Nuclear Ribosomal DNA (nrDNA) Sequence based Molecular Markers for Plant Phylogeny: Potential and Pitfalls

Author: Inamul Haque

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Abstract

Phylogenies play a valuable role in our understanding of biological diversity. They help to structure classifications and provide us with insights into the events that took place during the course of evolution. For the assessment of phylogeny, historically used morphological data is now being replaced by the more advantageous molecular data, specifically DNA sequence data. One of the most important region used for phylogenetic inference is the nuclear ribosomal DNA (nrDNA) region. The ITS1-5.8S-ITS2, ITS2, intergenic spacer and external transcribed spacer regions have been routinely used for phylogenetic analysis. Evaluating accurate phylogenetic inference with the advent of molecular data has its own set of challenges. If the background of the genes or sequences included in the analysis are not considered and understood, it can lead to major pitfalls resulting in inaccurate phylogenetic reconstructions. A better understanding of the different molecular processes which operate in these regions is of paramount importance since they can directly affect the phylogenetic analysis. This review summarizes the different problems that can arise when using nrDNA sequences for phylogenetic analysis, and how to overcome them.

Keywords

Phylogeny, molecular markers, internal transcribed spacer, external transcribed spacer, nuclear ribosomal DNA

Conclusion

The wealth of knowledge on the phylogeny of life is largely attributed to morphological data. The hierarchical classification systems that have been developed using morphological datasets do share similar phylogenetic nodes with those predicted by sequence based markers. Despite their limited resolution, these classifications establish a foundation of diagnostic anchor points (Caddah et al., 2022). DNA sequence analyses can then serve to validate, clarify, reinforce, and enhance accuracy for phylogenetic areas that lack sufficient morphological data, using these anchor points as a framework. The reason behind DNA data overtaking morphology in phylogenetic studies is that a substantial amount of the valuable morphological diversity has already undergone meticulous examination. The nrDNA region of eukaryotes do serve as a valuable marker for phylogenetic analyses due to their high sequence level variability, conserved flanking regions, rapid concerted evolution under similar functional constraints, and their small size. There are multiple challenges associated with the usage of these sequence. These challenges can be overcome with a proper understanding of the sequences and considerable precautions have to be undertaken for phylogenetic analyses to be accurate. Studies have consistently demonstrated that integrating both ITS and 5' ETS datasets in phylogenetic analyses tends to yield higher support and resolution of trees. Therefore, incorporating a 5' ETS dataset into an existing ITS-based phylogeny appears to be a promising approach for enhancing phylogenetic accuracy (Chen et al., 2022). Rather than relying solely on nrDNA sequences for phylogenetic analysis, it is beneficial to consider using single-copy nuclear genes as an alternative. These genes, which are inherited from both parents, are becoming more prevalent in phylogenetic analysis. They typically avoid concerted evolution and feature codons that limit alignment ambiguity, making it easier to conduct homologous comparisons.

References

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How to cite this article

Inamul Haque (2023). Nuclear Ribosomal DNA (nrDNA) Sequence based Molecular Markers for Plant Phylogeny: Potential and Pitfalls. Biological Forum – An International Journal, 15(5): 886-892.