DOI: 10.6075/j0dz06qq
title: Data from: Laboratory culture of the California Sea Firefly Vargula tsujii (Ostracoda: Cypridinidae): developing a model system for the evolution of marine bioluminescence

description: 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.
description: <strong>Femto pulse results
 (Femto_pulse_results.svg):</strong> Agilent Femto Pulse capillary
 electrophoresis measuring the length distribution of HMW DNA extracted
 from <em>Vargula tsujii </em>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. <strong>Whole genome assembly (2
 haplotypes - 20180114_pseudohap2.1.fasta.gz and
 20180114_pseudohap2.2.fasta.gz):</strong> Whole genome assembly of
 the sequencing data from sample # 5047 / TCO4 (SRR9308458) with the
 Supernova v2.0.0 genome assembly software, using default
 parameters. <strong>Raw assembly graph
 (20180114_raw.gfa.gz): </strong>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).
description: