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Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of noncollinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared with other reptiles, and harbor a higher genetic load compared with green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage. This work was completed in part with resources provided by the University of Massachusetts' Green High Performance Computing Cluster (GHPCC). Funding was provided by the University of Massachusetts Amherst, NSF-IOS (grant #1904439 to L.M.K.), NOAA-Fisheries, National Research Council postdoctoral fellowship program to L.M.K., VGP, Rockefeller University, to E.D.J., HHMI to E.D.J., the Sanger Institute, Max-Planck-Gesellschaft, and grant contributions from Tom Gilbert, Paul Flicek, R.W.M., Karen A. Bjorndal, Alan B. Bolten, Ed Braun, N.J.G., T.M.-B., and A.F.S. We acknowledge CONICYT-DAAD for scholarship support to T.C.-V., the São Paulo Research Foundation to E.K.S.R.–FAPESP (grant #2020/10372-6). BeGenDiv is partially funded by the German Federal Ministry of Education and Research (BMbF, Förderkennzeichen 033W034A). The work of F.T.-N. and P.M. was supported by the Intramural Research Program of the National Library of Medicine, NIH. The work of M.P. was partially funded through the Federal Ministry of Education and Research (grant 01IS18026C). H.P. was supported by a Formació de Personal Investigador fellowship from Generalitat de Catalunya (FI_B100131). M.K. was supported by “la Caixa” Foundation (ID 100010434; code LCF/BQ/PR19/11700002), the Vienna Science and Technology Fund (WWTF), and the City of Vienna (VRG20-001). Funding for green turtle resequencing was provided by a Welsh Government Sêr Cymru II and the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 663830-BU115 and the Sea Turtle Conservancy, Florida Sea Turtle Grants Program (17-033R).

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1,2,3,4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences., We thank them for their permission to publish. A.R., S.K., B.P.W. and A.M.P. were supported by the Intramural Research Program of the NHGRI, NIH (1ZIAHG200398). A.R. was also supported by the Korea Health Technology R&D Project through KHIDI, funded by the Ministry of Health & Welfare, Republic of Korea (HI17C2098). S.A.M., I.B. and R.D. were supported by Wellcome Trust grant WT207492; W.C., M. Smith, Z.N., Y.S., J.C., S. Pelan, J.T., A.T., J.W. and Kerstin Howe by WT206194; L.H., F.M., Kevin Howe and P. Flicek by WT108749/Z/15/Z, WT218328/B/19/Z and the European Molecular Biology Laboratory. O.F. and E.D.J. were supported by Howard Hughes Medical Institute and Rockefeller University start-up funds for this project. J.D. and H.A.L. were supported by the Robert and Rosabel Osborne Endowment. M.U.-S. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement (750747). F.T.-N., J. Hoffman, P. Masterson and K.C. were supported by the Intramural Research Program of the NLM, NIH. C.L., B.J.K., J. Kim and H.K. were supported by the Marine Biotechnology Program of KIMST, funded by the Ministry of Ocean and Fisheries, Republic of Korea (20180430). M.C. was supported by Sloan Research Fellowship (FG-2020-12932). S.C.V. was funded by a Max Planck Research Group award from the Max Planck Society, and a Human Frontiers Science Program (HFSP) Research grant (RGP0058/2016). T.M.L., W.E.J. and the Canada lynx genome were funded by the Maine Department of Inland Fisheries & Wildlife (F11AF01099), including when W.E.J. held a National Research Council Research Associateship Award at the Walter Reed Army Institute of Research (WRAIR). C.B. was supported by the NSF (1457541 and 1456612). D.B. was funded by The University of Queensland (HFSP - RGP0030/2015). D.I. was supported by Science Exchange Inc. (Palo Alto, CA). H.W.D. was supported by NSF grants (OPP-0132032 ICEFISH 2004 Cruise, PLR-1444167 and OPP-1955368) and the Marine Science Center at Northeastern University (416). G.J.P.N. and the thorny skate genome were funded by Lenfest Ocean Program (30884). M.P. was funded by the German Federal Ministry of Education and Research (01IS18026C). M. Malinsky was supported by an EMBO fellowship (ALTF 456-2016). The following authors’ contributions were supported by the NIH: S. Selvaraj (R44HG008118); C.V.M., S.R.F., P.V.L. (R21 DC014432/DC/NIDCD); K.D.M. (R01GM130691); H.C. (5U41HG002371-19); M.D. (U41HG007234); and B.P. (R01HG010485). D.G. was supported by the National Key Research and Development Program of China (2017YFC1201201, 2018YFC0910504 and 2017YFC0907503). F.O.A. was supported by Al-Gannas Qatari Society and The Cultural Village Foundation-Katara, Doha, State of Qatar and Monash University Malaysia. C.T. was supported by The Rockefeller University. M. Hiller was supported by the LOEWE-Centre for Translational Biodiversity Genomics (TBG) funded by the Hessen State Ministry of Higher Education, Research and the Arts (HMWK). H.C. was supported by the NHGRI (5U41HG002371-19). R.H.S.K. was funded by the Max Planck Society with computational resources at the bwUniCluster and BinAC funded by the Ministry of Science, Research and the Arts Baden-Württemberg and the Universities of the State of Baden-Württemberg, Germany (bwHPC-C5). B.V. was supported by the Biomedical Research Council of A*STAR, Singapore. T.M.-B. was funded by the European Research Council under the European Union’s Horizon 2020 research and innovation programme (864203), MINECO/FEDER, UE (BFU2017-86471-P), Unidad de Excelencia María de Maeztu, AEI (CEX2018-000792-M), a Howard Hughes International Early Career award, Obra Social “La Caixa” and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). E.C.T. was supported by the European Research Council (ERC-2012-StG311000) and an Irish Research Council Laureate Award. M.T.P.G. was supported by an ERC Consolidator Award 681396-Extinction Genomics, and a Danish National Research Foundation Center Grant (DNRF143). T.W. was supported by the NSF (1458652). J. M. Graves was supported by the Australian Research Council (CEO561477). E.W.M. was partially supported by the German Federal Ministry of Education and Research (01IS18026C). Complementary sequencing support for the Anna’s hummingbird and several genomes was provided by Pacific Biosciences, Bionano Genomics, Dovetail Genomics, Arima Genomics, Phase Genomics, 10X Genomics, NRGene, Oxford Nanopore Technologies, Illumina, and DNAnexus. All other sequencing and assembly were conducted at the Rockefeller University, Sanger Institute, and Max Planck Institute Dresden genome labs. Part of this work used the computational resources of the NIH HPC Biowulf cluster (https://hpc.nih.gov). We acknowledge funding from the Wellcome Trust (108749/Z/15/Z) and the European Molecular Biology Laboratory., With funding from the Spanish government through the "Severo Ochoa Centre of Excellence" accreditation (CEX2018-000792-M).

