Phylogenetic Analysis of Ribosomal DNA Sequences

Phylogenetic analysis of ribosomal DNA (rDNA) sequences exploits the evolutionary information encoded within the tandemly repeated ribosomal RNA gene clusters, notably the internal transcribed spacers (ITS1 and ITS2) flanking the 5.8S rRNA gene. These spacers evolve faster than the conserved rRNA coding regions, rendering them ideal markers for distinguishing closely related taxa. Analysis typically involves PCR amplification of the ITS regions, alignment informed by secondary‐structure models, and tree reconstruction using methods such as maximum likelihood or Bayesian inference. Secondary‐structure constraints guide alignment, while compensatory base changes (CBCs) in paired regions can signal species boundaries. Concerted evolution acts to homogenise rDNA repeats, although intragenomic polymorphisms and pseudogene formation may complicate interpretation. The integration of sequence data, structural modelling and novel distance metrics now provides enhanced resolution across scales from microbial lineages to angiosperm clades. Practical applications span species delimitation, community barcoding, conservation genetics and tracing hybridisation events, underscoring global significance in biodiversity assessment and evolutionary biology.

Research from Nature Portfolio

Recent studies have revealed unexpected patterns of intragenomic diversity within rDNA arrays of yeasts, challenging the assumption of complete homogenisation. High‐coverage sequencing of Metschnikowia pulcherrima isolates demonstrated extensive variation in ITS and D1/D2 domains, indicating chimeric genome evolution and non‐standard modes of diversification. These findings underscore the need for careful marker selection and awareness of pseudogene interference when reconstructing yeast phylogenies. In parallel, global surveys of seed‐plant ITS2 variation established average genetic‐distance thresholds for species delineation, showing that angiosperms exhibit a mean ITS2 divergence of around 4 per cent between sister species, whereas gymnosperms display approximately half that value. These thresholds offer a quantitative framework for molecular taxonomy and barcoding across diverse plant lineages, facilitating more objective species identification and informing studies of life‐history evolution.

Phylogenetic Analysis of Ribosomal DNA Sequences publication trend

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

Technical terms

Ribosomal DNA (rDNA): Tandem arrays of genes encoding ribosomal RNA, including conserved rRNA units and rapidly evolving internal spacers.

Internal Transcribed Spacer (ITS): Non-coding regions (ITS1, ITS2) between rRNA genes, used as molecular markers due to high interspecific variability.

Phylogenetic Marker: A DNA sequence with appropriate rate of evolution for inferring evolutionary relationships at a given taxonomic level.

Secondary Structure: The folding pattern of RNA (stems, loops) determined by base pairing, used to guide alignment and assess functional constraints.

Compensatory Base Change (CBC): Paired nucleotide substitutions in RNA stems that maintain base-pairing, often correlating with species-level divergence.

Concerted Evolution: The process by which repetitive DNA sequences within a genome evolve in a coordinated manner, reducing intragenomic variation.

GC Content: The proportion of guanine and cytosine nucleotides in a DNA or RNA region, influencing stability and evolutionary dynamics.

References

1. Structure-Based GC Investigation Sheds New Light on ITS2 Evolution in Corydalis Species. International Journal of Molecular Sciences (2023).
2. High intragenomic, intergenomic, and phenotypic diversity in pulcherrimin-producing Metschnikowia yeasts indicates a special mode of genome evolution. Scientific Reports (2024).
3. Compensatory Base Changes in ITS2 Secondary Structure Alignment, Modelling, and Molecular Phylogeny: An Integrated Approach to Improve Species Delimitation in Tulasnella (Basidiomycota). Journal of Fungi (2023).
4. Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. Biology Direct (2010).
5. Molecular thresholds of ITS2 and their implications for molecular evolution and species identification in seed plants. Scientific Reports (2017).