin-Qiao
• Format: Article
• Language: English
• Subjects: 631/181; 631/208; 631/449; Chloroplasts; Evolution; Evolution, Molecular; Genetic diversity; Genetic Variation - genetics; Genome, Chloroplast - genetics; Genomes; Germplasm; Humanities and Social Sciences; multidisciplinary; Mutation; Phylogeny; Prunus; Prunus davidiana; Prunus dulcis; Prunus dulcis - classification; Prunus dulcis - genetics; Prunus kansuensis; Prunus mongolica; Prunus pedunculata; Prunus persica; Prunus tangutica; Prunus tenella; Prunus tomentosa; Prunus triloba; RpoB protein; Science; Science (multidisciplinary); Sequence analysis; Species; Species Specificity
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-67264-3

As a source of genetic variation, almond germplasm resources are of great significance in breeding. To better reveal the mutation characteristics and evolution patterns of the almond chloroplast (cp) genome, the complete cp genomes from six almond species were analyzed. The lengths of the chloroplast genome of the six almond species ranged from 157,783 bp to 158,073 bp. For repeat sequence analysis, 53 pairs of repeats (30 bp or longer) were identified. A total of 117 SSR loci were observed, including 96 polymorphic SSR loci. Nine highly variable regions with a nucleotide variability (Pi) higher than 0.08, including rps16 , rps16 - psbK , atpF - atpH , rpoB , ycf3 - rps4 , rps4 - ndhJ , accD - psaI and rps7 - orf42 (two highly variable regions) were located. Based on the chloroplast genome evolution analysis, three species ( P. tenella , P. pedunculata and P. triloba ) and wild cherry ( P. tomentosa ) were grouped into clade I. Clade II consisted of two species ( P. mongolica and P. tangutica ) and wild peach ( P. davidiana ). Clade III included the common almond ( P. dulcis ), cultivated peach ( P. persica ) and GanSu peach ( P. kansuensis ). This result expands the researchers’ vision of almond plant diversity and promotes an understanding of the evolutionary relationship among almond species. In brief, this study provides abundant resources for the study of the almond chloroplast genome, and has an important reference value for study of the evolution and species identification of almond.