OBADIRE, Tobi Tejumade and Covenant University, Theses Masters (2024) MUTATION PROFILING OF RBCL AND MATK GENES AND PHYLOGENETIC RELATIONSHIPS OF SELECTED MEMBERS OF THE FABACEAE FAMILY. Masters thesis, Covenant University.
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Abstract
Gene mutation profiling involves detecting the type and effect of mutation on a gene. The rbcL and matK genes are chloroplast genes involved in photosynthesis; mutations on these genes can be deleterious or beneficial to the plant. Integrating underutilized legumes into genetic studies alongside major legumes using barcoding methodologies is essential for their genetic improvement. This research aimed to provide detailed mutation information on the rbcL and matK genes of the selected legumes and gain insight into their classification based on DNA barcodes. The sequences of sixteen legumes were used in the study. Five amino acid sequence entries from these species, reference sequences and complete chloroplast genomes were retrieved from the National Center for Biotechnology Information database. The gene sequences were aligned with their reference sequences using MULTALIN to identify amino acid substitutions in the genes. The type and effect of these mutations on protein function and stability were predicted using the SIFT, PROVEAN, and I-MUTANT v.2.0 online servers. The rbcL and MatK genes of Macrotyloma geocarpum were isolated, amplified, and sequenced. Consensus sequences of the sequence entries from 15 species were generated and aligned with those sequenced using the Muscle algorithm. Phylogenetic analysis was conducted using the neighbor-joining algorithm in MEGA 11 software. Results revealed 32 and 22 amino acid substitutions in the matK and rbcL genes, respectively. Five substitutions in the matK gene across three species were predicted to be deleterious by all three predictive software, and one substitution in the rbcL gene was predicted to be beneficial. The double barcodes (matK+rbcL) and single barcode (rbcL) classified the selected legumes randomly, however, matK gene classified the legumes down to the genus and species levels. It also revealed that Cajanus cajan, an underutilized legume, is the closest to Vigna unguiculata, implying the possibility of genetically improving C. cajan using the V. unguiculata genome. The matK gene also gave similar result to that of chloroplast genome. Consequently, matK gene is recommended as a core barcode sequence in the Fabaceae family.
| Item Type: | Thesis (Masters) |
|---|---|
| Uncontrolled Keywords: | Mutation, rbcL, matK, Underutilized legumes, Phylogenetic Analysis |
| Subjects: | Q Science > QH Natural history Q Science > QH Natural history > QH301 Biology |
| Divisions: | Faculty of Medicine, Health and Life Sciences > School of Biological Sciences |
| Depositing User: | Patricia Nwokealisi |
| Date Deposited: | 24 Oct 2024 12:45 |
| Last Modified: | 24 Oct 2024 12:45 |
| URI: | http://eprints.covenantuniversity.edu.ng/id/eprint/18537 |
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