Phylogenomics and genome size evolution in Amomum s. s. (Zingiberaceae): Comparison of traditional and modern sequencing methods
Language English Country United States Media print-electronic
Document type Journal Article, Research Support, Non-U.S. Gov't
PubMed
36384185
DOI
10.1016/j.ympev.2022.107666
PII: S1055-7903(22)00279-2
Knihovny.cz E-resources
- Keywords
- Chromosome counts, Elettariopsis, Hyb-Seq, ITS, Polyploidy, cpDNA,
- MeSH
- Amomum * genetics MeSH
- Genome Size MeSH
- DNA, Chloroplast MeSH
- DNA, Plant genetics MeSH
- Phylogeny MeSH
- Genome, Plant MeSH
- DNA, Ribosomal genetics MeSH
- Zingiberaceae * genetics MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- DNA, Chloroplast MeSH
- DNA, Plant MeSH
- DNA, Ribosomal MeSH
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.
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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