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The European sardine (Sardina pilchardus Walbaum, 1792) is culturally and economically important throughout its distribution. Monitoring studies of sardine populations report an alarming decrease in stocks due to overfishing and environmental change, which has resulted in historically low captures along the Iberian Atlantic coast. Important biological and ecological features such as population diversity, structure, and migratory patterns can be addressed with the development and use of genomics resources. Agência financiadora Portuguese national funds from FCT-Foundation for Science and Technology: UID/Multi/04326/2016; European Regional Development Fund (FEDER): 22153-01/SAICT/2016; ALG-01-0145-FEDER-022121; ALG-01-0145-FEDER-022231; MAR2020 operational programme of the European Maritime and Fisheries Fund (project SARDI-NOMICS): MAR-01.04.02-FEAMP-0024; European Union's Horizon 2020 research and innovation programme: 654008 info:eu-repo/semantics/publishedVersion

Venom research is a highly multidisciplinary field that involves multiple subfields of biology, informatics, pharmacology, medicine, and other areas. These different research facets are often technologically challenging and pursued by different teams lacking connection with each other. This lack of coordination hampers the full development of venom investigation and applications. The COST Action CA19144-European Venom Network was recently launched to promote synergistic interactions among different stakeholders and foster venom research at the European level. ispartof: GIGASCIENCE vol:10 issue:3 ispartof: location:United States status: published

Abstract Background The teleost fish Monopterus albus is emerging as a new model for biological studies due to its natural sex transition and small genome, in addition to its enormous economic and potential medical value. However, no genomic information for the Monopterus is currently available. Findings Here, we sequenced and de novo assembled the genome of M. albus and report the de novochromosome assembly by FISH walking assisted by conserved synteny (Cafs). Using Cafs, 328 scaffolds were assembled into 12 chromosomes, which covered genomic sequences of 555 Mb, accounting for 81.3% of the sequences assembled in scaffolds (∼689 Mb). A total of 18 ,660 genes were mapped on the chromosomes and showed a nonrandom distribution along chromosomes. Conclusions We report the first reference genome of the Monopterus and provide an efficient Cafs strategy for a de novo chromosome-level assembly of the Monopterus genome, which provides a valuable resource, not only for further studies in genetics, evolution, and development, particularly sex determination, but also for breed improvement of the species.

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. Rede Nacional de Espectrometria de Massa | Ref. LISBOA-01-0145-FEDER-022125 Biotechnology and Biological Sciences Research Council | Ref. BB/M009122/1 COMPETE and North Portugal Regional Operational Programme | Ref. Norte2020 Biotechnology and Biological Sciences Research Council | Ref. BB/N020146/1 Vedecká Grantová Agentúra MŠVVaŠ SR a SAV | Ref. SFRH/BD/126560/2016 Netherlands Organization for Scientific Research | Ref. 825.09.016 Rede Nacional de Espectrometria de Massa | Ref. ROTEIRO/0028/2013 European Regional Development Fund | Ref. UID/Multi/04423/2019 Vedecká Grantová Agentúra MŠVVaŠ SR a SAV | Ref. 1/0458/18 Vedecká Grantová Agentúra MŠVVaŠ SR a SAV | Ref. 1/0684/16 Portuguese Science Foundation | Ref. PTDC/MAR/115347/2009 Portuguese Science Foundation | Ref. COMPETE-FCOMP-01-012 Portuguese Science Foundation | Ref. FP7-PEOPLE-2010-IEF Deutsche Forschungsgemeinschaft | Ref. HO 5569/2-1 Portuguese Science Foundation | Ref. FEDER-015453 Danish National Research Foundation | Ref. DNRF94 Danish National Research Foundation | Ref. DNRF96 Novo Nordisk Foundation | Ref. NNF14CC0001 DeiC National Life Science Supercomputer European Molecular Biology Laboratory Wellcome Trust | Ref. WT108749/Z/15/Z Lundbeck Foundation | Ref. R52-A4895 Lundbeck Foundation | Ref. R52–5062 David and Lucile Packard Foundation Villum Fonden | Ref. VKR023446 National Science Foundation

Abstract Background With more than 30,000 species, fish—including bony, jawless, and cartilaginous fish—are the largest vertebrate group, and include some of the earliest vertebrates. Despite their critical roles in many ecosystems and human society, fish genomics lags behind work on birds and mammals. This severely limits our understanding of evolution and hinders progress on the conservation and sustainable utilization of fish. Results Here, we announce the Fish10K project, a portion of the Earth BioGenome Project aiming to sequence 10,000 representative fish genomes in a systematic fashion within 10 years, and we officially welcome collaborators to join this effort. As a step towards this goal, we herein describe a feasible workflow for the procurement and storage of biospecimens, as well as sequencing and assembly strategies. Conclusions To illustrate, we present the genomes of 10 fish species from a cohort of 93 species chosen for technology development.