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Abstract BackgroundUniversal single-copy orthologs are the most conserved components of genomes. Although they are routinely used for studying evolutionary histories and assessing new assemblies, current methods do not incorporate information from available genomic data. ResultsHere, we first determine the influence of evolutionary history on universal gene content and find that across 11,098 genomes of plants, fungi, and animals comprising 2606 taxonomic groups, 215 groups significantly vary from their respective lineages in terms of BUSCO (Benchmarking Universal Single Copy Orthologs) completeness. Additionally, 169 groups display an elevated complement of duplicated orthologs, likely from ancestral whole genome duplication events. Secondly, we investigate the extent of taxonomic congruence in broad BUSCO-derived phylogenies. For 275 suitable families out of 543 tested, sites evolving at higher rates produce at most 23.84% more taxonomically concordant, and at least 46.15% less terminally variable phylogenies compared to lower-rate sites. We find that BUSCO concatenated and coalescent trees have comparable accuracy and conclude that higher rate sites from concatenated alignments produce the most congruent and least variable phylogenies. Finally, we show that undetected, yet pervasive BUSCO gene loss events lead to misrepresentations of assembly quality. To overcome this, we filter a Curated set of BUSCOs (CUSCOs) that provide up to 6.99% fewer false positives compared to the standard search and introduce novel methods for comparing assemblies using gene synteny. ConclusionsOverall, we highlight the importance of considering evolutionary histories during assembly evaluations and release the phyca software toolkit that reconstructs consistent phylogenies and offers more precise assembly assessments. 

Abstract PremisePectocarya recurvata(Boraginaceae, subfamily Cynoglossoideae), a species native to the Sonoran Desert (North America), has served as a model system for a suite of ecological and evolutionary studies. However, no reference genomes are currently available in Cynoglossoideae. A high‐quality reference genome forP. recurvatawould be valuable for addressing questions in this system and across broader taxonomic scales. MethodsUsing PacBio HiFi sequencing, we assembled a reference genome forP. recurvataand annotated coding regions with full‐length transcripts from an Iso‐Seq library. We assessed genome completeness with BUSCO andk‐mer analysis, and estimated the genome size of six individuals using flow cytometry. ResultsThe chromosome‐scale genome assembly forP. recurvatawas 216.0 Mbp long (N50 = 12.1 Mbp). Previous observations indicatedP. recurvatais 2n = 24. Our assembly included 12 primary contigs (158.3 Mbp) containing 30,655 genes with telomeres at 23 out of 24 ends. Flow cytometry measurements from the same population included two plants with 1C = 196.9 Mbp, the smallest measured for Boraginaceae, and four with 1C = 385.8 Mbp, which is consistent with tetraploidy in this population. DiscussionTheP. recurvatagenome assembly and annotation provide a high‐quality genomic resource in a sparsely represented area of the angiosperm phylogeny. This new reference genome will facilitate answering open questions in ecophysiology, biogeography, and systematics. 

Abstract Terrestrial planets in the habitable zone (HZ) of Sun-like stars are priority targets for detection and observation by the next generation of space telescopes. Earth's long-term habitability may have been tied to the geological carbon cycle, a process critically facilitated by plate tectonics. In the modern Earth, plate motion corresponds to a mantle convection regime called mobile lid. The alternate, stagnant-lid regime is found on Mars and Venus, which may have lacked strong enough weathering feedback to sustain surface liquid water over geological timescales if initially present. Constraining observational strategies able to infer the most common regime in terrestrial exoplanets requires quantitative predictions of the atmospheric composition of planets in either regime. We use end-member models of volcanic outgassing and crust weathering for the stagnant- and mobile-lid convection regimes, which we couple to models of atmospheric chemistry and climate and ocean chemistry to simulate the atmospheric evolution of these worlds in the HZ. In our simulations under the two alternate regimes, we find that the fraction of planets possessing climates consistent with surface liquid water is virtually the same. Despite this unexpected similarity, we predict that a mission capable of detecting atmospheric CO₂abundance above 0.1 bar in 25 terrestrial exoplanets is extremely likely (≥95% of samples) to infer the dominant interior convection regime in that sample with strong evidence (10:1 odds). This offers guidance for the specifications of the Habitable Worlds Observatory NASA concept mission and other future missions capable of probing samples of habitable exoplanets. 

