Characterizing the genetic basis of a novelty in a charismatic non-model system: bioluminescent ostracods (California Sea Firefly)

Abstract

Bioluminescence, the production of light via living organisms, is a complex phenomenon that is of great interest to scientists from many disciplines. Bioluminescence has independently evolved at least eighty times on land and in the ocean, making it a fascinating system to study. Although the bioluminescent biochemistry has been extensively studied, the genes that make up the bioluminescent pathway are largely unknown. The bioluminescent ostracod Vargula tsujii, use bioluminescence for defense and a, secrete the enzyme luciferase and substrate luciferin from the light organ located in a glandular structure near the mouth of the organism. We propose to use gene co-expression network-based approach to identify genes responsible for the production of luciferin and elucidate the luciferin metabolic pathway.  In the laboratory of Dr. Todd Oakley, we measured hundreds of wild-collected animals and performed analyses to quantify the instar stages of V. tsujii, while raising a full life cycle in the laboratory, a first for any luminous ostracod. This successful rearing has created the opportunity for us to investigate the evolutionary origins of bioluminescence by characterizing the genes responsible for the synthesis of luciferin. We use gene co-expression network-based analyses combined with functional enrichment in R, Python and other assembled bioinformatics pipelines to identify candidate genes responsible for the synthesis of luciferin. After extracting RNA from ostracods induced to express bioluminescence throughout various times of the day, we outsourced those isolated transcriptomes for sequencing. The sequences were returned, formatted and assembled into a matrix consisting of gene IDs and expression counts. This matrix was input into a WGCNA pipeline developed in R, and a high throughput network analysis was conducted to create modules consisting of highly co-expressed genes. Using bait sequences of luciferase from other species of ostracod to find close homologs in the Tsujii transcriptome, we then selected the modules that were found to contain those homologs as modules of high interest. We hypothesize that genes responsible for the synthesis of luciferin, a molecule with a fundamental and functional role in light production behavior in the context of courtship signaling and defense, are co-regulated with luciferase in these modules.