Although the evolutionary drivers of genome size change are known, the general patterns and mechanisms of plant genome size evolution are yet to be established. Here we aim to assess the relative importance of proliferation of repetitive DNA, chromosomal variation (including polyploidy), and the type of endoreplication for genome size evolution of the Pleurothallidinae, the most species-rich orchid lineage. Phylogenetic relationships between 341 Pleurothallidinae representatives were refined using a target enrichment hybrid capture combined with high-throughput sequencing approach. Genome size and the type of endoreplication were assessed using flow cytometry supplemented with karyological analysis and low-coverage Illumina sequencing for repeatome analysis on a subset of samples. Data were analyzed using phylogeny-based models. Genome size diversity (0.2-5.1 Gbp) was mostly independent of profound chromosome count variation (2n = 12-90) but tightly linked with the overall content of repetitive DNA elements. Species with partial endoreplication (PE) had significantly greater genome sizes, and genomic repeat content was tightly correlated with the size of the non-endoreplicated part of the genome. In PE species, repetitive DNA is preferentially accumulated in the non-endoreplicated parts of their genomes. Our results demonstrate that proliferation of repetitive DNA elements and PE together shape the patterns of genome size diversity in orchids.

CEITEC Masaryk University Brno CZ 62500 Czech Republic

Department of Botany Faculty of Science Charles University Benátská 2 Prague CZ 12800 Czech Republic

Department of Botany University of Innsbruck Sternwartestraße 15 Innsbruck 6020 Austria

Department of Experimental Plant Biology Faculty of Science Charles University Viničná 5 Prague CZ 12844 Czech Republic

Faculty of Science Masaryk University Brno CZ 62500 Czech Republic

Institute of Botany of the Czech Academy of Sciences Zámek 1 Průhonice CZ 25243 Czech Republic

Prague Botanical Garden Trojská 800 196 Prague CZ 17100 Czech Republic

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