A draft genome sequence of the elusive giant squid, Architeuthis dux

ABSTRACT Background The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked. Findings We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.Villum Fonden | Ref. VKR023446Portuguese Science Foundation | Ref. PTDC/MAR/115347/2009Portuguese Science Foundation | Ref. COMPETE-FCOMP-01-012Portuguese Science Foundation | Ref. FEDER-015453Portuguese Science Foundation | Ref. FP7-PEOPLE-2010-IEFDanish National Research Foundation | Ref. DNRF96Danish National Research Foundation | Ref. DNRF94Rede Nacional de Espectrometria de Massa | Ref. ROTEIRO/0028/2013Rede Nacional de Espectrometria de Massa | Ref. LISBOA-01-0145-FEDER-022125COMPETE and North Portugal Regional Operational Programme | Ref. Norte2020European Regional Development Fund | Ref. UID/Multi/04423/2019Wellcome Trust | Ref. WT108749/Z/15/ZEuropean Molecular Biology LaboratoryLundbeck Foundation | Ref. R52–5062Lundbeck Foundation | Ref. R52-A4895Novo Nordisk Foundation | Ref. NNF14CC0001Biotechnology and Biological Sciences Research Council | Ref. BB/N020146/1Biotechnology and Biological Sciences Research Council | Ref. BB/M009122/1David and Lucile Packard FoundationNetherlands Organization for Scientific Research | Ref. 825.09.016Deutsche Forschungsgemeinschaft | Ref. HO 5569/2-1Vedecká Grantová Agentúra MŠVVaŠ SR a SAV | Ref. 1/0684/16Vedecká Grantová Agentúra MŠVVaŠ SR a SAV | Ref. 1/0458/18Vedecká Grantová Agentúra MŠVVaŠ SR a SAV | Ref. SFRH/BD/126560/2016National Science FoundationDeiC National Life Science Supercompute