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Data from: Laboratory culture of the California Sea Firefly Vargula tsujii (Ostracoda: Cypridinidae): developing a model system for the evolution of marine bioluminescence

Citation

Goodheart, Jessica A. et al. (2020), Data from: Laboratory culture of the California Sea Firefly Vargula tsujii (Ostracoda: Cypridinidae): developing a model system for the evolution of marine bioluminescence, Dryad, Dataset, https://doi.org/10.6075/J0DZ06QQ

Abstract

Bioluminescence, or the production of light by living organisms via chemical reaction, is widespread across Metazoa. Laboratory culture of bioluminescent organisms from diverse taxonomic groups is important for determining the biosynthetic pathways of bioluminescent substrates, which may lead to new tools for biotechnology and biomedicine. Some bioluminescent groups may be cultured, including some cnidarians, ctenophores, and brittle stars, but those use luminescent substrates (luciferins) obtained from their diets, and therefore are not informative for determination of the biosynthetic pathways of the luciferins. Other groups, including terrestrial fireflies, do synthesize their own luciferin, but culturing them is difficult and the biosynthetic pathway for firefly luciferin remains unclear. An additional independent origin of endogenous bioluminescence is found within ostracods from the family Cypridinidae, which use their luminescence for defense and, in Caribbean species, for courtship displays. Here, we report the first complete life cycle of a luminous ostracod (Vargula tsujii Kornicker & Baker, 1977, the California Sea Firefly) in the laboratory. We also describe the late-stage embryogenesis of Vargula tsujii and discuss the size classes of instar development. We find embryogenesis in V. tsujii ranges from 25-38 days, and this species appears to have five instar stages, consistent with ontogeny in other cypridinid lineages. We estimate a complete life cycle at 3-4 months. We also present the first complete mitochondrial genome for Vargula tsujii. Bringing a luminous ostracod into laboratory culture sets the stage for many potential avenues of study, including learning the biosynthetic pathway of cypridinid luciferin and genomic manipulation of an autogenic bioluminescent system.

Methods

Femto pulse results (Femto_pulse_results.svg): Agilent Femto Pulse capillary electrophoresis measuring the length distribution of HMW DNA extracted from Vargula tsujii adult females. Run D18-2980 (Panel C; red star), corresponds to the DNA sample #5047, which was used for the Chromium library preparation. As this size distribution measurement was made after library preparation and after shipment of the extracted DNA from the Hudson Alpha Institute of Biotechnology Genomic Services lab (HAIB-GSL) to MIT, we cannot strictly state if the small size distribution is due to the extraction conditions or due to shearing from refreezing and shipping, however the poor results of the Supernova assembler from the produced chromium library suggest the input DNA was already small.

Whole genome assembly (2 haplotypes - 20180114_pseudohap2.1.fasta.gz and 20180114_pseudohap2.2.fasta.gz): Whole genome assembly of the sequencing data from sample # 5047 / TCO4 (SRR9308458) with the Supernova v2.0.0 genome assembly software, using default parameters.

Raw assembly graph (20180114_raw.gfa.gz): The ‘raw’ assembly graph with full headers was first output to FASTA format using supernova ‘mkoutput’, and was then converted to the GFA assembly graph format using the supernova2gfa utility of gfaview (https://github.com/lh3/gfa1).

Usage Notes

 

 

Funding

Arnold and Mabel Beckman Foundation, Award: Beckman Young Investigator Award to Jing-Ke Weng

University of California, Santa Barbara, Award: Faculty Seed Grant to Todd Oakley