Sequence analysis of rbcL and matK regions for a comparison study of Senna species

Patcharawarin Ruanto, Somrutai Tunma, Nattiya Chaichana

Abstract


Background: DNA barcoding is an efficient molecular biology technique that utilizes a short genetic locus with sufficient variability to enable precise organism identification. Typically, regions such as ribulose-bisphosphate carboxylase (rbcL) and maturase K (matK) in plants are widely used due to their balance between interspecific divergence and intraspecific conservation. These standardized genomic fragments are amplified by Polymerase Chain Reaction (PCR) and subsequently sequenced for comparative analysis. Every species has its own characteristic DNA barcode, which can be matched against curated reference libraries, enabling accurate identification even when morphological traits are ambiguous, damaged, or insufficient for taxonomic classification. This approach has been particularly transformative in biodiversity monitoring, ecological studies, and the detection of cryptic or invasive species. Presenting DNA barcodes in a graphical form provides an alternative and powerful way to store and display sequence information as it facilitates cross-comparison. The generated graphical outputs can be incorporated into machine learning algorithms for species recognition in further large-scale ecological and conservation research.

Methods: The matK and rbcL genes of the collected five senna species were selected as DNA barcodes to confirm and distinguish these plant samples. An alternative method was also presented to extract the characteristics of the DNA sequences with graphical operation based on Chaos Game Representation (CGR).

Results: It was found that the power to discriminate between species was high enough when a two-locus barcode approach was applied with 90% successful amplification using the provided protocol optimization. The similarity/dissimilarity comparison of the collected plant samples was also achieved by the obtained CGR.

Conclusion: Grouping of individuals based on genetic relationship was consistent with morphology and taxonomy, particularly when the primers for matK were used, whereas the rbcL barcode was less effective in distinguishing species.

Keywords:

DNA barcode, matK, rbcL, Senna species, Chaos Game Representation


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References


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DOI: https://doi.org/10.62940/als.v13i1.3252

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