Biology subjects

Brown, A.

Publications and source records attributed to Brown, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Proteome-wide in silico screening for human protein-protein interactions

Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational screen for human PPIs. First, a classifier called KIRC (Knowledge-Informed Rapid Classifier), trained on biological features, was used to rank all 200 million possible protein pairs in the human proteome by their interaction likelihood. Second, the [~]1.6 million top-ranked KIRC pairs were subjected to structure prediction by AlphaFold-Multimer and ranked using SPOC (Structure Prediction and Omics Classifier), which identifies functional predictions based on biological and structural features. This pipeline revealed 16,000 high-confidence PPIs ([~]90% precision), of which more than 5,000 were not previously recognized and more than 12,000 have not been structurally resolved. We use this "predictome" to formulate new hypotheses in different areas of biology, reinterpret low-resolution cryo-EM maps, and identify and validate novel PPIs that may support replication-coupled chromatin assembly. The predicted PPIs, viewable at predictomes.org, are expected to accelerate characterization of the molecular interactions that underlie vertebrate cell physiology.

bioinformatics↗

bioRxiv2025

NF-kB-Dependent Transcriptional Regulation of Piezo1 Mediates Bacterial Clearance on Stiffened Lung

Respiratory pathogens, such as Pseudomonas aeruginosa damage the alveolar-capillary barrier leading to lung injury and stiffness. Lung stiffness is a key macrophage signal for bacterial clearance, but it remains unknown how stiffness-sensing mechanosensitive ion channels in macrophages are regulated during pneumonia. Macrophage Piezo1 is critical to bacterial clearance in experimental pneumonia in vivo; however, identification of putative matrix-derived signals and the mechanism of their effects remain to be determined. To our knowledge, our work is the first to show that during pneumonia, transcription of the mechanosensitive ion channel Piezo1 is increased in macrophages by the NF-{kappa}B transcription factor, p65, through its signaling adaptor protein, MyD88, leading to increased Piezo1 Ca2+ channel activity. Piezo1 mRNA abundance is increased in association with open chromatin at the Piezo1 promoter in macrophages. The enhanced level of Piezo1 increases the abundance of transcription factor EB (Tfeb) resulting in lysosome biogenesis and stiffness-dependent phagolysosome maturation, a critical step for macrophage bacterial clearance. Our data support the mechanism whereby transcription of macrophage Piezo1 is enhanced by p65 to augment bacterial clearance on an injured, stiffened lung matrix during pneumonia. Therefore, Piezo1 is a future therapeutic target against pneumonia-induced lung injury.

immunology↗

bioRxiv2025

Axonemal dynein contributions to flagellar beat types and waveforms

Eukaryotic flagella, or motile cilia, are iconic molecular machines whose beating drives cell propulsion and fluid transport across diverse organisms. Beat type and waveform are tailored to function, differing between species and cell types, and individual flagella can switch between beat types. Aberrant beating causes ciliopathies and infertility in humans1 and prevents unicellular parasite transmission2. Eight distinct dynein motor protein complexes bind to axonemal doublet microtubules (DMTs) within flagella and drive beating, yet despite extensive structural analysis3-5, how this machinery achieves different beat types is unknown. Here, using the flagellate unicellular parasite Leishmania, we show a division of labour where specific dyneins drive specific beat types. Using cryo-EM, we determined the structure of the 96-nm repeat unit of the DMT and identified its dynein composition. We used CRISPR-Cas9 to systematically delete all 96-nm repeat proteins, comprehensively mapping necessity for swimming, and determined the contribution of each dynein to incidence and waveform of the preferred beat types. Outer dynein arms (ODAs) were required for symmetric tip-to-base beats, specific single-headed inner dynein arms (IDAs) were important for asymmetric base-to-tip beats (IDAd), and double-headed IDAf important for both. This systematic analysis indicates that the prevailing dogma that ODAs drive and IDAs shape the beat6-9 is either incomplete or not universal, and establishes new hypotheses for how different species, cell types and individual flagella achieve their necessary beat types.

biophysics↗

bioRxiv2025

Multi-trophic metacommunity responses to habitatnfragmentation in the Brazilian Atlantic Forest

