Chloroplast Genome Evolution and Phylogenetic Analysis in Zingiberaceae

The chloroplast genomes of Zingiberaceae exhibit a highly conserved quadripartite architecture comprising a large single-copy region, a small single-copy region and two inverted repeats. Genome sizes typically range from 155 to 165 kb, encoding around 110–113 unique genes that include protein-coding genes, transfer RNAs and ribosomal RNAs. Despite this conservation, lineage-specific expansions or contractions of inverted repeats, shifts at single-copy/inverted-repeat boundaries and variations in simple sequence repeats and long repeats generate hotspots of sequence divergence. Comparative analyses have uncovered genes under positive selection, offering insights into adaptive evolution, while highly variable intergenic regions serve as robust molecular markers. Phylogenomic reconstructions based on whole chloroplast sequences have resolved intergeneric relationships, clarified sectional delimitations within Zingiber, Kaempferia and Alpinia, and provided a framework for taxonomic revision, conservation management and authentication of medicinal species.

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Chloroplast Genome Evolution and Phylogenetic Analysis in Zingiberaceae publication trend

The graph below shows the total number of articles in chloroplast genome evolution and phylogenetic analysis in zingiberaceae across all publications each year (not limited to Nature Index journals).

Technical terms

Quadripartite structure: Organisation of the chloroplast genome into two single-copy regions (LSC, SSC) separated by two inverted repeats (IRs).

Inverted repeat (IR): Two identical or near-identical sequences that stabilise genome structure and influence genome size.

Simple sequence repeat (SSR): Short tandem repeats used as polymorphic markers for population genetics and species identification.

Positive selection: Evolutionary process favouring advantageous mutations, detectable by elevated nonsynonymous substitution rates.

Hotspot region: Genomic segment exhibiting high sequence variability, often targeted for molecular marker development.

Single-nucleotide polymorphism (SNP): A single-base variation used to infer phylogenetic relationships and population structure.

Phylogenetic inference: Reconstruction of evolutionary relationships among taxa using molecular sequence data.

References

1. Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae). BMC Genomics (2023).
2. Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae). BMC Plant Biology (2021).
3. Chloroplast Genome Evolution in Four Montane Zingiberaceae Taxa in China. Frontiers in Plant Science (2022).