Peach chloroplast genome variation architecture and phylogenomic signatures of cpDNA introgression in Prunus

The complete chloroplast genome of peach provides essential information required for the assessment of phylogenetic relationships among Prunus species. Here, we compared the complete chloroplast DNA (cpDNA) genome between two peach cultivars and a wild relative, Prunus mira. The cpDNA genomes of the...

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Bibliographic Details
Published in:Canadian journal of plant science 2019-12, Vol.99 (6), p.885-896
Main Authors: Amar, Mohamed Hamdy, Magdy, Mahmoud, Wang, Lu, Zhou, Hui, Zheng, Beibei, Jiang, Xiaohan, Atta, Aiman H, Han, Yuepeng
Format: Article
Language:English
Subjects:
Chloroplast DNA
Chloroplasts
code à barres de l’ADN
Cultivars
DNA barcoding
Expressed sequence tags
Genetic diversity
Genomes
InDel
introgression
Microsatellites
Nucleotide sequence
Phylogeny
Plant sciences
Prunus
Prunus kansuensis
Prunus mira
Prunus persica
Simple sequence repeats
SNV
Species
SSR
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Summary:The complete chloroplast genome of peach provides essential information required for the assessment of phylogenetic relationships among Prunus species. Here, we compared the complete chloroplast DNA (cpDNA) genome between two peach cultivars and a wild relative, Prunus mira. The cpDNA genomes of the three peach specimens ranged from 157 330 to 157 744 bp in length and all contained 133 genes and 128 intergenic spacer (IGS) regions with an average GC content of 36.8%. The cpDNA genome of peach contained approximately 600 simple sequence repeats (SSRs), with hexa-nucleotide repeats being the most frequent microsatellites. Most SSRs have undergone divergence between cultivated and wild peaches. A total of 331 single nucleotide variants were identified in the cpDNA genomes. Fifty-one multiple-base pair indels were detected, which are mainly responsible for the cpDNA genome size variation. The cpDNA genomes contained 45 hypervariable regions, with 78% in the large single copy region (LSC). Phylogenomic analysis revealed that Prunus persica is more closely related to Prunus kansuensis than to other wild relatives, and a frequency of introgression of the chloroplast genome between Prunus species was deduced. Collectively, various genetic variations in the cpDNA genomes can serve as molecular markers for genomic studies of Prunus species, such as DNA barcoding, phylogeny, and systematics.
ISSN:0008-4220
1918-1833
DOI:10.1139/cjps-2019-0129