The structure of ecological communities is profoundly altered by anthropogenic disturbance to landscapes. However, most reported impacts rely on the quantification of diversity estimates for single trophic levels or impacts on key species of interest. In this analysis we integrate measures of community structure, comparisons of interaction networks and measures of {beta}-diversity across four trophic levels: plants, bats, bat ectoparasites and bacteria within the ectoparasites. Our data show that bat, bat fly, and bacterial communities are significantly nested across forest fragments, with specialist consumers in all groups being found in fewer fragments than generalists. We found substantial {beta}-diversity in both species richness and interaction richness across fragments but no decline in interaction redundancy with decreasing fragment size, likely because even intact forest networks had very low redundancy in our dataset. Despite the loss of species and interactions, our data provide support for the conservation value of even the smallest and most disturbed forest fragments where essential seed dispersal services are potentially maintained by Artibeus, Carollia and Sturnira and distinct sets of taxa and interactions are supported. These species may be key in the potential recovery of these habitats, but our data highlight the fragility of these communities which have contracted around these disturbance-tolerant species.

ecology↗

bioRxiv2025

Collateral fitness effects of mutation are not commonly caused by protein misfolding

Mutations in coding sequences are often assumed to harm cells by destabilizing proteins and creating toxic misfolded species. Here we directly test how fitness scales with predicted folding stability. Using deep mutational scanning of a gratuitously expressed protein in S. cerevisiae ({approx}2,000 YFP single-amino-acid variants) and meta-analyses of seven additional scans of gratuitous proteins in yeast and E. coli, we find that collateral fitness effects, costs that arise independently of protein function, do not correlate with predicted destabilization ({Delta}{Delta}G). Even variants predicted or biochemically shown to misfold frequently had no measurable collateral cost. In contrast, across matched datasets where the same proteins were required for growth, predicted destabilization strongly tracked primary fitness costs, and this association intensified as functional demand increased. These conclusions were robust to multiple stability predictors and to competitive fitness assays with high sensitivity. Together, our results indicate that misfolding is not a common driver of collateral fitness costs, whereas it often underlies primary costs when function matters. These findings overturn the long-standing assumption that misfolding universally drives the collateral costs of mutation, reframing misfolded proteins as only one piece of a broader puzzle and opening the way to identify alternative cellular vulnerabilities that shape evolution, disease, and aging.

molecular biology↗

bioRxiv2025

ESPWA: a deep learning-enabled tool for precision-based use of endocrine therapy in resource-limited settings

Immunohistochemistry for estrogen receptor (ER) expression is often unavailable in low-and-middle-income countries (LMICs), leading to empiric use of endocrine therapy (ET) and unnecessary toxicity in ER-negative patients. To address this unmet need, we developed ESPWA, a deep-learning model trained on 3448 H&E slides and tissue-matched ER status from breast cancer patients treated at Zanmi Lasante (ZL), Haiti. A model trained on The Cancer Genome Atlas (TCGA) exhibited substantial domain shift when applied to the ZL cohort, with AUROCs dropping from 0.846 on TCGA cross-validation to 0.671 on the ZL cohort. In contrast, ESPWA demonstrated improved performance on ZL cross-validation (AUROC=0.790; p=0.005). In an independent test set of 134 Haitian patients with parallel slides prepared and scanned in Mirebalais Hospital (Haiti) and Brigham and Womens Hospital, ESPWA was robust to variations in slide preparation, quality, and scanners, achieving AUROCs of 0.794 on BWH-prepared WSIs and 0.805 on Mirebalais-prepared WSIs. Prospective studies using ESPWA are underway in sub-Saharan Africa to evaluate its utility in informing precision-based use of ET.

cancer biology↗

bioRxiv2025

Ketone body driven lipid remodeling supports thermogenic adaptation to fasting

Metabolic adaptation to fasting may have conferred survival advantage to early humans and predicts weight gain caused by overnutrition in modern societies. Fasting suppresses brown adipose tissue (BAT) thermogenesis; however, it is unclear how BAT rewires cellular metabolism to balance between energy conservation and heat generation. Here, we report that BAT in mice under fasting and cold challenge consumed ketone bodies, specifically acetoacetate (AcAc). Ablating liver ketogenesis decreased, while enhancing hepatic AcAc output defended, body temperature in mice facing the dual challenge. Using stable isotope tracing in brown adipocytes in vitro combined with quantitative analysis of metabolic fluxes and lipidomics in BAT from genetic mouse models, we disentangled the two metabolic fates of AcAc - terminal oxidation in the mitochondria and lipid biosynthesis in the cytosol. Notably, AcAc-sourced carbon preferentially supported polyunsaturated fatty acid synthesis in BAT, linking to the positive impact of intermittent fasting on lipid profiles in both mice and humans. Therefore, ketone body utilization by thermogenic adipocytes contributes to metabolic resilience of mammals and can be targeted to optimize benefits of dietary regimens.

