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

Rute R Da Fonseca ,Qiye Li ,Olivier Fédrigo ,Hugo Osório ,Tomáš Vinař ,Oleg Simakov ,Caroline B Albertin ,Iñigo Barrio-Hernandez ,Graham Alexander ,Mateus Patrício ,Broňa Brejová ,Jan M Strugnell ,André M Machado ,Blagoy Blagoev ,Tobias Baril ,Chong Chu ,Rasmus Nielsen ,Ângela Maria Ribeiro ,Alexandre Campos ,Mehboob‐Ur Rahman ,Paul Geeleher ,Filipe Silva ,Sara Rocha ,Agostinho Antunes ,Jakob Vinther ,Bent Petersen ,Remo Sanges ,Bárbara Frazão ,L Filipe C Castro ,Davide Pisani ,Alex Hayward ,Erich D Jarvis ,Thomas Sicheritz-Pontén ,Henk-Jan T Hoving ,Bin Ma ,Yufeng Wu ,Alvarina Couto ,Ricardo Tafur-Jimenez ,Simon Rasmussen ,Inger E Winkelmann ,Fernando Peñaloza ,Guojie Zhang ,Francesco Musacchia ,M Thomas P Gilbert

doi:10.1093/gigascience/giz152

Abstract

ABSTRACTBackgroundThe 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.FindingsWe 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.ConclusionsThis 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.

Highlights

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
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
Cephalopod populations are thought to be currently increasing in some regions for a variety of reasons [3], including potential predator release as a consequence of the depletion of fish stocks [4]

Summary

Conclusions

Because of its astonishing proportions, and for the lack of knowledge of the key facets of its deep-sea lifestyle, the giant squid has long captured the imagination of scientists and the general public alike. With the release of this annotated giant squid genome, we set the stage for future research into the enigmas that enshroud this awe-inspiring creature. The datasets supporting the results of this article are available in the NCBI database via Bioproject PRJNA534469. The 3 transcriptome datasets (TSA) have IDs GHKK01000000, GHKL01000000, and GHKH01000000 and the sequence data used for the genome assemblies have ID VCCN01000000. Proteomics data are available via ProteomeXchange with identifier PXD016522. Supporting data are available via the Gigascience repository GigaDB [69]

Methods

Findings

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