Chloroplast Genomics and Phylogenetic Analysis in Angiosperms

The chloroplast genome has emerged as a pivotal resource for resolving evolutionary relationships among flowering plants. Typically organised into a quadripartite structure—comprising two inverted repeats flanking large and small single-copy regions—chloroplast DNA offers conserved coding sequences alongside variable intergenic spacers. Comparative analyses across angiosperm lineages have elucidated patterns of gene loss, expansion or contraction of inverted repeats and the distribution of simple sequence repeats, all of which inform species delimitation, biogeographical history and adaptive radiations. Advances in high-throughput sequencing and genome skimming now enable rapid assembly and annotation of complete plastomes, underpinning robust phylogenetic trees that integrate molecular clocks and biogeographical models. These data guide the development of molecular markers for breeding programmes, support the authentication of medicinal and agricultural crops and contribute to conservation strategies by clarifying cryptic diversity in threatened taxa.

Research from Nature Portfolio

Recent studies have harnessed entire chloroplast sequences as ‘super-barcodes’ to distinguish closely related cultivars, demonstrating that complete plastomes yield greater resolution than individual loci. Comparative genomics of multiple species within an economically important arum genus revealed variation in inverted-repeat boundaries and intron content, highlighting lineage-specific structural rearrangements that correlate with phylogenetic branching. Foundational work in a large neotropical genus established a set of highly divergent intergenic regions and protein-coding genes that serve as reliable markers for inferring relationships both within the genus and across its family, providing a framework for future studies of genome evolution in tropical angiosperms.

Chloroplast Genomics and Phylogenetic Analysis in Angiosperms publication trend

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

Technical terms

Chloroplast genome (plastome): The circular DNA molecule within chloroplasts that encodes genes for photosynthesis and gene expression.

Quadripartite structure: The four-part organisation of a plastome, including two inverted repeats (IRs) and two single-copy regions (LSC and SSC).

Inverted repeat (IR): Two identical or nearly identical DNA segments in reverse orientation, separating the large and small single-copy regions.

Simple sequence repeat (SSR): Short, tandemly repeated DNA motifs used as molecular markers for genetic diversity and population studies.

Molecular marker: A DNA sequence variant used to distinguish taxa or traits, often employed in phylogenetics and breeding.

Phylogenetic analysis: The reconstruction of evolutionary relationships based on genetic data, typically represented as a branching tree diagram.

References

1. Identification of three cultivated varieties of Scutellaria baicalensis using the complete chloroplast genome as a super-barcode. Scientific Reports (2023).
2. Comparative analysis of complete chloroplast genome sequences of four major Amorphophallus species. Scientific Reports (2019).
3. Chloroplast genomes of Byrsonima species (Malpighiaceae): comparative analysis and screening of high divergence sequences. Scientific Reports (2018).
4. Application of chloroplast genome in the identification of Phyllanthus urinaria and its common adulterants. Frontiers in Plant Science (2023).
5. Comparative analysis of chloroplast genomes of Pulsatilla species reveals evolutionary and taxonomic status of newly discovered endangered species Pulsatilla saxatilis. BMC Plant Biology (2024).