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Phylogeny offers a powerful framework for understanding mechanisms driving community assembly. Yet, most empirical studies in community phylogenetics rely on observational approaches. In this study, we explore how two important drivers of community assembly-habitat size and predator presence-shape species richness and phylogenetic relatedness of prey communities by altering colonization and extinction processes. Using bromeliad invertebrate communities as our study system, we combined surveys of natural communities with experiments that manipulated habitat size and predator presence. Colonization and extinction were isolated in separate experiments to test whether effects of habitat size and predator presence differed across stages of community assembly. Following species-area theory, we expected larger habitats to increase species richness and, given the strong consumptive effects of the top predator (a damselfly larvae), we expected species richness to decline in the presence of predators. Under a community phylogenetics framework, if traits mediating responses to these factors are phylogenetically conserved, we expected the phylogenetic structure of the community (i.e., relatedness) to have deterministic patterns along both gradients. Specifically, if habitat size functions as an environmental filter, small bromeliads would host phylogenetically clustered assemblages; alternatively, if it functions as a mediator for coexistence among close relatives, larger habitats would exhibit greater relatedness. Likewise, we expected the generalist top predators to increase relatedness when closely related taxa have shared defensive traits. As traits mediating community assembly may vary in their phylogenetic distribution across lineages, we also anticipated relatedness patterns to vary across taxonomic scales. We found a positive effect of habitat size on species richness, which was driven by colonization mechanisms. Habitat size also affected relatedness, but the direction depended on the taxonomic scale, with positive relationships at broad scales and negative relationships at narrower scales. By contrast, predators reduced species richness through extinction mechanisms, although these effects were masked in natural communities by continuous replacement of individuals through colonization. Predator effects on relatedness were variable across taxonomic scales, suggesting the involvement of multiple traits at different phylogenetic depths. Together, our findings highlight the complex interplay between environmental factors and community assembly in structuring taxonomic and phylogenetic dimensions of diversity.

Huanglongbing (HLB, 'Candidatus Liberibacter asiaticus') is one of the most devastating pathogens in citrus domain. Here, we present the nearly complete genome sequence of a CR-NGP1 strain obtained a from symptomatic Nagpur Mandarin (Citrus reticulata) tree in the Nagpur region of Central India. High-throughput sequencing on the Illumina NovaSeq 6000 platform generated ~ 85.7 million paired-end reads, 63.5 million paired-end reads and 14.8 million paired-end reads for sample CLas_001, CLas_002 and CLas_003 each with 150 bp read length, respectively. Two assembly strategies were used: (i) reference-based assembly with SPAdes produced a draft genome of ~ 1.19 Mb with assembly comprised 149 contigs, with an N50 of 14,173 bp, longest contig of 39,711 bp, and an overall GC content of 36.27%. (ii) KBase CONCOCT binning v1.1 applied to all 3 samples produced a nearly complete CR-NGP1 genome of ~ 1,156,009 bases with assembly of 93 contig, with an N50 of 17,668 bp, a longest contig of 39,711 bp, and an overall GC content of 36.4%. This resource of a CLas genome from Central India provides important insights to understand genetic diversity of CLas strains and will facilitate comparative genomics and epidemiological studies of Huanglongbing.

Overlap detection is a key step in de novo genome assembly pipelines based on the Overlap-Layout-Consensus (OLC) paradigm. Existing methods for overlap detection either rely on heuristic seed-and-extension strategies or locality-sensitive hashing (LSH), both of which struggle to handle repetitive genomic regions and the computational burden of large-scale datasets. Here, we present FEDRANN, a novel strategy for overlap graph construction that integrates feature extraction, dimensionality reduction (DR), and approximate nearest neighbor (ANN) search. We find the pipeline combining inverse document frequency (IDF) transformation, sparse random projection (SRP), and NNDescent enables accurate detection of overlaps across diverse datasets. We developed an efficient open-source implementation of this pipeline named Fedrann (https://github.com/jzhang-dev/fedrann). Through systematic benchmarking on real long-read sequencing data, we demonstrate that Fedrann produces overlap graphs comparable to or better than those generated by existing state-of-the-art tools, including MECAT2, minimap2, and wtdbg2, while maintaining competitive runtime. By integrating Fedrann into the Shasta assembler, we successfully reconstructed human whole genomes, achieving high assembly contiguity and quality. Despite being implemented primarily in Python, Fedrann achieves performance parity with tools written in compiled languages by leveraging C-accelerated numerical libraries and optimized batch-based matrix operations. Our results suggest that the combination of dimensionality reduction and ANN techniques offers a robust, scalable framework for accurate overlap detection in long-read assembly and broader sequence similarity search tasks.

