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.
Insights into the evolution of non-model organisms are limited by the lack of reference genomes of high accuracy, completeness, and contiguity. Here, we present a chromosome-level, ...karyotype-validated reference genome and pangenome for the barn swallow (Hirundo rustica). We complement these resources with a reference-free multialignment of the reference genome with other bird genomes and with the most comprehensive catalog of genetic markers for the barn swallow. We identify potentially conserved and accelerated genes using the multialignment and estimate genome-wide linkage disequilibrium using the catalog. We use the pangenome to infer core and accessory genes and to detect variants using it as a reference. Overall, these resources will foster population genomics studies in the barn swallow, enable detection of candidate genes in comparative genomics studies, and help reduce bias toward a single reference genome.
Display omitted
•Generation of a high-quality annotated reference genome and pangenome for barn swallow•Generation of comprehensive barn swallow genetic variants catalog•Multispecies alignment and variants catalog detected list of candidate genes•Pangenome improves read mapping and variant calling
Secomandi et al. present a chromosome-level genome and pangenome for the barn swallow. They generate a large catalog of worldwide genetic variants and identify genomic regions potentially under selection. They also compare the barn swallow genome with that of other bird species to detect conserved and accelerated genes.
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 >100-fold, closes >23,000 gaps of the CanFam3.1 reference assembly and improves gene annotation by identifying >1200 new protein-coding transcripts. The assembly and annotation are available at NCBI under the accession GCF_000002285.5.
Societal Impact Statement
Society anticipates a world in which more food and fiber must be produced at warmer temperatures, which, on the contrary, have greater constraints on the use of water and ...fertilizers. Tree legumes are often the climax vegetation on the semi‐arid and arid lands, covering ~25% of the planet, but the knowledge of their genomes is limited. A draft genome sequence for Prosopis alba, a salt and heat tolerant tree that is able to fix nitrogen under harsh conditions, yields new clues about its adaptations. Its rich genetic and ecological diversity makes Prosopis well‐suited to the investigation of gene functions important to its own greater utilization and/or the improvement of climate resilience of other crops.
Summary
In arid lands that comprise 41% of the Earth's surface and are growing, tree legumes are often the climax vegetation. Now found in much of arid America, Prosopis alba is a salt‐tolerant nitrogen‐fixing tree native to Argentina.
We present a Prosopis alba genome assembly that is 707 Mb in size, comprising of 6087 contigs of up to 2,077,851 bp in length and of ~359.3 Mb (50.8%) being repetitive elements dominated (20.3%) by long terminal repeats (LTR) retrotransposons. Among a total of 57,572 coding sequences (CDS), 42,475 are putative protein coding genes with median length of 2748 bp. The Prosopis alba genome shares the legume‐common tetraploidy (LCT) but has not reduplicated, evolving 3.5% and 23.1% faster than Phaseolus vulgaris and Glycine max, respectively, since the LCT.
The 50 most expanded gene families include many that are involved in ion homeostasis, perhaps related to drought and/or salt adaptation, together with photosynthetic genes carbonic anhydrase (CA), malate dehydrogenase (MDH) and malic enzyme and gene families involved in circadian clock systems, synthesis of brassinosteroids, auxin and gibberellin. Some expanded gene families include members showing molecular signatures of positive selection, as do numerous multi‐copy orthologous groups with features associated with pathogen resistance and single‐copy orthogroups related to drought and salt stress response, root and root hair development, nodulation, heavy metal detoxification and stay‐green habit.
Coupling genomics‐based clues about possible causes of its striking physiological adaptations with rich diversity in ecological context offers means to further investigate functional roles of specific Prosopis genes/alleles.
Society anticipates a world in which more food and fiber must be produced at warmer temperatures, which, on the contrary, have greater constraints on the use of water and fertilizers. Tree legumes are often the climax vegetation on the semi‐arid and arid lands, covering ~25% of the planet, but the knowledge of their genomes is limited. A draft genome sequence for Prosopis alba, a salt and heat tolerant tree that is able to fix nitrogen under harsh conditions, yields new clues about its adaptations. Its rich genetic and ecological diversity makes Prosopis well‐suited to the investigation of gene functions important to its own greater utilization and/or the improvement of climate resilience of other crops.
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.
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 (
) and green (
) 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.
Despite high sequence identity among mammalian prion proteins (PrPs), 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, which 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 on 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 PrPs 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.
The article considers a particular case of Richard Kearney's characteristic hermeneutical exploration of `the possible' as an `imaginative' way of casting light upon philosophical issues. This ...particular case is his recent hermeneutical and phenomenological consideration of `Otherness' in the context of philosophy of religion. This consideration, strongly influenced by philosophers such as Heidegger, Levinas, Ricoeur and Derrida, is developed in two of his recent works Strangers, Gods and Monsters and The God Who May Be.
The article examines how he seeks to navigate an interpretation of divine otherness as an ethical appeal which escapes the dilemma of a God either so transcendent as to be anonymous or so immanent as to be a mere projection. It outlines how, rejecting onto-theology in favour of eschatology, Kearney envisages the divine as an ethically enabling possibility. This possibility, he claims, enables us to achieve, beyond our own intrinsic resources, an ethical order of justice and love through which the kingdom of God — the God Who May Be — is accomplished. There is a co-relativity between the divine as enabling possibility and humanity which accomplishes this possibility.
It investigates the way in which Kearney seeks to legitimize, within a phenomenological frame of reference, an experiential affirmation of this conception of divine transcendence as eschatological possibility. It argues that this phenomenological consideration needs to be qualified and complemented by certain metaphysical considerations which Kearney disputes.
PDF