The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes.We use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes.The AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures.

The domestic dog has evolved to be an important biomedical model for studies regarding the genetic basis of disease, morphology and behavior. Genetic studies in the dog have relied on a draft reference genome of a purebred female boxer dog named “Tasha” initially published in 2005. Derived from a Sanger whole genome shotgun sequencing approach coupled with limited clone-based sequencing, the initial assembly and subsequent updates have served as the predominant resource for canine genetics for 15 years. While the initial assembly produced a good-quality draft, as with all assemblies produced at the time, it contained gaps, assembly errors and missing sequences, particularly in GC-rich regions, which are found at many promoters and in the first exons of protein-coding genes. Here, we present Dog10K_Boxer_Tasha_1.0, an improved chromosome-level highly contiguous genome assembly of Tasha created with long-read technologies that increases sequence contiguity &gt, 100-fold, closes &gt, 23,000 gaps of the CanFam3.1 reference assembly and improves gene annotation by identifying &gt, 1200 new protein-coding transcripts. The assembly and annotation are available at NCBI under the accession GCF_000002285.5.

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are only available for a few non-microbial species1–4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling the most accurate and complete reference genomes to date. Here we summarize these developments, introduce a set of quality standards, and present lessons learned from sequencing and assembling 16 species representing major vertebrate lineages (mammals, birds, reptiles, amphibians, teleost fishes and cartilaginous fishes). We confirm that long-read sequencing technologies are essential for maximizing genome quality and that unresolved complex repeats and haplotype heterozygosity are major sources of error in assemblies. Our new assemblies identify and correct substantial errors in some of the best historical reference genomes. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an effort to generate high-quality, complete reference genomes for all ~70,000 extant vertebrate species and help enable a new era of discovery across the life sciences.

BackgroundHalyomorpha halys(Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species’ feeding and habitat traits, defining potential targets for pest management strategies.ResultsAnalysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely supportH. halys’ capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications.ConclusionsAvailability of theH. halysgenome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls.

Background The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes. Results We use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes. Conclusion The AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures.

