The centromere has a conserved function across eukaryotes; however, the associated DNA sequences exhibit remarkable diversity in both size and structure. In plants, some species possess well-defined centromeres dominated by tandem satellite repeats and centromeric retrotransposons, while others have centromeric regions composed almost entirely of retrotransposons. Using a combination of bioinformatic, molecular, and cytogenetic approaches, we analyzed the centromeric landscape of Humulus lupulus. We identified novel centromeric repeats and characterized two types of centromeric organization. Cytogenetic localization on metaphase chromosomes confirmed the genomic distribution of the major repeats and revealed unique centromeric organization specifically on chromosomes 2, 8, and Y. Two centromeric types are composed of the major repeats SaazCEN and SaazCRM1 (Ty3/Gypsy) which are further accompanied by chromosome-specific centromeric satellites, Saaz40, Saaz293, Saaz85, and HuluTR120. Chromosome 2 displays unbalanced segregation during mitosis and meiosis, implicating an important role for its centromere structure in segregation patterns. Moreover, chromosome 2-specific centromeric repeat Saaz293 is a new marker for studying aneuploidy in hops. Our findings provide new insights into chromosome segregation in hops and highlight the diversity and complexity of the centromere organization in H. lupulus.

Advanced Genomics Center National Institute of Genetics Mishima 411 8540 Shizuoka Japan

Department of Experimental Biology Faculty of Science Masaryk University 62500 Brno Czech Republic

Department of Plant Developmental Genetics Institute of Biophysics of the Czech Academy of Sciences 61200 Brno Czech Republic

Graduate School of Environmental and Life Science Okayama University 1 1 Tsushima naka Kita ku Okayama 700 8530 Japan

Hop Research Institute Co Ltd 43846 Žatec Czech Republic

Institute of Experimental Botany of the Czech Academy of Sciences Centre of Plant Structural and Functional Genomics 77900 Olomouc Czech Republic

Research Institute Suntory Global Innovation Center Ltd 8 1 1 Seikadai Seika Soraku Kyoto 619 0284 Japan

School of Life Science and Technology Institute of Science Tokyo Tokyo 152 8550 Japan

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