Castro L. Filipe C.

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L. Filipe C.

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  • Article
    A 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.
  • Article
    Basal gnathostomes provide unique insights into the evolution of vitamin B12 binders
    (Oxford University Press, 2014-12-31) Lopes-Marques, Monica ; Ruivo, Raquel ; Delgado, Ines ; Wilson, Jonathan M. ; Aluru, Neelakanteswar ; Castro, L. Filipe C.
    The uptake and transport of vitamin B12 (cobalamin; Cbl) in mammals involves a refined system with three evolutionarily related transporters: transcobalamin 1 (Tcn1), transcobalamin 2 (Tcn2), and the gastric intrinsic factor (Gif). Teleosts have a single documented binder with intermediate features to the human counterparts. Consequently, it has been proposed that the expansion of Cbl binders occurred after the separation of Actinopterygians. Here, we demonstrate that the diversification of this gene family took place earlier in gnathostome ancestry. Our data indicates the presence of single copy orthologs of the Sarcopterygii/Tetrapoda duplicates Tcn1 and Gif, and Tcn2, in Chondrichthyes. In addition, a highly divergent Cbl binder was found in the Elasmobranchii. We unveil a complex scenario forged by genome, tandem duplications and lineage-specific gene loss. Our findings suggest that from an ancestral transporter, exhibiting large spectrum and high affinity binding, highly specific Cbl transporters emerged through gene duplication and mutations at the binding pocket.