Computational Biology
@ Comenius University in Bratislava

Rute R. {da Fonseca}, Alvarina Couto, Andre M. Machado, Brona Brejova, Carolin B. Albertin, Filipe Silva, Paul Gardner, Tobias Baril, Alex Hayward, Alexandre Campos, Angela M. Ribeiro, Inigo Barrio-Hernandez, Henk-Jan Hoving, Ricardo Tafur-Jimenez, Chong Chu, Barbara Frazao, Bent Petersen, Fernando Penaloza, Francesco Musacchia, Graham C. Alexander, Hugo Osorio, Inger Winkelmann, Oleg Simakov, Simon Rasmussen, M. Ziaur Rahman, Davide Pisani, Jakob Vinther, Erich Jarvis, Guojie Zhang, Jan M. Strugnell, L. Filipe C. Castro, Olivier Fedrigo, Mateus Patricio, Qiye Li, Sara Rocha, Agostinho Antunes, Yufeng Wu, Bin Ma, Remo Sanges, Tomas Vinar, Blagoy Blagoev, Thomas Sicheritz-Ponten, Rasmus Nielsen, M. Thomas P. Gilbert. A draft genome sequence of the elusive giant squid, Architeuthis dux. Gigascience, 9(1). 2020.

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Download from publisher: http://dx.doi.org/10.1093/gigascience/giz152

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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.