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ArticleA draft genome sequence of the elusive giant squid, Architeuthis dux(Oxford University Press, 2020-01-16) da Fonseca, Rute R. ; Couto, Alvarina ; Machado, Andre M. ; Brejova, Brona ; Albertin, Carolin B. ; Silva, Filipe ; Gardner, Paul ; Baril, Tobias ; Hayward, Alex ; Campos, Alexandre ; Ribeiro, Ângela M. ; Barrio-Hernandez, Inigo ; Hoving, Henk-Jan ; Tafur-Jimenez, Ricardo ; Chu, Chong ; Frazão, Barbara ; Petersen, Bent ; Peñaloza, Fernando ; Musacchia, Francesco ; Alexander, Graham C., Jr. ; Osório, Hugo ; Winkelmann, Inger ; Simakov, Oleg ; Rasmussen, Simon ; Rahman, M. Ziaur ; Pisani, Davide ; Vinther, Jakob ; Jarvis, Erich ; Zhang, Guojie ; Strugnell, Jan M. ; Castro, L. Filipe C. ; Fedrigo, Olivier ; Patricio, Mateus ; Li, Qiye ; Rocha, Sara ; Antunes, Agostinho ; Wu, Yufeng ; Ma, Bin ; Sanges, Remo ; Vinar, Tomas ; Blagoev, Blagoy ; Sicheritz-Ponten, Thomas ; Nielsen, Rasmus ; Gilbert, M. Thomas P.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.
ArticleIdentification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain(BMC, 2022-05-18) Petrosino, Giuseppe ; Ponte, Giovanna ; Volpe, Massimiliano ; Zarrella, Ilaria ; Ansaloni, Federico ; Langella, Concetta ; Di Cristina, Giulia ; Finaurini, Sara ; Russo, Monia T. ; Basu, Swaraj ; Musacchia, Francesco ; Ristoratore, Filomena ; Pavlinic, Dinko ; Benes, Vladimir ; Ferrante, Maria I. ; Albertin, Carolin B. ; Simakov, Oleg ; Gustincich, Stefano ; Sanges, RemoBackground Transposable elements (TEs) widely contribute to the evolution of genomes allowing genomic innovations, generating germinal and somatic heterogeneity, and giving birth to long non-coding RNAs (lncRNAs). These features have been associated to the evolution, functioning, and complexity of the nervous system at such a level that somatic retrotransposition of long interspersed element (LINE) L1 has been proposed to be associated to human cognition. Among invertebrates, octopuses are fascinating animals whose nervous system reaches a high level of complexity achieving sophisticated cognitive abilities. The sequencing of the genome of the Octopus bimaculoides revealed a striking expansion of TEs which were proposed to have contributed to the evolution of its complex nervous system. We recently found a similar expansion also in the genome of Octopus vulgaris. However, a specific search for the existence and the transcription of full-length transpositionally competent TEs has not been performed in this genus. Results Here, we report the identification of LINE elements competent for retrotransposition in Octopus vulgaris and Octopus bimaculoides and show evidence suggesting that they might be transcribed and determine germline and somatic polymorphisms especially in the brain. Transcription and translation measured for one of these elements resulted in specific signals in neurons belonging to areas associated with behavioral plasticity. We also report the transcription of thousands of lncRNAs and the pervasive inclusion of TE fragments in the transcriptomes of both Octopus species, further testifying the crucial activity of TEs in the evolution of the octopus genomes. Conclusions The neural transcriptome of the octopus shows the transcription of thousands of putative lncRNAs and of a full-length LINE element belonging to the RTE class. We speculate that a convergent evolutionary process involving retrotransposons activity in the brain has been important for the evolution of sophisticated cognitive abilities in this genus.