Résumé
In P. notatum, apomixis is expressed mainly at the polyploid (tetraploid) level. The trait is controlled by a non-recombinant, hemizygous region, known as the Apomixis Controlling Locus (ACL). Genetic analyses have estimatedthat the ACL spans approximately 36 Mbp and is syntenic to segments of rice chromosomes 2 and 12. Recently,we assembled the genomes of three tetraploid genotypes, the obligate apomictic Q4117, the experimentallyobtained facultative apomictic (highly sexual) Q3664 and the fully sexual Q4188, using a chromosome-levelassembly of a diploid sexual cytotype as a reference. The aim of this study was to resolve the ACL genomicsequence in these plants, identify possible structural variations and annotate its gene contents. To achieve this,ONT long-read sequencing was used to obtain 30x-70x genome coverage for the three genotypes. Several contigscarrying ACL-linked markers identified in the Q4117 de novo assembly were used to create a custom database fortargeted coverage enrichment via ONT adaptive sampling, in which the obligate apomictic tetraploid genotypeQ3775 was included. In addition, the whole assembly of Q4117 was improved using Bionano optical mappingdata. Two ACL-linked scaffolds were reconstructed and aligned against the reference genome. The ACL consistsof a 35-Mb insertion into the pericentromeric region of chromosome 9. Its structure comprises duplicatedfragments from chromosomes 5 and 8 (homeologous to rice chromosomes 2 and 12) arranged in a mosaicpattern associated with repetitive elements, and 1648 intact and fragmented genes. Several of them are relatedto reproduction, growth and development. Comparative analysis showed a high degree of ACL conservation inthe two obligate apomictic genotypes Q4117 and Q3775, while it is absent in Q3664 and Q4188.