TY - JOUR
T1 - A draft genome sequence of the elusive giant squid, Architeuthis dux
AU - da Fonseca, Rute R.
AU - Couto, Alvarina
AU - Machado, Andre M.
AU - Brejova, Brona
AU - Albertin, Carolin B.
AU - Silva, Filipe
AU - Gardner, Paul
AU - Baril, Tobias
AU - Hayward, Alex
AU - Campos, Alexandre
AU - Ribeiro, Ângela M.
AU - Barrio-Hernandez, Inigo
AU - Hoving, Henk-Jan
AU - Tafur-Jimenez, Ricardo
AU - Chu, Chong
AU - Frazão, Barbara
AU - Petersen, Bent
AU - Peñaloza, Fernando
AU - Musacchia, Francesco
AU - Alexander, Graham C.
AU - Osório, Hugo
AU - Winkelmann, Inger
AU - Simakov, Oleg
AU - Rasmussen, Simon
AU - Rahman, M. Ziaur
AU - Pisani, Davide
AU - Vinther, Jakob
AU - Jarvis, Erich
AU - Zhang, Guojie
AU - Strugnell, Jan M.
AU - Castro, L. Filipe C.
AU - Fedrigo, Olivier
AU - Patricio, Mateus
AU - Li, Qiye
AU - Rocha, Sara
AU - Antunes, Agostinho
AU - Wu, Yufeng
AU - Ma, Bin
AU - Sanges, Remo
AU - Vinar, Tomas
AU - Blagoev, Blagoy
AU - Sicheritz-Pontén, Thomas
AU - Nielsen, Rasmus
AU - Gilbert, M. Thomas P.
PY - 2020
Y1 - 2020
N2 - 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.
AB - 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.
KW - cephalopod
KW - genome assembly
KW - invertebrate
U2 - 10.1093/gigascience/giz152
DO - 10.1093/gigascience/giz152
M3 - Journal article
C2 - 31942620
AN - SCOPUS:85077940907
VL - 9
JO - GigaScience
JF - GigaScience
SN - 2047-217X
IS - 1
M1 - giz152
ER -