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Abstract The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10×, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world's smallest cetacean, to investigate blue whale's unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research. 

Abstract Evolutionary innovations generate phenotypic and species diversity. Elucidating the genomic processes underlying such innovations is central to understanding biodiversity. In this study, we addressed the genomic basis of evolutionary novelties in the glassy-winged sharpshooter (Homalodisca vitripennis, GWSS), an agricultural pest. Prominent evolutionary innovations in leafhoppers include brochosomes, proteinaceous structures that are excreted and used to coat the body, and obligate symbiotic associations with two bacterial types that reside within cytoplasm of distinctive cell types. Using PacBio long-read sequencing and Dovetail Omni-C technology, we generated a chromosome-level genome assembly for the GWSS and then validated the assembly using flow cytometry and karyotyping. Additional transcriptomic and proteomic data were used to identify novel genes that underlie brochosome production. We found that brochosome-associated genes include novel gene families that have diversified through tandem duplications. We also identified the locations of genes involved in interactions with bacterial symbionts. Ancestors of the GWSS acquired bacterial genes through horizontal gene transfer (HGT), and these genes appear to contribute to symbiont support. Using a phylogenomics approach, we inferred HGT sources and timing. We found that some HGT events date to the common ancestor of the hemipteran suborder Auchenorrhyncha, representing some of the oldest known examples of HGT in animals. Overall, we show that evolutionary novelties in leafhoppers are generated by the combination of acquiring novel genes, produced both de novo and through tandem duplication, acquiring new symbiotic associations that enable use of novel diets and niches, and recruiting foreign genes to support symbionts and enhance herbivory. 

Fungi shape the diversity of life. Characterizing the evolution of fungi is critical to understanding symbiotic associations across kingdoms. In this study, we investigate the genomic and metabolomic diversity of the genus Escovopsis , a specialized parasite of fungus-growing ant gardens. Based on 25 high-quality draft genomes, we show that Escovopsis forms a monophyletic group arising from a mycoparasitic fungal ancestor 61.82 million years ago (Mya). Across the evolutionary history of fungus-growing ants, the dates of origin of most clades of Escovopsis correspond to the dates of origin of the fungus-growing ants whose gardens they parasitize. We reveal that genome reduction, determined by both genomic sequencing and flow cytometry, is a consistent feature across the genus Escovopsis, largely occurring in coding regions, specifically in the form of gene loss and reductions in copy numbers of genes. All functional gene categories have reduced copy numbers, but resistance and virulence genes maintain functional diversity. Biosynthetic gene clusters (BGCs) contribute to phylogenetic differences among Escovopsis spp., and sister taxa in the Hypocreaceae. The phylogenetic patterns of co-diversification among BGCs are similarly exhibited across mass spectrometry analyses of the metabolomes of Escovopsis and their sister taxa. Taken together, our results indicate that Escovopsis spp. evolved unique genomic repertoires to specialize on the fungus-growing ant-microbe symbiosis. 

Abstract The futureRicochetexperiment aims at searching for new physics in the electroweak sector by providing a high precision measurement of the Coherent Elastic Neutrino-Nucleus Scattering (CENNS) process down to the sub-100 eV nuclear recoil energy range. The experiment will deploy a kg-scale low-energy-threshold detector array combining Ge and Zn target crystals 8.8 m away from the 58 MW research nuclear reactor core of the Institut Laue Langevin (ILL) in Grenoble, France. Currently, theRicochetCollaboration is characterizing the backgrounds at its future experimental site in order to optimize the experiment’s shielding design. The most threatening background component, which cannot be actively rejected by particle identification, consists of keV-scale neutron-induced nuclear recoils. These initial fast neutrons are generated by the reactor core and surrounding experiments (reactogenics), and by the cosmic rays producing primary neutrons and muon-induced neutrons in the surrounding materials. In this paper, we present theRicochetneutron background characterization using$$^3$$ ${}^3$He proportional counters which exhibit a high sensitivity to thermal, epithermal and fast neutrons. We compare these measurements to theRicochetGeant4 simulations to validate our reactogenic and cosmogenic neutron background estimations. Eventually, we present our estimated neutron background for the futureRicochetexperiment and the resulting CENNS detection significance. Our results show that depending on the effectiveness of the muon veto, we expect a total nuclear recoil background rate between 44 ± 3 and 9 ± 2 events/day/kg in the CENNS region of interest, i.e. between 50 eV and 1 keV. We therefore found that theRicochetexperiment should reach a statistical significance of 4.6 to 13.6 $$\sigma $$ $\sigma$for the detection of CENNS after one reactor cycle, when only the limiting neutron background is considered. 

