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.

The hard clam genome reveals massive expansion and diversification of inhibitors of apoptosis in Bivalvia

“…To ensure the representativeness and reliability of phylostratigraphic tree, we included 11 species—whose genomes are currently available—from each representative family in molluscs (Mytilidae, Pteriidae, Ostreidae, Pectinidae, and Veneridae for bivalves; Aplysiidae, Planorbidae, Lottiidae, and Peltospiridae for Gastropods; Architeuthidae and Octopodidae for Cephalopods) and 7 species from other phyla for downstream analysis. Hence, the nucleotide and protein sequences of those 18 species ( P. fucata ; C. virginica; M. philippinarum ; A. farreri ; Ruditapes philippinarum (Rph) [ 83 ]; Chrysomallon squamiferum (Csq): GCA_012295275.1; L. gigantea ; Biomphalaria glabrata (Bgl) : GCA_000457365.1 ASM45736v1; Aplysia californica (Aca): GCF_000002075.1; Architeuthis dux (Adu) [ 84 ]; O. bimaculoides ; Capitella teleta (Cte): GCA_000328365.1 Capca1; Helobdella robusta (Hro): GCA_000326865.1; Apis mellifera (Ame): GCF_003254395.2_Amel_HAv3.1; Drosophila melanogaster (Dme): GCF_000001215.4_Release_6_plus_ISO1_MT; Homo sapiens (Hsa): GCF_000001405.38_GRCh38.p12; B. floridae; Nematostella vectensis (Nve): GCA_000209225.1 ASM20922v1) were downloaded from public databases (see also database IDs above). The longest transcript was selected from alternate splice transcripts for each gene, and genes with ≤ 30 amino acids were removed.…”

The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

“…Bivalvia 21 , Cephalopoda 72 , Gastropoda 74 and Polyplacophora 80 , most Bivalvia seem to retain the gene composition expected for lophotrochozoans: Hox1, Hox2, Hox3, Hox5, Lox, Antp, Lox4, Lox2, Post2, Post1 for the Hox cluster and Gsx, Xlox, Cdx for the ParaHox cluster 81 .…”

“…65,66,70 ). Given the disparate body plans in molluscan classes, the study of Hox cluster composition, organization and gene expression has practically become a standard in Mollusca genome assembly studies 21,22,[78][79][80][81][82]57,[71][72][73][74][75][76][77] . Homeobox genes are divided into four classes, of which the Antennapedia (ANTP)-class (Hox, ParaHox, NK, Mega-homeobox, SuperHox) is the best studied, particularly the Hox and ParaHox clusters 57,70,75 .…”

Krüppel-like factor/specificity protein evolution in the Spiralia and the implications for cephalopod visual system novelties

“…However, a lack of sequence data has made it difficult to assess the importance of this mechanism in most metazoan species until recently. Cephalopods, a group of molluscs that include squid, cuttlefish, octopus, and nautilus, have recently benefited from genome and transcriptome sequencing and are exceptional subjects for the study of morphological novelty because they have evolved a diversity of complex, class-specific traits [5][6][7][8][9][10][11][12].…”