Phylogenetic Analysis of Dioscorea and Related Species

The genus Dioscorea, commonly known as yams, comprises over 600 species of global agronomic and ecological importance. Phylogenetic analyses have progressively clarified relationships within this diverse lineage, revealing deep splits among tropical African, Asian and Atlantic clades. Early efforts relied on plastid loci such as rbcL, matK and trnL-F, which provided coarse resolution of sectional boundaries. Advances in high-throughput sequencing have since enabled whole plastome and low-coverage nuclear data to refine species-level relationships, uncover intraspecific divergence and identify mutation hotspots suitable for DNA barcoding. Comparative plastome studies demonstrate a conserved quadripartite genome architecture across Dioscorea, yet reveal lineage-specific expansions and contractions at inverted repeat boundaries. Integration of plastid phylogenomics with nuclear microsatellite markers has illuminated patterns of regional diversification, domestication and dispersal among cultivated and wild taxa. These insights underpin ongoing efforts in molecular breeding, conservation of wild germplasm and the accurate delimitation of cryptic species within this economically vital genus.

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Phylogenetic Analysis of Dioscorea and Related Species publication trend

The graph below shows the total number of articles in phylogenetic analysis of dioscorea and related species across all publications each year (not limited to Nature Index journals).

Technical terms

Plastome: The complete chloroplast genome of a plant, typically arranged as two inverted repeats separated by large and small single-copy regions.

Simple sequence repeat (SSR): A class of molecular marker consisting of tandemly repeated short DNA motifs, used for assessing genetic diversity and population structure.

Inverted repeat (IR): Two identical sequences in opposite orientation within the plastome that separate single-copy regions and contribute to genome stability.

Hotspot region: A segment of the genome exhibiting elevated levels of nucleotide diversity, often targeted for DNA barcoding or marker development.

Phylogenomic analysis: Reconstruction of evolutionary relationships using genome-scale data, such as entire plastomes or concatenated nuclear gene sets, to improve resolution and support.

References

1. Pan-Plastome of Greater Yam (Dioscorea alata) in China: Intraspecific Genetic Variation, Comparative Genomics, and Phylogenetic Analyses. International Journal of Molecular Sciences (2023).
2. Molecular phylogeny of Dioscorea (Dioscoreaceae) in East and Southeast Asia. Blumea - Biodiversity Evolution and Biogeography of Plants (2013).
3. Low-coverage whole genome sequencing of eleven species/subspecies in Dioscorea sect. Stenophora (Dioscoreaceae): comparative plastome analyses, molecular markers development and phylogenetic inference. Frontiers in Plant Science (2023).
4. Complete Chloroplast Genome of Four Thai Native Dioscorea Species: Structural, Comparative and Phylogenetic Analyses. Genes (2023).