Dna Barcoding: Efficiency of Rbcl Gene for Sequence Characterisation of Cyperus Esculentus in Nigeria

Abstract

Background Plants have been classified based on morphological traits. However, there are biases associated with this classification. The limitation can be prevented by using DNA barcoding. Therefore, the efficiency of the Ribulose -bisphosphate carboxylase (rbcL) marker was investigated to identify Tiger Nut (Cyperus esculentus), which belongs to the family of Cyperaceae. In this study, C. esculentus samples were collected from two villages in northern Nigeria. For DNA barcoding, the rbcL region of C. esculentus samples were amplified, sequenced in both directions, and subsequently analysed. The amplified sequences' biological sequence homology, sequence divergence, and phylogenetic tree construction were studied using Basic Local Alignment Tool (BLAST), Codon Code Aligner and MEGA X respectively. Results A 100% identity of rbcL locus with several other Cyperus species was obtained from BLAST result. The region seems highly conserved among several Cyperus species as variation within this marker locus’s sequence is minimal. However, a G/T variation at a nucleotide position could differentiate the tested samples from 40% of the other data bank species. The phylogenetic tree analysis clustered the 20 samples and the retrieved sequences based on the very few sequence variations without distinctly separating C. esculentus samples from other Cyperus species. Conclusions These findings showed that rbcL marker could only identify our samples up to genius level. Therefore, other DNA barcoding markers are needed to identify and characterise C. esculentus since the characterization based on rbcL gene sequences conducted in this work could not identify C. esculentus up to the species level.