Phylogenomics and genome size evolution in Amomum s. s. (Zingiberaceae): Comparison of traditional and modern sequencing methods

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Authors	HLAVATÁ Kristýna LEONG-ŠKORNIČKOVÁ Jana ZÁVESKÁ Eliška ŠÍDA Otakar NEWMAN Mark MALÍK MANDÁKOVÁ Terezie LYSÁK Martin MARHOLD Karol FÉR Tomáš
Year of publication	2023
Type	Article in Periodical
Magazine / Source	Molecular Phylogenetics and Evolution
MU Faculty or unit	Central European Institute of Technology
Citation
Web	https://doi.org/10.1016/j.ympev.2022.107666
Doi	http://dx.doi.org/10.1016/j.ympev.2022.107666
Keywords	Chromosome counts; cpDNA; Elettariopsis; Hyb-Seq; ITS; Polyploidy
Description	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.
Related projects:	e-Infrastruktura CZ