We have developed a novel laser heterodyne radiometer using a fiber-coupled distributed feedback laser as the local oscillator to perform spectroscopic measurements of small molecules in the near-infrared (NIR) spectral region. Here, we demonstrate measurement of HCN and C O 2 in the lab and C H 4 and C O 2 in the atmospheric column. In addition, we demonstrate detection of a neutral iron, Fe(I), Fraunhofer line in the spectrum of the sun, at a vacuum wavelength of 1559.252 nm, that can be used to calibrate the wavelength scale of the instrument and enable verification of proper system operation for field applications.

The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55 000 organisms (>4800 viruses, >40 000 prokaryotes and >10 000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.

Despite high sequence identity among mammalian prion proteins, mammals have varying rates of susceptibility to prion disease resulting in a so-called species barrier. The species barrier follows no clear pattern, with closely related species or similar sequences being no more likely to infect each other, and remains an unresolved enigma. Variation of the conformationally flexible regions may alter the thermodynamics of the conformational change, commonly referred to as the conformational conversion, that occurs in the pathogenic process of the mammalian prion protein. A conformational ensemble scenario is supported by the species barrier in prion disease and evidence that there are strains of pathogenic prion with different conformations within species. To study how conformational flexibility has evolved in the prion protein, an investigation was undertaken of the evolutionary dynamics of structurally disordered regions in the mammalian prion protein, non-mammalian prion protein that is not vulnerable to prion disease, and remote homologs Doppel and Shadoo. Structural disorder prediction analyzed in an evolutionary context revealed that the occurrence of increased or altered conformational flexibility in mammalian prion proteins coincides with key events among PrP, Doppel, and Shadoo. Comparatively rapid evolutionary dynamics of conformational flexibility in the prion protein suggest that the species barrier is not a static phenomenon. A small number of amino acid substitutions can repopulate the conformational ensemble and have a disproportionately large effect on pathogenesis.

Protein structure is commonly regarded to be conserved and to dictate function. Most proteins rely on conformational flexibility to some degree. Are regions that convey conformational flexibility conserved over evolutionary time? Can changes in conformational flexibility alter protein function? Here, the evolutionary dynamics of structurally ordered and disordered (flexible) regions are investigated genome-wide in flaviviruses, revealing that the amount and location of structural disorder fluctuates highly among related proteins. Some regions are prone to shift between structured and flexible states. Increased evolutionary dynamics of structural disorder is observed for some lineages but not in others. Lineage-specific transitions of this kind could alter the conformational ensemble accessible to the same protein in different species, causing a functional change, even if the predominant function remains conserved. Thus, rapid evolutionary dynamics of structural disorder is a potential driving force for phenotypic divergence among flaviviruses.

