My research area pertains to molecular genetics with the focus of this project being molecular evolution. The purpose of this research is to understand the evolutionary relationship between papain-like cysteine proteases (PLCPs) in the Carica papaya genome to establish context for further investigation into the enzymes’ functions in various C. papaya tissues at different stages of development. Additionally, papain is used in industrial settings and understanding the enzymatic activity of PLCPs other than papain could provide valuable information about more enzymatically efficient members of the gene family. This portion of the project was conducted by obtaining coding sequences from the Phytozome database which could then be manipulated using the Molecular Evolutionary Genetics Analysis (MEGA) software to align the sequences using different parameters. Two alignments were generated: an alignment of the sequences’ codons (groups of three nucleotides that code for amino acids) and an alignment of the sequences translated to amino acids. RAxML Black Box software was used to generate phylogenetic trees annotated with bootstrap values at each branch point. The bootstrap values provide support for the accuracy of the trees, aiding in the selection of a tree that represents the evolutionary relationships between members of the gene family. Based on the bootstrap values, the amino acid alignment is most accurate for depicting the evolutionary relationships. The next step in this research is to identify which members are differentially expressed in the tissues of C. papaya. Since this is an ongoing project, no conclusions can be made at this time. My goal is to enroll in a Ph.D. or Master’s program in molecular biology following graduation. This research has given me hands-on experience with bioinformatics principles that can be applied to this field. The next steps of this project will provide additional experience in analyzing molecular mechanisms in cellular systems.
Author: William Dunphy Gregor, Botany
Advisor: Richard Moore, Biology
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