Abstract A thorough understanding of adaptation and speciation requires model organisms with both a history of ecological and phenotypic study as well as a complete set of genomic resources. In particular, high-quality genome assemblies of ecological model organisms are needed to assess the evolution of genome structure and its role in adaptation and speciation. Here, we generate new genomes of cactophilic Drosophila, a crucial model clade for understanding speciation and ecological adaptation in xeric environments. We generated chromosome-level genome assemblies and complete annotations for seven populations across Drosophila mojavensis, Drosophila arizonae, and Drosophila navojoa. We use these data first to establish the most robust phylogeny for this clade to date, and to assess patterns of molecular evolution across the phylogeny, showing concordance with a priori hypotheses regarding adaptive genes in this system. We then show that structural evolution occurs at constant rate across the phylogeny, varies by chromosome, and is correlated with molecular evolution. These results advance the understanding of the D. mojavensis clade by demonstrating core evolutionary genetic patterns and integrating those patterns to generate new gene-level hypotheses regarding adaptation. Our data are presented in a new public database (cactusflybase.arizona.edu), providing one of the most in-depth resources for the analysis of inter- and intraspecific evolutionary genomic data. Furthermore, we anticipate that the patterns of structural evolution identified here will serve as a baseline for future comparative studies to identify the factors that influence the evolution of genome structure across taxa. 

Abstract Soil microorganisms are pivotal in the global carbon cycle, but the viruses that affect them and their impact on ecosystems are less understood. In this study, we explored the diversity, dynamics, and ecology of soil viruses through 379 metagenomes collected annually from 2010 to 2017. These samples spanned the seasonally thawed active layer of a permafrost thaw gradient, which included palsa, bog, and fen habitats. We identified 5051 virus operational taxonomic units (vOTUs), doubling the known viruses for this site. These vOTUs were largely ephemeral within habitats, suggesting a turnover at the vOTU level from year to year. While the diversity varied by thaw stage and depth‐related patterns were specific to each habitat, the virus communities did not significantly change over time. The abundance ratios of virus to host at the phylum level did not show consistent trends across the thaw gradient, depth, or time. To assess potential ecosystem impacts, we predicted hostsin silicoand found viruses linked to microbial lineages involved in the carbon cycle, such as methanotrophy and methanogenesis. This included the identification of viruses ofCandidatusMethanoflorens, a significant global methane contributor. We also detected a variety of potential auxiliary metabolic genes, including 24 carbon‐degrading glycoside hydrolases, six of which are uniquely terrestrial. In conclusion, these long‐term observations enhance our understanding of soil viruses in the context of climate‐relevant processes and provide opportunities to explore their role in terrestrial carbon cycling. 

Abstract The Madrean Sky Islands are mountain ranges isolated by a ‘desert sea’. This area is a biodiversity hotspot currently threatened by climate change. Here, we studied soil microbial communities along elevational gradients in eight Madrean Sky Islands in southeastern Arizona (USA). Our results showed that while elevational microbial richness gradients were weak and not consistent across different mountains, soil properties strongly influenced microbial community composition (overall composition and the abundance of key functional groups) along elevational gradients. In particular, warming is associated with a higher abundance of soil‐borne fungal plant pathogens that concomitantly might facilitate upward elevational shifts of plant species released from negative plant–soil feedbacks. Furthermore, projected warming and drought in the area aggravated by anthropogenic nitrogen deposition on mountain tops (and thus, decreasing nitrogen limitation) can enhance a shift from ectomycorrhizal to arbuscular mycorrhizal fungi. Overall, these results indicate that climate change effects on plant–soil interactions might have profound ecosystem consequences. 

