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High quality phased assembly of grape genome offer new opportunities in chimera detection
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Edité par CCSD -
International audience. In perennial plants and especially those propagated through cuttings, several genotypes can coexist in a single individ-ual, thus leading to chimeras. When the variant induces a noticeable phenotype modification, it can lead to a new cultivar. Viticulture already took economic advantage of this natural phenomenon: for instance, the berry skin of 'Pinot gris' derived from 'Pinot noir' by the selection of a chimera. Chimeras could also impact other crucial traits without be-ing visually identified. Periclinal chimera where the variant has entirely colonized a cell layer is the most stable and can be propagated through cuttings. In grapevine, two function-al cell layers are present in leaves, L1 and L2. However, lat-eral roots are formed from the L2 cell layer only. Thus, com-paring DNA sequences of roots and leaves could allow chi-mera detection. In this study we used new generation Hifi long reads sequencing and recent bioinformatics tools ap-plied to 'Merlot' to detect periclinal chimeras. Sequencing of 'Magdeleine Noire des Charentes' and 'Cabernet franc', the parents of 'Merlot', allowed haplotype resolved assem-bly. Pseudomolecules were built with few contigs, in some occasions only one per chromosome. This high resolution allowed haplotype comparison. Annotation from PN40024 was transferred to all pseudomolecules. Through variant de-tection, periclinal chimeras were found on both haplotypes. These results open new perspectives on chimera detection, which is an important resource to improve cultivars through clonal selection or breed new ones. Detailed results will be presented and discussed.
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