Fylogenomika, evoluce genomu a dynamika repetitivních elementů v rodu Amomum Roxb. (Zingiberaceae)

Hlavatá, Kristýna

Amomum Roxb. s.l. (black cardamom) is a complicated genus in the ginger family Zingiberaceae (subfamily Alpinioideae) that according to some definitions includes groups of species recognized as separate genera, e.g. genus Elettariopsis Baker. Phylogenetic studies have so far failed to elucidate both the position of Amomum within Alpinioideae and the relationship between Amomum and other genera like Elettariopsis. In this work, Amomum was subjected to a detailed morphological analysis of the largest possible sampling, together with a phylogenetic analysis. Amomum was recircumscribed, Amomum s.s. and three new genera were established, three genera were resurrected, and genus Elettariopsis was merged into Amomum. Meanwhile, new species were described and others epitypified. A well-resolved nuclear-gene phylogeny of Amomum s.s. was obtained using next-generation sequencing (Hyb-Seq) and showed the existence of four clades (A, B, C, D) within the genus. Clade D, the former genus Elettariopsis, was further divided into three subclades (D1-D3). A chloroplast DNA-based phylogeny supported this structure, but additional phylogenies based on ribosomal DNA were incongruent with it, indicating that the frequently used ITS marker and other rDNA markers may not be suitable for reconstructing deeper phylogenetic...

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