Evidence map›Paper›PMID 41839682›Full record

ArticleJournal, genetic engineering & biotechnology2026

Structural analysis of clingstone and freestone peach (Prunus persica L.) plastome genome: provides insight into phylogeny and time diversification.

Mokhtar Said Rizk, Alsamman M Alsamman, Heba A M AbdAlla, Mohamed Abd S El Zayat, Ahmed H Hassan, El-Shaimaa Saad El-Demerdash, Mohamed Z S Ahmed, Yuepeng Han, Mohamed Hamdy Amar, Achraf El Allali

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Article in Journal, genetic engineering & biotechnology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

10 authors.

Mokhtar Said RizkGenetic Resources Department, Desert Research Center (DRC), Cairo, Egypt; Laboratory of Genomics and Genome Editing, South Sinai Regional Plant Gene Bank, Desert Research Center, Cairo, 11753, Egypt.
Alsamman M AlsammanDepartment of Genome Mapping, Molecular Genetics and Genome Mapping Laboratory, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Genetic Engineering Research Institute, Giza 12619, Egypt; International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt; Bioinformatics Laboratory, College of Computing, University Mohammed VI Polytechnic, Ben Guerir 43150, Morocco.
Heba A M AbdAllaBotany Department, Agriculture and Biological Institute, National Research Centre, Giza, Egypt.
Mohamed Abd S El ZayatGenetic Resources Department, Desert Research Center (DRC), Cairo, Egypt; Laboratory of Genomics and Genome Editing, South Sinai Regional Plant Gene Bank, Desert Research Center, Cairo, 11753, Egypt.
Ahmed H HassanGenetic Resources Department, Desert Research Center (DRC), Cairo, Egypt; Laboratory of Genomics and Genome Editing, South Sinai Regional Plant Gene Bank, Desert Research Center, Cairo, 11753, Egypt.
El-Shaimaa Saad El-DemerdashGenetic Resources Department, Desert Research Center (DRC), Cairo, Egypt.
Mohamed Z S AhmedGenetic Resources Department, Desert Research Center (DRC), Cairo, Egypt.
Yuepeng HanState Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China.
Mohamed Hamdy AmarLaboratory of Genomics and Genome Editing, South Sinai Regional Plant Gene Bank, Desert Research Center, Cairo, 11753, Egypt.; Center for Converging Sciences and Emerging Technologies (CoSET), Benha National University, El-Obour City, P.O. 11828, Egypt. Electronic address: mohamed.amar@drc.gov.eg.
Achraf El AllaliBioinformatics Laboratory, College of Computing, University Mohammed VI Polytechnic, Ben Guerir 43150, Morocco. Electronic address: achraf.elalalli@um6p.ma.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundThe complete plastome genome of peach represents a valuable genomic resource for elucidating the evolutionary history and phylogenetic relationships within Prunus species.

methodsThis study performed plastome sequencing of two peach cultivars Clingstone (CLS) and Freestone (FRS) along with the wild relative Prunus mira, using the Illumina HiSeq 2500 platform. In this study, the plastomes of two peach cultivars-Clingstone (CLS) and Freestone (FRS)-and the wild relative Prunus mira were sequenced using the Illumina HiSeq 2500 platform. A broad comparative assessment was enabled by comparing these sequences with 22 previously sequenced Prunus plastomes.

resultsAll 25 plastomes exhibited a conserved quadripartite structure, with genome sizes ranging from 157,685 to 158,955 bp and an average GC content of 37.72 %. Structural variations were observed, including gene rearrangements and boundary shifts between the IR, LSC,and Small Single-Copy (SSC) regions. These boundary shifts, together with the identified sequence rearrangements, highlighted potential mutational hotspot regions. Considerable diversity was detected in Simple Sequence Repeats (SSRs), including polymorphic loci with total counts ranging from 559 to 1064 per plastome, comprising mono-, di-, penta-, and hexa-nucleotide motifs.Variable Simple Sequence Repeats (SSRs) and codon usage patterns were identified as evolutionary hotspots. Out of 40 genes, 28 single-copy and 12 multi-copy were consistently found across all plastomes. Such variation patterns underscore regions with high phylogenetic informativeness. Phylogenomic analysis revealed well-supported monophyletic clades, clarifying evolutionary relationships among peach, cherry, and almond groups. Divergence time estimates place the split between cultivated peach (Prunus persica, including CLS and FRS) and P. mira in the Eocene.

conclusionThis comprehensive plastome-based study enriches our understanding of the evolutionary dynamics of peach cultivars, particularly Clingstone and Freestone, in relation to wild Prunus relatives. The identified SSR loci, codon usage features, and structural variations offer potential molecular markers for peach genetic evolution and precise taxonomic resolution at the subspecies level.

Indexed as

ClingstoneDivergence time estimationFreestonePlastome genomePlastome phylogenomicPrunus persicaSimple Sequence Repeats (SSRs)

Identifiers

PMID41839682
PMCPMC12966720

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