Genomic and Transcriptomic Analyses of Bioluminescence Genes in the Enope Squid Watasenia scintillans

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: 3D modelling; Cephalopod; Firefly squid; RNA editing; Repetitive elements.

Fig. 1

RE frequency comparison of three cephalopod genomes

Fig. 2

Partial sequences of symplectin-like proteins in Watasenia scintillans assembly (contig# s249267, s334436, s464828) and in arm tip transcriptome (c144950). a Amino acid sequence alignment among Sthenoteuthis oualaniensis symplectin (PDB ID; C6KYS2), W. scintillans sequences and human vanin-1 (Uniprot Accession; 4CYG). Red triangle is the location of a catalytic site on vanin-1. The number at the last of the alignment is the length of the sequence. b Predicted three-dimensional structure of s249267 based on the structure of human vanin-1. The sequence runs from blue to red. Three catalytic residues are shown in stick model. The structure of human vanin-1 was determined with RR6 inhibitor, which is shown in purple stick model. The catalytic residues are well aligned to RR6, which is expected to be replaced by coelenterazine in symplectin-like protein. s249267 does not have about 50 residues at the N-terminal side and 240 residues at the C-terminal side compared with human vanin-1. The C-terminal side can be located in the yellow background region, and the residue corresponding to Cys390 of S. oualaniensis symplectin can be located at the far side of the putative coelenterazine-binding site