Abstract The Cryogenic Underground Observatory for Rare Events (CUORE) is the most sensitive experiment searching for neutrinoless double-beta decay (0 νββ ) in 130 Te. CUORE uses a cryogenic array of 988 TeO 2 calorimeters operated at ∼10 mK with a total mass of 741 kg. To further increase the sensitivity, the detector response must be well understood. Here, we present a non-linear thermal model for the CUORE experiment on a detector-by-detector basis. We have examined both equilibrium and dynamic electro-thermal models of detectors by numerically fitting non-linear differential equations to the detector data of a subset of CUORE channels which are well characterized and representative of all channels. We demonstrate that the hot-electron effect and electric-field dependence of resistance in NTD-Ge thermistors alone are inadequate to describe our detectors' energy-dependent pulse shapes. We introduce an empirical second-order correction factor in the exponential temperature dependence of the thermistor, which produces excellent agreement with energy-dependent pulse shape data up to 6 MeV. We also present a noise analysis using the fitted thermal parameters and show that the intrinsic thermal noise is negligible compared to the observed noise for our detectors. 

Abstract An array of twelve 0.28 kg lithium molybdate (LMO) low-temperature bolometers equipped with 16 bolometric Ge light detectors, aiming at optimization of detector structure for CROSS and CUPID double-beta decay experiments, was constructed and tested in a low-background pulse-tube-based cryostat at the Canfranc underground laboratory in Spain. Performance of the scintillating bolometers was studied depending on the size of phonon NTD-Ge sensors glued to both LMO and Ge absorbers, shape of the Ge light detectors (circular vs. square, from two suppliers), in different light collection conditions (with and without reflector, with aluminum coated LMO crystal surface). The scintillating bolometer array was operated over 8 months in the low-background conditions that allowed to probe a very low, μBq/kg, level of the LMO crystals radioactive contamination by 228 Th and 226 Ra. 

Abstract CUPID is a next-generation bolometric experiment aiming at searching for neutrinoless double-beta decay with ∼250 kg of isotopic mass of 100 Mo. It will operate at ∼10 mK in a cryostat currently hosting a similar-scale bolometric array for the CUORE experiment at the Gran Sasso National Laboratory (Italy). CUPID will be based on large-volume scintillating bolometers consisting of 100 Mo-enriched Li 2 MoO 4 crystals, facing thin Ge-wafer-based bolometric light detectors. In the CUPID design, the detector structure is novel and needs to be validated. In particular, the CUORE cryostat presents a high level of mechanical vibrations due to the use of pulse tubes and the effect of vibrations on the detector performance must be investigated. In this paper we report the first test of the CUPID-design bolometric light detectors with NTD-Ge sensors in a dilution refrigerator equipped with a pulse tube in an above-ground lab. Light detectors are characterized in terms of sensitivity, energy resolution, pulse time constants, and noise power spectrum. Despite the challenging noisy environment due to pulse-tube-induced vibrations, we demonstrate that all the four tested light detectors comply with the CUPID goal in terms of intrinsic energy resolution of 100 eV RMS baseline noise. Indeed, we have measured 70–90 eV RMS for the four devices, which show an excellent reproducibility. We have also obtained high energy resolutions at the 356 keV line from a 133 Ba source, as good as Ge semiconductor γ detectors in this energy range.