[Editors' Note: Dr. Patrick Masterson, out-going President of the EUI, presented these remarks at the Celebration of the 25th Anniversary of the EUROPEAN UNIVERSITY INSTITUTE in the Badia Fiesolana, Fiesole, Italy, on 7 November 2001. The Editors wish to express gratitude to President Masterson for allowing GLJ to publish his speech] Your Excellencies, President Prodi, distinguished Commissioners, dear Colleagues, Ladies and Gentlemen: [1] It is a great pleasure to welcome you here this afternoon to our birthday celebration which we will continue to celebrate with special events during the coming year. For it is a special birthday, namely our 25th anniversary. From our modest beginnings in 1976 we have grown to be an important independent intellectual resource for Europe, the largest European doctorate programme in our disciplines of law, economics, social and political science and history and civilization and a significant postdoctoral centre for research and advanced studies in the social sciences. [2] Funded by the Member States, the institutions of the European Union, and endowed research funds, the European University Institute is the intellectual alma mater for over 500 doctoral students, 50 professors and about 60 visiting senior researchers - this European intellectual powerhouse is splendidly sustained by a dedicated multinational support staff to all of whom I express warm appreciation and sincere thanks. [3] We will have the pleasure of brief remarks by the President of the Commission, Professor Prodi, the second President of the Institute, Professor Maihofer, the President elect Professor Yves Meny and a young doctorate researcher, Jesse Scott, all of whom I heartily welcome. [4] The founding President of the Institute, Dr Max Kohnstamm, had hoped to be with us today but on medical advice was unable to travel. He has asked me to convey the following greeting on this auspicious day. [5] Ladies and Gentlemen, I am extremely sorry not to be in your midst this afternoon but very grateful to the Institute's President for allowing me nevertheless to join you for a few moments. [6] What strikes me most, thinking back to the solemn opening of the Institute's first academic year, is the incredible development of the Institute that since has taken place. That beginning was indeed extremely modest, some ten professors for the four departments all together, some sixty students chosen from about one hundred applicants and a small administrative staff. [7] I intended to mention a few names from members of the then High Council, the Academic Council, the student body and the administration who made that beginning possible. But I soon realized, however, that that was impossible. I would have to name everybody or no-one because the beginning became a joint effort of all who participated in the adventure, sometimes not without having serious difficulties. and, yes, in the adventure, because an adventure it was! However, I cannot omit to mention the generosity of the Italian Government of those early days which allowed the Institute to settle at the Badia instead of the government's original wish and plan. It then set to restore the Badia with utmost care to its original and actual splendour. Without the continuing generosity of following Italian governments the development we commemorate today would not have happened. Neither would the installation at the Badia have taken place without the good will shown by the then resident Scolopi Fathers who still share the Badia with the Institute. [7] Permit me to make a very few exceptions to the self-imposed rule not to mention anyone especially. I do want to mention two men who are no longer with us. The first one is Ambassador Cattani. He may well be the only person who, during the 21 years that separated the original proposal made by the German delegation at the Conference of Messina in 1955, during all those years never gave up to push for the realization of the proposal. The second one is Marcello Buzzonetti, the Institute's first Secretary General. Without his finesse d'esprit and his total devotion to the Institute the final launching of it might well never have taken place. Forgive me also if I mention the names of two people, happily still present here today. I mentioned them twenty five years ago as examples to us all for their constant good humour, gentleness and presence at work from early morning to late in the evening. One, our first portiere Gastone, and the second his wife Marisa who looked after the very young children of some of our students in order to enable them to concentrate on their studies. [8] At a birthday party one normally takes part and brings a present. Not being present, may I turn this around and express two wishes? The first one: that the Institute's authorities commission a full-blown history of the European University Institute from its inception at Messina in 1955 until the end of the actual President's tenure. The development of the Institute definitively deserves this to be done! My second and last wish goes back to a regret I mentioned 25 years ago. It concerned the absence of a professorial post in the Institute for philosophy. From time to time one of the departments helped through an appointment to at least partly deal with this lacuna - or, if by a happy coincidence a philosopher happened to become the Institute's President! [9] Probably the most important problem our world is now faced with is world order and world governance. It seems to me that political philosophy has a contribution to make in dealing with this problem. It should do this both through studying what philosophers of the past and present have written about the political consequences of their thinking and in exploring new ways of thinking and acting about this central problem now facing us all. This seems to me even more necessary now. Ladies and Gentlemen, may I thank you for your kindness for listening for a moment to someone who would have loved to be with you today. [10] Sadly one of the former Presidents of the Institute, Emile Noel died a few years ago but I am glad to welcome his widow Madame Gobeil Noel here today. Emile Noel will have been well known personally and by repute to our many distinguished visitors here today. I wish to pay a special tribute to his memory and to record the crucial role he played in developing the specifically European focus of so much of the research at the Institute and in developing relations of mutual regard and cooperation between the Institute as an autonomous research resource for Europe and the evolving institutions of the European Union. [11] The research at the Institute speaks for itself and needs no praise from me. Therefore I will confine myself on this happy occasion to just one reflection, namely that over and above the splendid research achievement there is a personal enrichment of people at the Institute which constitutes a precious European added value. [12] We hear much talk today in these difficult times of the clash of cultures and civilizations. I would like to record that the experience here at the Institute gives living evidence that, while respecting diversity, a fruitful level of overlapping cultural consensus is not only possible but can actually be achieved and with most beneficial results. Young researchers coming from Budapest, Berlin, Paris, Dublin, Stockholm, Madrid, the U.S., Africa, Australia and Asia arrive with very diverse culturally embedded frameworks of human experience, value systems and norms of rational enquiry. They come here to what is not any one of these frameworks but rather a pilgrim province of the mind. They find that alternative viewpoints, outlooks and approaches are not just a threat but more profoundly, a challenge, and a possibility of a new comparative way of addressing an issue. They experience not just the possibility but the achieved reality of overlapping cultural consensus - achieved not without difficulty but with great benefit. In this work and experience virtues of tolerance, mutual respect and openness to the value of the Other are pre-reflectively absorbed and consciously developed. This is the real European added value of our experience at the Institute, and the evidence of it is all around you. It provides hope that, on a wider scale, the much-reported clash of cultures and civilizations is not the inevitable end-product of current tensions, but a new opportunity for dialogue and exploration. It provides hope that a fruitful consensus is an achievable ideal. [13] The European University Institute, together with other universities in many other countries, has a significant role to play in this, our common task. Without doubt, this is the confident birthday message that the Institute has for the wider community on its 25th anniversary.

Masterson Patrick, Lefèvre Charles. La définition du fini implique-t-elle l'infini ?. In: Revue Philosophique de Louvain. Troisième série, tome 62, n°73, 1964. pp. 39-68.