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<p>This study leveraged plastome genomics to resolve the evolutionary relationships and clarify the phylogenetic structure among six Egyptian domesticated barley cultivars (<i>Hordeum vulgare</i> subsp. <i>vulgare</i>, Thell.) and their wild progenitor (<i>H. vulgare</i> subsp. <i>spontaneum</i>, K. Koch). Complete chloroplast genomes ranging from 136,460 to 136,462&#xa0;bp were assembled using NOVOPlasty and subjected to comparative genomic analyses encompassing single nucleotide polymorphism (SNP) profiling, simple sequence repeat (SSR) characterization, codon usage bias assessment, and phylogenetic reconstruction. Maximum likelihood phylogenetic reconstruction identified a well-defined evolutionary framework, highlighting the emergence of two discrete lineage divergences among the taxa under investigation, with cultivar G130 exhibiting phylogenetic congruence with the reference plastome (NC_056985.1), while all remaining genotypes constituted a discrete monophyletic assemblage encompassing five domesticated cultivars and the wild subspecies. Chloroplast genomes from six Egyptian barley cultivars and their wild ancestor were examined at 23 loci. Most genotypes showed high heteroplasmy (mean 0.988–0.990, median &gt; 0.998), indicating allelic diversity, while G130 had only three variable sites and near-complete homoplasmy, reflecting plastome uniformity. Relative synonymous codon usage (RSCU) profiling revealed conservation of AT-rich codon preferences between wild and domesticated lineages, reflecting fundamental translational constraints transcending domestication processes. Comparative assessment of three canonical chloroplast barcode markers (<i>trnL</i>, <i>matK</i>, <i>rbcL</i>) demonstrated phylogenetic discrimination capacity of <i>trnL</i> sequences (2377&#xa0;bp), exhibiting the most extensive chromatic diversification patterns. The systematic identification of cultivar-specific molecular markers provides essential tools for barley authentication and quality control applications. This investigation furnishes insights into chloroplast genome evolutionary dynamics throughout the domestication continuum, establishing robust frameworks for optimizing Egyptian barley breeding strategies and germplasm utilization while contributing fundamental knowledge to cereal crop phylogenomics and agricultural genomics applications. (269 words).</p>

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Plastome phylogenomics of egyptian barley: evolution, mutational landscapes, and DNA barcoding

  • 期刊论文

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  • 发表日期：

    2025年12月29日

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  • Abeer Al-Andal

摘要

This study leveraged plastome genomics to resolve the evolutionary relationships and clarify the phylogenetic structure among six Egyptian domesticated barley cultivars (Hordeum vulgare subsp. vulgare, Thell.) and their wild progenitor (H. vulgare subsp. spontaneum, K. Koch). Complete chloroplast genomes ranging from 136,460 to 136,462 bp were assembled using NOVOPlasty and subjected to comparative genomic analyses encompassing single nucleotide polymorphism (SNP) profiling, simple sequence repeat (SSR) characterization, codon usage bias assessment, and phylogenetic reconstruction. Maximum likelihood phylogenetic reconstruction identified a well-defined evolutionary framework, highlighting the emergence of two discrete lineage divergences among the taxa under investigation, with cultivar G130 exhibiting phylogenetic congruence with the reference plastome (NC_056985.1), while all remaining genotypes constituted a discrete monophyletic assemblage encompassing five domesticated cultivars and the wild subspecies. Chloroplast genomes from six Egyptian barley cultivars and their wild ancestor were examined at 23 loci. Most genotypes showed high heteroplasmy (mean 0.988–0.990, median > 0.998), indicating allelic diversity, while G130 had only three variable sites and near-complete homoplasmy, reflecting plastome uniformity. Relative synonymous codon usage (RSCU) profiling revealed conservation of AT-rich codon preferences between wild and domesticated lineages, reflecting fundamental translational constraints transcending domestication processes. Comparative assessment of three canonical chloroplast barcode markers (trnL, matK, rbcL) demonstrated phylogenetic discrimination capacity of trnL sequences (2377 bp), exhibiting the most extensive chromatic diversification patterns. The systematic identification of cultivar-specific molecular markers provides essential tools for barley authentication and quality control applications. This investigation furnishes insights into chloroplast genome evolutionary dynamics throughout the domestication continuum, establishing robust frameworks for optimizing Egyptian barley breeding strategies and germplasm utilization while contributing fundamental knowledge to cereal crop phylogenomics and agricultural genomics applications. (269 words).