physiology↗

bioRxiv2025

Integrated Histology and Molecular Profiling of Postmortem Human Auditory and Vestibular Organs via a Poly(Methyl Methacrylate)-Based Workflow

Hearing and balance disorders are the most prevalent sensory impairments, affecting hundreds of millions worldwide, yet their underlying cellular and molecular pathologies remain poorly understood. This knowledge gap stems from the inaccessibility of the ears sensory organs--embedded within the temporal bone (TB), the hardest bone in the body--which cannot be biopsied in living patients without causing irreversible damage. Conventional histopathology workflows rely on postmortem en bloc extraction of TBs, followed by lengthy decalcification, celloidin embedding, and manual serial sectioning of these large specimens--a process that takes one to two years, is labor- and cost-intensive, and lacks compatibility with most modern protein, DNA, and RNA assays. Here, we present a rapid, reversible polymethyl methacrylate (rPMMA) workflow that enables advanced molecular histopathology studies on formalin-fixed, calcified TBs. Our protocol uses low-temperature (-40 {degrees}C to +4 {degrees}C) resin embedding, precision near-serial sectioning (10-50 {micro}m) via femtosecond laser microtomy or precision diamond wire sawing, and subsequent deacrylation to fully restore tissue accessibility for high-fidelity histomorphology, multiplexed immunofluorescence, whole-genome sequencing, and in situ mRNA detection (RNAscope) assays. Compared to the gold-standard celloidin workflow, our method reduces processing time and costs by approximately 90% while integrating equivalent histomorphology with advanced molecular assays, providing a new benchmark for multidimensional studies in human hearing and balance pathologies.

pathology↗

bioRxiv2025

A conserved mechanism for the retrieval of polyubiquitinated proteins from cilia

The temporospatial distribution of proteins within cilia is regulated by intraflagellar transport (IFT), wherein molecular trains shuttle between the cell body and cilium. Defects in this process impair various signal-transduction pathways and cause ciliopathies. Although K63-linked ubiquitination appears to trigger protein export from cilia, the mechanisms coupling polyubiquitinated proteins to IFT remain unclear. Using a multidisciplinary approach, we demonstrate that a complex of CFAP36, a conserved ciliary protein of previously unknown function, and ARL3, a GTPase involved in ciliary import, binds polyubiquitinated proteins and links them to retrograde IFT trains. CFAP36 uses a coincidence detection mechanism to simultaneously bind two IFT subunits accessible only in retrograde trains. Depleting CFAP36 accumulates K63-linked ubiquitin in cilia and disrupts Hedgehog signaling, a pathway reliant on the retrieval of ubiquitinated receptors. These findings advance our understanding of ubiquitin-mediated protein transport and ciliary homeostasis, and demonstrate how structural changes in IFT trains achieve cargo selectivity.

molecular biology↗

bioRxiv2025

Cell-to-cell signalling mediated via CO2: activity dependent CO2 production in the axonal node opens Cx32 in the Schwann cell paranode.

Loss of function mutations of Cx32, which is expressed in Schwann cells, cause X-linked Charcot Marie Tooth disease, a slowly progressive peripheral neuropathy. Cx32 is thus essential for the maintenance of myelin. During action potential propagation, Cx32 hemichannels in the Schwann cell paranode are thought to open and release ATP. As Cx32 hemichannels are directly sensitive to CO2, we have tested whether CO2 produced in the axon, as a consequence of the energetic demands of action potential propagation, might gate Cx32 hemichannels. Using isolated sciatic nerve from the mouse, we have shown that the critical components required for intercellular CO2 signalling are present (nodal mitochondria, the source of CO2; a CO2-permeable aquaporin, AQP1; paranodal Cx32; and carbonic anhydrase). We have used a membrane impermeant fluorescent dye FITC, which can permeate Cx32 hemichannels, to demonstrate the opening of Cx32 in Schwann cells in response to an external CO2 stimulus or during action potential propagation in the isolated nerve. Pharmacological blockade of AQP1 or allosteric enhancement of carbonic anhydrase activity greatly reduced Cx32 gating during action potential firing. By contrast, inhibition of carbonic anhydrase with acetazolamide greatly increased Cx32 gating. Cx32 gating was unabected by the G-protein blocker GDP{beta}S, indicating that it was not mediated by G protein coupled receptors. By expressing a modified Cx32 subunit, Cx32DN, that coassembles with Cx32WT, we have shown that the activity dependent dye loading of Schwann cells depends upon CO2 binding to Cx32. This CO2-dependent opening of Cx32 also mediates an activity dependent Ca2+ influx into the paranode and, by increasing the leak current across the myelin sheath, slows the conduction velocity. Our data demonstrate that CO2 can act via connexins to mediate neuron-to-glia signalling and that CO2 permeable aquaporins and carbonic anhydrase are key components of this signalling mechanism.

