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U.S.A."],"published-print":{"date-parts":[[2026,5,26]]},"abstract":"<jats:p>Mutations that arise in the shoot apical meristems can become fixed, but typically only in one of the meristem layers. Therefore, in long-lived, clonally propagated species, polymorphic genomes coexist in the form of periclinal chimeras. Given their evolutionary and economic impact, it is critical to understand the dynamics and phenotypic implications of layer-specific variation. Here, we \u03b3-irradiated axillary buds from an elite peppermint clone and obtained 261 independent mutants carrying large indels. We produced a haplotype-aware, high-continuity assembly of this sterile allohexaploid and, using short-read sequencing, detected, on average, six large indels per mutant. Importantly, most of these mutants were periclinal chimeras: comparison of mutation frequency in root (derived solely from the L2\/3 layer) and leaves (which contain cells from all three layers) demonstrated that the indels are confined to either the outer, L1-derived layer, or the inner L2\/3 layers. We observed that the L1 layer was more often mutated, confirming that mutation rate in the shoot apical meristem is potentially optimized to each meristematic layer. To assess whether deletion of a single haplotype in a single meristematic layer could affect plant function, we characterized mutants under field conditions, detecting variation in secondary metabolite production. Two mutants produced an oil with very low (\u2212)-menthol levels, associated with the loss of a single haplotype of the menthone-menthol reductase gene in the epidermal layer. These results highlight the evolutionary relevance of layer-specific genetic variation and present opportunities for improvement of clonally propagated crops that suffer from genetic diversity bottlenecks.<\/jats:p>","DOI":"10.1073\/pnas.2532794123","type":"journal-article","created":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T09:47:42Z","timestamp":1778579262000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":1,"title":["Layer-specific genetic variation unlocks secondary metabolite diversity in long-lived clonal peppermint"],"prefix":"10.1073","volume":"123","author":[{"given":"Nestor","family":"Kippes","sequence":"first","affiliation":[{"name":"Department of Plant Biology and Genome Center, University of California at Davis","place":["Davis"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meric C.","family":"Lieberman","sequence":"additional","affiliation":[{"name":"Department of Plant Biology and 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Lieberman N. Kippes L. Comai I. M. Henry Chromosome-scale assembly of a polyploid mint (Mentha aquatica var citrata 14). Figshare. https:\/\/doi.org\/10.6084\/M9.FIGSHARE.30153271. Deposited 18 September 2025."},{"key":"e_1_3_4_58_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.278090.123"},{"key":"e_1_3_4_59_2","unstructured":"H. Li Aligning sequence reads clone sequences and assembly contigs with BWA-MEM. arXiv [Preprint] (2013). https:\/\/doi.org\/10.48550\/arXiv.1303.3997."},{"key":"e_1_3_4_60_2","doi-asserted-by":"publisher","DOI":"10.14806\/ej.17.1.200"},{"key":"e_1_3_4_61_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts635"},{"key":"e_1_3_4_62_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt656"},{"key":"e_1_3_4_63_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8"},{"key":"e_1_3_4_64_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu638"},{"key":"e_1_3_4_65_2","unstructured":"N. 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