|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.
Keywords: cephalopod; invertebrate; genome assembly|