neuroscience↗

bioRxiv2025

Hyphal growth determines spatial organization and coexistence in a pathogenic polymicrobial community within alveoli-like geometries

The bodies of macroorganisms host microbes living in multi-species communities. Sequencing approaches have revealed that different organs host different microbiota and tend to be infected by different pathogens, drawing correlations between environmental parameters at the organ level and microbial composition. However, less is known about the microscale dimension of microbial ecology, particularly during infection. In this study, we focus on the role of microscale spatial structure, studying its influence on the ecology of a polymicrobial infection of P. aeruginosa, S. aureus and C. albicans. Although these pathogens are commonly found together in the lungs of chronically ill patients, it is unclear whether they coexist or compete and segregate in different niches. We find that, while P. aeruginosa quickly outcompetes C. albicans and S. aureus on large surfaces, robust spatial organization and coexistence emerges in microfluidic microchambers that mimic the spatial characteristics of alveoli. In these microenvironments, slowly growing C. albicans is able to leverage fast eccentric hyphal growth to conquer boundary spaces, where it establishes itself excluding the other pathogens. We show that the emerging spatial patterning is robust to changes in the virulence of the community, enabling coexistence and potentially determining infection severity and outcomes. Our findings reveal a previously unrecognized role of mechanical forces in shaping infection dynamics, suggesting that microenvironmental structure is a critical determinant of pathogen coexistence, virulence, and treatment outcomes. Because adaptations, such as changes in morphology, are widespread among microbes, these results are generalizable to other ecologies and environments.

microbiology↗

bioRxiv2024

An improved neural network model enables worm tracking in challenging conditions and increases signal-to-noise ratio in phenotypic screens

High-resolution posture tracking of C. elegans has applications in genetics, neuroscience, and drug screening. While classic methods can reliably track isolated worms on uniform backgrounds, they fail when worms overlap, coil, or move in complex environments. Model-based tracking and deep learning approaches have addressed these issues to an extent, but there is still significant room for improvement in tracking crawling worms. Here we train a version of the DeepTangle algorithm developed for swimming worms using a combination of data derived from Tierpsy tracker and hand-annotated data for more difficult cases. DeepTangleCrawl (DTC) outperforms existing methods, reducing failure rates and producing more continuous, gap-free worm trajectories that are less likely to be interrupted by collisions between worms or self-intersecting postures (coils). We show that DTC enables the analysis of previously inaccessible behaviours and increases the signal-to-noise ratio in phenotypic screens, even for data that was specifically collected to be compatible with legacy trackers including low worm density and thin bacterial lawns. DTC broadens the applicability of high-throughput worm imaging to more complex behaviours that involve worm-worm interactions and more naturalistic environments including thicker bacterial lawns.

animal behavior and cognition↗

bioRxiv2024

IL-33 protects from recurrent C. difficile infection by restoration of humoral immunity

Clostridioides difficile infection (CDI) recurs in one of five patients. Monoclonal antibodies targeting the virulence factor TcdB reduce disease recurrence, suggesting that an inadequate anti-TcdB response to CDI leads to recurrence. In patients with CDI, we discovered that IL-33 measured at diagnosis predicts future recurrence, leading us to test the role of IL-33 signaling in the induction of humoral immunity during CDI. Using a mouse recurrence model, IL-33 was demonstrated to be integral for anti-TcdB antibody production. IL-33 acted via ST2+ ILC2 cells, facilitating germinal center T follicular helper (GC-Tfh) cell generation of antibodies. IL-33 protection from reinfection was antibody-dependent, as MT KO mice and mice treated with anti-CD20 mAb were not protected. These findings demonstrate the critical role of IL-33 in generating humoral immunity to prevent recurrent CDI. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=176 SRC="FIGDIR/small/623943v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@9ec4aeorg.highwire.dtl.DTLVardef@1827bd3org.highwire.dtl.DTLVardef@18f761dorg.highwire.dtl.DTLVardef@19396d4_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO IL-33 restoration induces toxin-B-specific antibody production via the ILC2-TFH axis. In the left panel, IL-33 remediation increases ILC2s, subsequently inducing TFH directly or indirectly. TFH cell induction is pivotal for the production of antibodies. IL-33 also downregulates type 1 and type 3 immunity, favoring type 2 immunity to enhance host survival and reduce morbidity. The middle panel illustrates antibiotic-induced dysbiosis, resulting in decreased IL-33 levels and reduced antibody production. The right panel demonstrates the protective effect in reinfection, attributed to toxin-specific antibodie generated by IL-33 remediation. C_FIG

immunology↗

bioRxiv2024

Fourth generation CAR Tregs with PDCD1-driven IL-10 have enhanced suppressive function