Abstract The assembly of genomes from pooled samples of genetically heterogenous samples of conspecifics remains challenging. In this study, we show that high‐quality genome assemblies can be produced from samples of multiple wild‐caught individuals. We sequenced DNA extracted from a pooled sample of conspecific herbivorous insects (Hemiptera: Miridae:Tupiocoris notatus) acquired from a greenhouse infestation in Tucson, Arizona (in the range of 30–100 individuals; 0.5 mL tissue by volume) using PacBio highly accurate long reads (HiFi). The initial assembly contained multiple haplotigs (>85% BUSCOs duplicated), but duplicate contigs could be easily purged to reveal a highly complete assembly (95.6% BUSCO, 4.4% duplicated) that is highly contiguous by short‐read assembly standards (N₅₀ = 675 kb; Largest contig = 4.3 Mb). We then used our assembly as the basis for a genome‐guided differential expression study of host plant‐specific transcriptional responses. We found thousands of genes (N = 4982) to be differentially expressed between our new data from individuals feeding onDatura wrightii(Solanaceae) and existing RNA‐seq data fromNicotiana attenuata(Solanaceae)‐fed individuals. We identified many of these genes as previously documented detoxification genes such as glutathione‐S‐transferases, cytochrome P450s, and UDP‐glucosyltransferases. Together our results show that long‐read sequencing of pooled samples can provide a cost‐effective genome assembly option for small insects and can provide insights into the genetic mechanisms underlying interactions between plants and herbivorous pests. 

ABSTRACT Many insects inhabiting temperate climates are faced with changing environmental conditions throughout the year. Depending on the species, these environmental fluctuations can be experienced within a single generation or across multiple generations. Strategies for dealing with these seasonal changes vary across populations. Drosophila mojavensis is a cactophilic Drosophila species endemic to the Sonoran Desert. The Sonoran Desert regularly reaches temperatures of 50°C in the summer months. As individuals of this population are rare to collect in the summer months, we simulated the cycling temperatures experienced by D. mojavensis in the Sonoran Desert from April to July (four generations) in a temperature- and light-controlled chamber, to understand the physiological and life history changes that allow this population to withstand these conditions. In contrast to our hypothesis of a summer aestivation, we found that D. mojavensis continue to reproduce during the summer months, albeit with lower viability, but the adult survivorship of the population is highly reduced during this period. As expected, stress resistance increased during the summer months in both the adult and the larval stages. This study examines several strategies for withstanding the Sonoran Desert summer conditions which may be informative in the study of other desert endemic species. 

Abstract Lichen thalli are formed through the symbiotic association of a filamentous fungus and photosynthetic green alga and/or cyanobacterium. Recent studies have revealed lichens also host highly diverse communities of secondary fungal and bacterial symbionts, yet few studies have examined the viral component within these complex symbioses. Here, we describe viral biodiversity and functions in cyanolichens collected from across North America and Europe. As current machine-learning viral-detection tools are not trained on complex eukaryotic metagenomes, we first developed efficient methods to remove eukaryotic reads prior to viral detection and a custom pipeline to validate viral contigs predicted with three machine-learning methods. Our resulting high-quality viral data illustrate that every cyanolichen thallus contains diverse viruses that are distinct from viruses in other terrestrial ecosystems. In addition to cyanobacteria, predicted viral hosts include other lichen-associated bacterial lineages and algae, although a large fraction of viral contigs had no host prediction. Functional annotation of cyanolichen viral sequences predicts numerous viral-encoded auxiliary metabolic genes (AMGs) involved in amino acid, nucleotide, and carbohydrate metabolism, including AMGs for secondary metabolism (antibiotics and antimicrobials) and fatty acid biosynthesis. Overall, the diversity of cyanolichen AMGs suggests that viruses may alter microbial interactions within these complex symbiotic assemblages.