The rifamycin synthetase (RIFS) from the bacterium Amycolatopsis mediterranei is a homodimeric assembly line that catalyzes 40+ chemical reactions to generate a complex precursor of the antitubercular drug rifampicin. It consists of an N-terminal substrate loading module (LM) followed by a decamodular polyketide synthase (PKS). While the catalytic functions are known for each domain of RIFS, how these activities are spatially and temporally coordinated during polyketide assembly remains incompletely defined. Here, we address this problem with thiol-selective crosslinking to understand the basis for conformational asymmetry during polyketide chain elongation. Our data suggest that C-terminal dimerization motifs-which are ubiquitous in bacterial PKS assembly lines-force their adjacent substrate carrier protein (CP) domains to co-migrate between two equivalent ketosynthase (KS) active site chambers. Cryogenic electron microscopy analysis of the first PKS module of RIFS (M1) further underscored this observation while revealing its unique architecture. Single-turnover kinetic analysis indicated that although changes to the C-terminus that reduced CP dimerization supported 2-fold greater KS:CP interactions, they were insufficient to overcome sub-stoichiometric product accumulation on the homodimeric protein. Our findings illuminate factors underlying asymmetry during polyketide antibiotic biosynthesis and should be instructive to future megasynth(et)ase engineers.

Microtubules polymerize from cytoplasmic pools of soluble αβ-tubulin heterodimers that support diverse cellular functions. The tubulin cofactors, TBCC, TBCD, and TBCE and the Arl2 GTPase, form TBC-DEG assemblies that regulate the assembly of α- and β-tubulin into heterodimers and their disassembly, yet their underlying mechanisms remain incompletely understood. Here, we reconstitute the human TBC-DE and TBC-DEG assemblies from eukaryotic cells copurified with monomeric β-tubulin intermediates and determine their cryo-EM structures. The structures reveal that TBC-DEG disassembles αβ-tubulin by releasing α-tubulin through a lever arm-like rotation in TBCE coupled to major conformational change in Arl2 upon its nucleotide release, while TBCD tightly holds β-tubulin. TBCD dissociates α-tubulin by refolding the β-tubulin H10-S8 loop at its intradimer interface. The TBC-DEG-β-tubulin or TBC-DE-β-tubulin assemblies undergo extensive back-to-back dimerization mediated by β-β-tubulin homodimers, formed through their dissociated H8 helices at unoccupied intradimer interfaces. Structural comparisons demonstrate that TBCE's mechanical rotation, driven by the Arl2 GTPase cycle, either delivers α-tubulin or removes it from beneath the TBCD-bound β-tubulin and is directionally regulated by TBCC stabilizing αβ-tubulin interfaces. Our findings suggest that TBC-DEG/TBCC catalyzing heterodimerization of α-tubulin with β-tubulin may have evolved to counteract β-tubulin's intrinsic tendency to form off-pathway toxic homodimers through its exposed α-tubulin-binding intradimer interface.

In this issue of Structure, Ren et al.1 show that the microtubule-associated protein Spef1 undergoes liquid-liquid phase separation mediated by its uniquely charged coiled-coil domain. These dynamic Spef1 condensates enrich tubulin to drive central-pair microtubule (CP-MT) assembly, providing a long-sought mechanistic explanation for CP-MT assembly and planar ciliary beating.

Carbohydrate-active enzymes (CAZymes) play an important role in the efficient deconstruction of lignocellulosic biomass (LCB) and chitin, which is essential for sustainable bioenergy production and for the development of industrially important value-added products. Fungi, especially members of Trichoderma spp., are known as efficient degraders of biomass and represent valuable resources for expanding the known repertoire of CAZymes. This study presents the first report of the sequencing and annotation of a high-quality hybrid genome assembly of Trichoderma caribbaeum IHBT, isolated from the western Himalayan region, along with RNA-seq analysis to identify CAZyme-encoding genes potentially involved in the biomass degradation process. The assembled genome was 36.2 Mb in size, with a N50 value of 1.2 Mb and a GC content of 48%, indicating a high-quality genome assembly. Genome mining enabled the identification and functional annotation of 362 putative CAZyme-encoding genes. Time-course transcriptome profiling of T. caribbaeum IHBT grown on sugarcane bagasse (SB) revealed an upregulation of several genes involved in carbohydrate metabolism, including members of the glycoside hydrolase (GH; XP_013945330.1, UKZ69522.1, UKZ67968.1, XP_013947289.1, XP_013940790.1, and UKZ68144.1) and auxiliary activity (AA; UKZ70991.1, XP_013940326.1, XP_013944427.1, UKZ71564, and UKZ60083.1) families, including lytic polysaccharide monooxygenases (LPMOs). Weighted Gene Co-Expression Network Analysis (WGCNA) identified eight potential Hub genes, of which XP_013943413.1, XP_013940723.1, XP_013945605, and XP_013942713 are directly implicated in biomass deconstruction. Overall, the identified CAZyme-encoding genes offer significant potential for further functional characterization and application in biomass valorization, thereby supporting the development of sustainable circular economic strategies in prospective studies.