The potency of regulatory T cell (Treg) therapy has been transformed through use of chimeric antigen receptors (CAR). However, to date, CAR Treg therapy has not achieved long-lasting tolerance in mouse models, suggesting that additional engineering is required to unlock the full potential of these cells. We previously found that human Tregs produce minimal amounts of IL-10 and have a limited capacity to control innate immunity in comparison to type I regulatory (Tr1) cells. Seeking to create "hybrid" CAR Tregs that were engineered with Tr1-like properties, we examined whether the PDCD1 locus could be exploited to endow Tregs with the ability to secrete high levels of IL-10 in a CAR-regulated manner. CRISPR-mediated PD1-deletion increased the activation potential of CAR Tregs without compromising in vivo stability. Knock-in of IL10 under control of the PD1 promoter facilitated CAR-mediated secretion of IL-10 in large quantities, and improved CAR Treg function, as determined by significant inhibition of dendritic cell antigen presentation and enhanced suppression of alloantigen- and islet autoantigen-specific T cells. Overall, CRISPR-mediated engineering to simultaneously remove an inhibitory signal and enhance suppressive mechanisms is a new approach to enhance the therapeutic potency of CAR Tregs.

immunology↗

bioRxiv2024

Synthetic G-quadruplex components for predictable, precise two-level control of mammalian recombinant protein expression

Control of mammalian recombinant protein expression underpins the in vitro manufacture and in vivo performance of all biopharmaceutical products. However, routine optimization of protein expression levels in these applications is hampered by a paucity of genetic elements that function predictably across varying molecular formats and host cell contexts. Herein, we describe synthetic genetic components that are specifically built to simplify bioindustrial expression cassette design processes. Synthetic G-quadruplex elements with varying sequence feature compositions were systematically designed to exhibit a wide-range of regulatory activities, and inserted into identified optimal positions within a standardized, bioindustry compatible core promoter-5UTR control unit. The resulting library tuned protein production rates over two orders of magnitude, where DNA and RNA G-quadruplexes could be deployed individually, or in combination to achieve synergistic two-level regulatory control. We demonstrate these components can predictably and precisely tailor protein expression levels in i) varying gene therapy and biomanufacturing cell hosts, and ii) both plasmid DNA and synthetic mRNA contexts. As an exemplar use-case, a vector design platform was created to facilitate rapid optimization of polypeptide expression ratios for difficult-to-express multichain products. Permitting simple, predictable titration of recombinant protein expression, this technology should prove useful for gene therapy and biopharmaceutical manufacturing applications.

bioengineering↗

bioRxiv2024

Global phylogenomic analysis of Staphylococcus pseudintermedius reveals genomic and prophage diversity in multi-drug resistant lineages

