BACKGROUND AND AIMS: A targeted enrichment NGS approach was used to construct the phylogeny of Amomum Roxb. (Zingiberaceae). Phylogenies based on hundreds of nuclear genes, the whole plastome and the rDNA cistron were compared with an ITS-based phylogeny. Trends in genome size (GS) evolution were examined, chromosomes were counted and the geographical distribution of phylogenetic lineages was evaluated. METHODS: In total, 92 accessions of 54 species were analysed. ITS was obtained for 79 accessions, 37 accessions were processed with Hyb-Seq and sequences from 449 nuclear genes, the whole cpDNA, and the rDNA cistron were analysed using concatenation, coalescence and supertree approaches. The evolution of absolute GS was analysed in a phylogenetic and geographical context. The chromosome numbers of 12 accessions were counted. KEY RESULTS: Four groups were recognised in all datasets though their mutual relationships differ among datasets. While group A (A. subulatum and A. petaloideum) is basal to the remaining groups in the nuclear gene phylogeny, in the cpDNA topology it is sister to group B (A. repoeense and related species) and, in the ITS topology, it is sister to group D (the Elettariopsis lineage). The former Elettariopsis makes a monophyletic group. There is an increasing trend in GS during evolution. The largest GS values were found in group D in two tetraploid taxa, A. cinnamomeum and A. aff. biphyllum (both 2n = 96 chromosomes). The rest varied in GS (2C = 3.54-8.78 pg) with a constant chromosome number 2n = 48. There is a weak connection between phylogeny, GS and geography in Amomum. CONCLUSIONS: Amomum consists of four groups, and the former Elettariopsis is monophyletic. Species in this group have the largest GS. Two polyploids were found and GS greatly varied in the rest of Amomum.

Central European Institute of Technology and Faculty of Science Masaryk University Kamenice 5 CZ 625 00 Brno Czech Republic

Department of Botany Faculty of Science Charles University Benátská 2 CZ 128 01 Prague Czech Republic

Department of Botany Faculty of Science Charles University Benátská 2 CZ 128 01 Prague Czech Republic; Department of Vascular Plant Taxonomy Institute of Botany Plant Science and Biodiversity Centre Slovak Academy of Sciences SK 845 23 Bratislava Slovak Republic

Department of Botany National Museum Prague Cirkusová 1840 CZ 193 00 Prague Czech Republic

Herbarium Royal Botanic Garden Edinburgh 20A Inverleith Row Edinburgh EH3 5LR UK

Institute of Botany Czech Academy of Science Zámek 1 CZ 252 43 Průhonice Czech Republic

The Herbarium Singapore Botanic Gardens National Parks Board 1 Cluny Road 259569 Singapore

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Ancient hybridization and repetitive element proliferation in the evolutionary history of the monocot genus Amomum (Zingiberaceae)