Phylogenetic Analysis of Chloroplast Genomes in Rosaceae

The Rosaceae family encompasses a wide array of economically and ecologically important taxa, including fruit crops, ornamentals and woody shrubs. Chloroplast genomes, with their conserved gene content and structure, have become indispensable for resolving phylogenetic relationships within this diverse lineage. Typical plastomes exhibit a quadripartite organisation, comprising large and small single-copy regions flanked by inverted repeats, and harbour markers such as simple sequence repeats and mutation hotspots. Comparative analyses across genera such as Rosa, Rubus and Paulownia have clarified deep divergences, revealed episodes of positive selection and uncovered reticulate evolution driven by hybridisation. Advances in high-throughput sequencing and bioinformatic pipelines now facilitate assembly of complete plastomes, identification of informative regions and the integration of RNA editing profiles. Such insights underpin robust phylogenetic frameworks, inform conservation of wild germplasm and support breeding strategies by pinpointing maternal lineages and lineage-specific markers.

Research from Nature Portfolio

Recent studies have assembled and compared multiple complete plastomes of Paulownia species, unravelling two principal clades that correspond to geographical distributions and demonstrating strong support for monophyly of the genus. Twelve hotspot regions and three genes under positive selection were identified, providing candidate loci for taxonomic clarification and evolutionary inference. In a separate investigation, eight endemic Rubus plastomes from Taiwan were characterised to reveal high sequence conservation and codon-usage patterns. Four intergenic spacer regions exhibited elevated variability, and 29 protein-coding genes showed signatures of positive selection. Phylogenomic analyses resolved three major lineages within the island’s endemics, furnishing a framework for broader infrageneric sampling and elucidation of plastome evolution in Rubus.

Phylogenetic Analysis of Chloroplast Genomes in Rosaceae publication trend

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

Technical terms

Chloroplast genome: The circular, typically 120–170 kb DNA molecule within chloroplasts encoding photosynthetic and housekeeping genes.

Quadripartite structure: The four-region architecture of plastomes, composed of one large single-copy region, one small single-copy region and two inverted repeats.

Hotspot region: A segment of the genome exhibiting elevated nucleotide variability useful for distinguishing closely related taxa.

Simple sequence repeat (SSR): A polymorphic locus formed by short tandem repeats, frequently used as high-resolution genetic markers.

RNA editing: The enzymatic alteration of RNA sequences after transcription, often resulting in changes to encoded amino acids.

References

1. Comparison of the complete plastomes and the phylogenetic analysis of Paulownia species. Scientific Reports (2020).
2. Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan. Scientific Reports (2021).
3. Complete chloroplast genomes of Rubus species (Rosaceae) and comparative analysis within the genus. BMC Genomics (2022).
4. Comparative Analysis of the Complete Chloroplast Genome Sequences of Three Closely Related East-Asian Wild Roses (Rosa sect. Synstylae; Rosaceae). Genes (2019).
5. Complex and reticulate origin of edible roses (Rosa, Rosaceae) in China. Horticulture Research (2022).