Staphylococcus pseudintermedius is the foremost cause of opportunistic canine skin and mucosal infections worldwide. Multidrug resistant (MDR) and methicillin-resistant S. pseudintermedius (MRSP) lineages have disseminated globally in the last decade and present significant treatment challenges. However, little is known regarding the factors that contribute to the success of MDR lineages. In this study, we compared the genome sequence of 110 UK isolates of S. pseudintermedius to 2,166 genomes of S. pseudintermedius populations from different continents. A novel core genome multi-locus typing scheme was generated to allow large scale, rapid and detailed analysis of S. pseudintermedius phylogenies, and was used to show that the S. pseudintermedius population structure is broadly segregated into an MDR population and a non-MDR population. MRSP lineages are predicted to either encode certain resistance genes chromosomally, or on plasmids, and this is associated with their MLST sequence type. Comparison of lineages most frequently implicated in disease, ST-45 and ST-71, with the phylogenetically related ST-496 lineage that has a comparatively low disease rate, revealed that ST-45 and ST-71 genomes encode distinct combinations of phage-defence systems and concurrently encode a high number of intact prophages. In contrast, ST-496 genomes encode a wider array of phage defence systems and lack intact, complete prophages. Additionally, we show that distinct prophages are widespread in S. pseudintermedius and appear to account for the vast majority of genomic diversity. These findings indicate that MRSP lineages have significant structural genomic differences, and that prophage integration, and differential antiviral systems correlate with the emergence of successful genotypes. Impact StatementStaphylococcus pseudintermedius is a major cause of soft tissue infections in dogs but may occasionally infect other companion animals and humans, most often veterinary professionals in primary care. Methicillin-resistant Staphylococcus pseudintermedius (MRSP) have emerged worldwide and are often linked to resistance to multiple antimicrobials, resulting in a significant health burden. Here, we analysed a large collection of S. pseudintermedius genome sequences, which has allowed a detailed characterisation of the molecular epidemiology and diversity of the species using a novel typing scheme. Here we show that closely related MRSP lineages differ in whether specific antibiotic resistance genes are encoded on potentially mobilisable plasmids, or more stably on the chromosome, indicating differing evolutionary trajectories of MRSP lineages. Comparison of the S. pseudintermedius types most frequently implicated in clinical cases to those associated with commensal carriage, showed that known genes thought to contribute to disease are universal, and therefore, not associated with the high incidence rates of disease of particular lineages. We demonstrate that MRSP sequence types linked to high disease rates lack specific phage-defence systems and are associated with a high burden of prophages. Data statementAll supporting data, code and protocols have been provided either within the article, through supplementary data files, or via Figshare and Zenodo. Six supplementary figures and one supplementary file are available with the online version of this article. Data summaryAll genome sequencing data (sequencing reads and genome assemblies) are available at the Sequence Read Archive (SRA) and Genomes repositories at NCBI, in Bioproject number PRJNA1153484. The information for the individual S. pseudintermedius genomes has been included in Supplementary File 1. Genome assemblies used in this study are available from https://zenodo.org/records/13692319, DOI 10.5281/zenodo.13692318. The S. pseudintermedius cgMLST scheme developed for this study has been made available via Zenodo (https://zenodo.org/records/13633136, DOI: 10.5281/zenodo.13633135) and Figshare (https://doi.org/10.6084/m9.figshare.26911654.v1, DOI: 10.6084/m9.figshare.26911654).

microbiology↗

bioRxiv2024

Long read sequencing and assembly of wild diploid relatives and cultivars in support of banana breeding programs

Banana is an important fruit and staple crop, which is vital for food and income security in developing countries. A genomics initiative was undertaken as part of the Global Alliance against TR4 (Tropical Race 4 of Fusarium Wilt of Banana) Alliance, with Bayer Crop Science, International Institute of Tropical Agriculture, and University of Queensland to collectively accelerate the breeding efforts in Eastern Africa. The goal of this project is to develop genomics resources to improve banana breeding, productivity, and quality traits amid a changing climate and shifting disease pressures for breeding. Here, we present the PacBio HiFi sequencing, assembly, and comparative analysis of seven genomes of wild and edible diploid banana accessions belonging to subspecies considered important progenitors to cultivated banana varieties and part of breeding programs. This banana genome resource will help power genome editing, a pangenome effort, and conventional breeding programs for germplasm improvement.

genomics↗

bioRxiv2024

Metagenomic insights into an enigmatic gammaproteobacterium that is important for carbon cycling in cave ecosystems worldwide

Caves are windows into the subsurface through which we can directly evaluate the microbiological processes responsible for rock weathering and biogeochemical cycling in more expansive areas of Earths subsurface. However, many cave microbial communities are dominated by microorganisms from uncultivated groups with unknown genomic capabilities that cannot be resolved from marker gene surveys alone. An example of this is a genus of Gammaproteobacteria known as "wb1-P19", which are ubiquitous and abundant in rRNA gene surveys from limestone and volcanic caves around the world. We recovered a nearly complete metagenome-assembled genome (MAG) representing a population of wb1-P19 from Lehman Caves in Great Basin National Park, Nevada, USA, and used it to identify additional MAGs representing this group from the Frasassi Caves in Italy and in publicly available databases. Although members of the wb1-P19 group have often been thought to be autotrophs that oxidize inorganic nitrogen compounds, we show that wb1-P19 are actually obligate or facultative methanotrophs capable of aerobic and anaerobic growth. Based on genomic classification, wb1-P19 are members of upland soil cluster {gamma} (USC{gamma}; part of the newly proposed order "Candidatus Methyloligotrophales"), and are likely important for methane consumption and carbon cycling in caves and other subterranean ecosystems globally.

microbiology↗