Date of Award
6-2025
Culminating Project Type
Thesis
Styleguide
apa
Degree Name
Biological Sciences - Cell and Molecular: M.S.
Department
Biology
College
College of Science and Engineering
First Advisor
Matthew Davis
Second Advisor
Angela McDonnell
Third Advisor
Sarah Gibson
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.
Keywords and Subject Headings
Genomics; Deep-sea Bioluminescence; Differential Gene Expression;
Abstract
Bioluminescence, the production and emission of light by a living organism, is a phenomenon that has fascinated people for centuries. However, the genomics that underlie this phenomenon has largely remained unexplored within vertebrates. Dragonfishes and their allies (Teleostei: Stomiiformes) include over 450 species of deep-sea fishes that are all known to be bioluminescent. Bioluminescence in dragonfishes is hypothesized to occur through intrinsic processes without the aid of bacteria, making them an ideal study system to explore the genetics associated with bioluminescence in vertebrates. Luminescent and non-luminescent tissue samples from four stomiiform species were freshly sampled, with the transcriptome from each tissue subsequently sequenced and assembled. Assessment of completeness, quality, and annotation of the transcriptomes was completed. Orthologous genes were identified across the four different species and tissue samples. Differential gene expression between luminous and non-luminous tissues was examined, with over forty upregulated genes found in luminescent tissues when compared to non-luminescent tissues. Candidate proteins of interest following transcript annotation based on previously published information on known luminescent systems in other taxa were modeled in 3D, with structural similarity analyses conducted to compare protein structure with known luciferases in other taxa. A flavoprotein identified in the bioluminescent barbel tissue of Stomias was successfully modeled with 100% confidence that showing significant structural similarity to luciferases previously characterized in corals and fireflies. Additional accessory functional domains and oxidoreductases were identified that could putatively support the metabolic infrastructure needed to support a light-producing reaction, further providing support for an intrinsic bioluminescent pathway in dragonfishes.
Recommended Citation
Larson, Meghan, "Lighting Up the Deep: Transcriptomic Analysis of Bioluminescent Organs in Stomiiformes (Teleostei)" (2025). Culminating Projects in Biology. 89.
https://repository.stcloudstate.edu/biol_etds/89
Comments/Acknowledgements
I would like to thank my advisor, Dr. Matthew Davis, my committee members, Dr. Sarah Gibson and Dr. Angela McDonnell, and my lab mates Allison Peck, Elizabeth Favor, Natalie Swearingen, and Aimee Hruska, for their advice, support, and feedback. I would also like to thank external collaborators on this project, including Dr. Wm. Leo Smith (University of Kansas) and Dr. Edward O. Wiley (University of Kansas).
I would like to thank St. Cloud State University for funding through the Student Research Mentor/Mentee Collaboration Grant. Additional funding for this work was provided by the University of Kansas (funds from collaborators Wm. Leo Smith and E.O. Wiley), and the Hellervik Prize (SCSU award to M.P. Davis). I would also like to thank the American Society of Ichthyologists and Herpetologists for supporting my professional development through the Cashner Award and providing support to attend the Joint Meeting of Ichthyologists and Herpetologists.
To my parents, family, and friends, thank you for the continuous support and encouragement throughout my academic endeavors. My life is infinitely better with you all in it.