Marine science student Omar Zayas shares a project update on his research of genetic connections between octopus species and populations in Puerto Rico, and how environmental and historical factors may contribute to these genetic differences.
Tell us what you have accomplished so far since starting your Seed Fund project?
Thanks to the funds I received from Isla Mar, I am now onto one of the project's final steps--data processing. By March, I had finished the laboratory work. I had sent 29 octopus samples for genetic sequencing and had completed sequencing for 23 others. I have completed the fieldwork (sampling) and laboratory work (DNA extraction and sequencing). I currently spend my time working on the computer, performing the processing, analysis, and interpretation of the data received.
What has been the most challenging aspect you have encountered? How did you overcome it, or how are you working to overcome it?
Processing and analyzing genomic data requires a command line interface, and the interface requires giving instructions to computer software. As this is my first time working firsthand with genomic data, it has been a challenge to learn how to use the Linux operating system since I had to learn the language that this system uses to give instructions to different software pipelines that I use to complete the data analysis. By using the manuals of each software and reading scientific articles with methods similar to the ones I am using, and above all, patience and perseverance, I was able to overcome my initial difficulties. It is important to remember that the manuals and scientific papers are just guides because each experimental design and study data is unique and must be processed differently.
Do you have any preliminary or final results to share?
I am still working on getting preliminary results regarding population genomics. The first step after receiving the sequenced DNA is to perform a quality control assay to see if the samples pass the sequencing step or if there has been trouble in the sequencing process--not what we want. Fortunately, the results obtained from the DNA samples were clear of issues and it was possible to retrieve readings with good coverage and quality.
Did you discover something new about your field of interest/your topic that you didn’t know before?
Though I had a basic understanding from the courses and workshops I've taken, this project was the first time I was able to work with this data type. This journey has led me to discover the world of bioinformatics and the analysis of genomic data. I feel more comfortable and familiar with the area than I did some months ago. There is still a long way to go, but I keep moving forward with the goal in sight.
What are the next steps to finish up your project and when do you aim to have it completed?
After processing and analyzing the data, I will interpret the results and reach conclusions from the study. We want to know what the results would mean for the field of population genomics and the conservation of marine organisms. By December 2023, I expect to have contributed to Malacology, Marine, and Fisheries Sciences in Puerto Rico and the Caribbean.
"We want to know what the results would mean for the field of population genomics and the conservation of marine organisms."
Omar’s Seed Fund project is supported by Medalla Light. Follow along here and on our social media for the final updates!