Phylogenetic Analysis of Rosaceae Systematics and Diversity
Summary
The Rosaceae family, comprising nearly 3 000 species and including economically vital fruit crops, ornamentals and timber trees, has long challenged taxonomists due to extensive hybridisation, polyploidy and morphological convergence. Recent advances in molecular phylogenetics, leveraging both nuclear and plastid genomes, have produced well-resolved trees that clarify subfamilial relationships, tribal circumscription and generic boundaries. Whole-genome duplication events uncovered through transcriptomic and genomic data appear to have driven major radiations and fruit-type innovations. Integrative analyses combining chloroplast genomes, nuclear markers and simple sequence repeat loci have refined the circumscription of problematic groups such as Maleae and Prunus, elucidated the origins of cherries and strawberries, and revealed biogeographic patterns linked to climatic and geological history. These phylogenomic frameworks inform the conservation of wild genetic resources, underpin crop-breeding strategies and deepen our understanding of angiosperm diversification.
Research from Nature Portfolio
Recent studies of the genus Filipendula employing complete chloroplast genome sequencing have revealed that, despite a highly conserved gene order and structure, lineage-specific rearrangements, gene losses and variations in simple sequence repeats distinguish Filipendula from other members of the Rosoideae. Identification of mutational hotspots in non-coding regions has yielded robust molecular markers for infrageneric classification. Molecular-dating analyses indicate that Filipendula diverged from related genera around 83 million years ago, with East Asian lineages splitting in the Miocene, providing a phylogenomic foundation for re-evaluating subtribal boundaries within the family.
Phylogenetic Analysis of Rosaceae Systematics and Diversity publication trend
The graph below shows the total number of articles in phylogenetic analysis of rosaceae systematics and diversity across all publications each year (not limited to Nature Index journals).
Technical terms
Chloroplast genome: The circular DNA molecule housed in chloroplasts, used extensively in plant phylogenetics for its conserved regions and uniparental inheritance.
Whole-genome duplication (WGD): An evolutionary event in which an organism’s entire genome is duplicated, often leading to increased diversity and novel traits.
Phylogenomics: The approach of using genome-scale data sets to infer evolutionary relationships among taxa.
Monophyly: A group of organisms that consists of a common ancestor and all its descendants, forming a single clade.
Inverted repeat (IR) regions: Two identical but oppositely oriented sequences in chloroplast genomes that contribute to structural stability and evolutionary dynamics.
References
- Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication. Molecular Biology and Evolution (2016).
- Comparative and phylogenetic analyses of the chloroplast genomes of Filipendula species (Rosoideae, Rosaceae). Scientific Reports (2023).
- Evolution of Cherries (Prunus Subgenus Cerasus) Based on Chloroplast Genomes. International Journal of Molecular Sciences (2023).
- Phylogeny of genera in Maleae (Rosaceae) based on chloroplast genome analysis. Frontiers in Plant Science (2024).
- Evolution of Rosaceae Plastomes Highlights Unique Cerasus Diversification and Independent Origins of Fruiting Cherry. Frontiers in Plant Science (2021).
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