Exploring The Significance of Coded And Non-Coding Regions in The Chloroplast Genome For Phylogenetic Studies: A Comparative Analysis.

Furan M. A., Genli G.

2. Çankaya International Congress Of scientific Research., Ankara, Turkey, 28 - 29 September 2023, pp.1-10

  • Publication Type: Conference Paper / Full Text
  • City: Ankara
  • Country: Turkey
  • Page Numbers: pp.1-10
  • Van Yüzüncü Yıl University Affiliated: Yes


Phylogenetic studies are paramount in comprehending the evolutionary connections between species and their gradual divergence across history. The chloroplast genome has been increasingly important in phylogenetics in recent years, primarily because of its distinct attributes, such as the inclusion of coding and non-coding sections. The current presentation aims to explore the significance of these particular regions within the context of phylogenetic study, with a specific focus on elucidating their divergences, merits, and drawbacks. The chloroplast genome serves as a valuable repository of evolutionary data, containing vital genes responsible for photosynthesis and several fundamental cellular mechanisms. Historically, phylogenetic study has primarily centered around these coding areas, as they offer significant insights into the interconnections across plant species. Nevertheless, the non-coding sections of the chloroplast genome, which were previously disregarded, have now been acknowledged as equally rich reservoirs of evolutionary data. Non-coding areas, including introns, intergenic spacers, and pseudogenes, exhibit a substantial degree of genetic variation and a varied mutation rate. This renders them indispensable in addressing complex inquiries pertaining to the theory of evolution. The objective of this presentation is to examine the distinctions between coded and non-coding areas within the chloroplast genome, with a particular focus on their distinct characteristics that play a role in phylogenetic inference. In this discussion, we shall examine the advantages associated with the utilization of coding regions, including conserved gene sequences and widely recognized alignment methods. Additionally, we will consider the disadvantages, such as the depletion of informative sites and the potential introduction of biases due to functional limitations. In addition, this discussion will encompass the advantages associated with the utilization of non-coding areas. These advantages include enhanced resolution for closely related species, the potential discovery of previously unidentified species, and the capacity to investigate more profound evolutionary distinctions. Nevertheless, it is imperative to acknowledge the obstacles linked to non-coding areas, including the complexities of alignment, the potential occurrence of homoplasy, and the necessity for reliable substitution models.


In conclusion, this presentation will emphasize the significance of using both coded and non-coding sections of the chloroplast genome in phylogenetic investigations. Through the strategic utilization of their individual strengths and the effective management of their limitations, researchers are able to acquire a more all-encompassing comprehension of evolutionary connections. This endeavor significantly contributes to the progression of our collective understanding of biodiversity, evolution, and ecology.