Genomic and Transcriptomic Analyses of Bioluminescence Genes in the Enope Squid Watasenia scintillans
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ORIGINAL ARTICLE
Genomic and Transcriptomic Analyses of Bioluminescence Genes in the Enope Squid Watasenia scintillans Masa-aki Yoshida 1 & Junichi Imoto 2,3 & Yuri Kawai 4 & Satomi Funahashi 4 & Ryuhei Minei 5 & Yuki Akizuki 5 & Atsushi Ogura 5 & Kazuhiko Nakabayashi 6 & Kei Yura 4,7 & Kazuho Ikeo 2 Received: 8 April 2020 / Accepted: 28 September 2020 # The Author(s) 2020
Abstract Watasenia scintillans, a sparkling enope squid, has bioluminescence organs to illuminate its body with its own luciferase activity. To clarify the molecular mechanism underlying its scintillation, we analysed high-throughput sequencing data acquired previously and obtained draft genome sequences accomplished with comparative genomic data among the cephalopods. The genome mapped by transcriptome data showed that (1) RNA editing contributed to transcriptome variation of lineage specific genes, such as W. scintillans luciferase, and (2) two types of luciferase enzymes were characterized with reasonable 3D models docked to a luciferin molecule. We report two different types of luciferase in one organism and possibly related to variety of colour types in the W. scintillans fluorescent organs. Keywords Firefly squid . Cephalopod . RNA editing . 3D modelling . Repetitive elements
Introduction Around the Japanese sea, especially off Toyama, the appearance of shoals of the sparkling enope squid, Watasenia scintillans, heralds the beginning of spring. The W. scintillans is also known as the “firefly squid,” which is important for both tourism and the fishing industry in Japan. W. scintillans emits light from three different types of photophores (Inamura et al. 1990). Five light organs are located around each eye, and a cluster of three light organs is located at the tip of the arms.
The squid also has dermal light organs producing ambient, greenish light. The dermal light organs are utilized for counter-illumination camouflage to match the brightness making it difficult for predators below to detect the squid (Young and Roper 1977). Young et al. (1979) reported that Enoploteuthis, the closest relative of W. scintillans, has dermal light organs similar to the ones of W. scintillans. The members of the Enoploteuthidae seems to have a common mechanism of bioluminescence. Several researches in the past have established the molecular mechanism of illumination that
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10126-020-10001-8) contains supplementary material, which is available to authorized users. * Masa-aki Yoshida [email protected] * Kei Yura [email protected] 1
2
Marine Biological Science Section, Education and Research Center for Biological Resources, Faculty of Life and Environmental Sciences, Shimane University, Oki, Japan Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
3
Present address: Fisheries Data Sciences Division, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Fukuura 2-12-4, Kanazaw
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