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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.

SUBMITTER: da Fonseca RR 

PROVIDER: S-EPMC6962438 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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

da Fonseca Rute R RR   Couto Alvarina A   Machado Andre M AM   Brejova Brona B   Albertin Carolin B CB   Silva Filipe F   Gardner Paul P   Baril Tobias T   Hayward Alex A   Campos Alexandre A   Ribeiro Ângela M ÂM   Barrio-Hernandez Inigo I   Hoving Henk-Jan HJ   Tafur-Jimenez Ricardo R   Chu Chong C   Frazão Barbara B   Petersen Bent B   Peñaloza Fernando F   Musacchia Francesco F   Alexander Graham C GC   Osório Hugo H   Winkelmann Inger I   Simakov Oleg O   Rasmussen Simon S   Rahman M Ziaur MZ   Pisani Davide D   Vinther Jakob J   Jarvis Erich E   Zhang Guojie G   Strugnell Jan M JM   Castro L Filipe C LFC   Fedrigo Olivier O   Patricio Mateus M   Li Qiye Q   Rocha Sara S   Antunes Agostinho A   Wu Yufeng Y   Ma Bin B   Sanges Remo R   Vinar Tomas T   Blagoev Blagoy B   Sicheritz-Ponten Thomas T   Nielsen Rasmus R   Gilbert M Thomas P MTP  

GigaScience 20200101 1


<h4>Background</h4>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.<h4>Findings</h4>We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Molecu  ...[more]

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