Phylogenetic Analysis of Grasses (Poaceae)

The grass family, Poaceae, comprises over 11 000 species that underpin global ecosystems and agriculture. Phylogenetic analyses have combined nuclear, plastid and mitochondrial sequence data to reconstruct relationships among its 12 subfamilies, elucidating the deep split between the BOP (Bambusoideae, Oryzoideae, Pooideae) and PACMAD (Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, Danthonioideae) clades. High-throughput sequencing and dense taxon sampling have resolved contentious nodes, clarified the timing of key divergences—often linked to whole-genome duplications and climatic shifts—and traced multiple independent origins of C4 photosynthesis. Plastome and nuclear gene phylogenies reveal patterns of gene retention, loss and transfer, while chloroplast genome assemblies provide detailed markers for barcoding and transplastomic applications. This robust evolutionary framework has informed studies on stress tolerance, invasive lineages and the adaptive significance of anatomical and physiological innovations, with immediate relevance for crop improvement and biodiversity conservation under changing climates.

Research from Nature Portfolio

Recent studies have employed extensive phylogenomic sampling to map whole-genome duplication (WGD) events across all 12 subfamilies. Analyses of 363 grass genomes revealed nine previously unknown WGDs, demonstrated differential retention of duplicate genes linked to environmental adaptation and morphogenesis, and suggested gene flow among bamboo lineages. This work illuminates how genome duplications have fuelled diversification and niche expansion within Poaceae. In parallel, the complete chloroplast genome of a model halophytic grass was assembled using long-read sequencing. Its quadripartite structure and comprehensive gene inventory have refined the placement of this species within the Chloridoideae and PACMAD clade, offering new loci for DNA barcoding and transplastomic research, and enhancing resolution in regions where plastome diversity is low.

Phylogenetic Analysis of Grasses (Poaceae) publication trend

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

Technical terms

Phylogenomics: The integration of genomic-scale data in phylogenetic analyses to infer evolutionary relationships with high resolution.

Whole-genome duplication (WGD): An event in which an organism’s entire set of chromosomes is duplicated, often facilitating gene diversification.

Chloroplast genome (plastome): The circular DNA within plant chloroplasts encoding genes vital for photosynthesis and used extensively in plant systematics.

Polyploidization: The process by which organisms acquire more than two complete sets of chromosomes, leading to polyploid lineages with potential adaptive advantages.

Paralogue: A gene that arises by duplication within a genome and may evolve novel functions or subfunctionalisation.

C3 and C4 photosynthesis: Carbon-fixation pathways in plants; C4 involves an additional biochemical pump that increases efficiency under high light, temperature or low CO₂ conditions.

References

1. Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages. Nature Communications (2024).
2. The newly assembled chloroplast genome of Aeluropus littoralis: molecular feature characterization and phylogenetic analysis with related species. Scientific Reports (2024).
3. Genome-wide analysis tracks the emergence of intraspecific polyploids in Phragmites australis. npj Biodiversity (2024).
4. The low level of plastome differentiation observed in some lineages of Poales hinders molecular species identification. Frontiers in Plant Science (2023).
5. A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C4 photosynthesis. Molecular Plant (2022).