Bitter gourd (Momordica charantia) is a widely cultivated vegetable and medicinal crop for its nutritional and pharmaceutical properties. Yet, the genomic basis of its domestication and key agronomic traits remains largely unexplored. Here, we present a high-quality, chromosome-level genome assembly specifically representing a smooth bitter gourd cultivar (Y1745), with a total assembly size of 327.14 Mb, a contig N50 of 11.33 Mb, and a scaffold N50 of 23.47 Mb. Comparative genomics reveals lineage-specific expansions of gene families related to stress responses and secondary metabolism. Population genomic analysis of 192 globally representative accessions identifies three distinct genetic groups (China, Southeast Asia, and South Asia Subcontinent), reflecting complex demographic histories, and uncovers strong signatures of selection associated with domestication and regional adaptation. In the genome-wide association study (GWAS) of 35 traits, we identify 893 significant trait-associated loci. Notably, two candidate genes (McWRKY and McFPF1-like 1) are associated with flowering time regulation, and one candidate gene (McEXLB1) with fruit size determination. Our work provides valuable genomic resources for understanding bitter gourd domestication and offers potential genetic targets for breeding.

Controlling collective behavior in the microscale is essential for advancing autonomous robotic systems in complex environments. While biohybrid microrobotic swarms offer considerable promise for targeted therapeutic and remediation applications, their programmable assembly and collective behavior remain challenging. Here, we describe an attractive light-triggered approach for enabling reconfigurable swarming of biohybrid microrobots based on the green microalga Chlamydomonas reinhardtii (CR). Such reversible swarming behavior is realized by combining the wavelength-dependent assembly ability of CR and its inherent phototactic properties with light exposures through a series of different mask openings that define the desired swarm geometry. Changes in the projected light enable dynamic modulation of the swarm shape and size, including real-time swarm splitting and merging behaviors. The concept was explored toward artificial intelligence-assisted wound targeting applications through the creation of microrobot swarms customized to exposed wound areas. Such powerful swarming capabilities offer considerable promise for the collective behavior of biohybrid microrobots toward important practical applications.

Protein condensates assemble actin filaments into diverse architectures, reminiscent of filopodia and stress fibers. During assembly, filament nucleation and elongation compete for a shared pool of actin monomers. Here we show that a balance between these processes is required to deform condensates of VASP, an actin polymerase, into high aspect ratio structures. Adding magnesium, which promotes filament nucleation, enhanced condensate deformation, while adding profilin, which favors elongation over nucleation, produced ring-like filament bundles that failed to deform condensates. Computational modeling predicted that a collection of short filaments would be more efficient at deforming condensates compared to a few long filaments. To test this prediction, filament capping protein was used to inhibit growth of long filaments. The resulting set of shorter filaments regained the ability to deform condensates, illustrating the importance of a balance between filament nucleation and elongation. More broadly, these findings illustrate how protein condensates balance actin nucleation, elongation, and bundling to direct the assembly of diverse cytoskeletal architectures.

Foliar endophytes contribute to plant nutrient acquisition, stress tolerance, and pathogen resistance, yet their responses to ecosystem-level processes remain poorly understood. Using a space-for-time substitution design, we investigated bacterial and fungal community dynamics in the foliar endosphere of four phylogenetically distinct plant hosts across a well-characterized successional chronosequence. Amplicon sequencing revealed that the ecosystem development stage (site age) significantly influenced endophyte community composition, particularly among fungi, but explained only a small proportion of the total variation. Host plant identity and associated leaf stoichiometry were stronger predictors of community structure, with sampling time within the growing season also contributing significantly. Together, these deterministic factors explained 10% and 11% of bacterial and fungal compositional variation, respectively, and 27% of predicted bacterial functional potential. Null model analyses indicated that remaining variation was mostly consistent with stochastic assembly processes, particularly ecological drift. Endophytic communities were characterized by a few persistent dominant taxa and many rare, transient members with overlapping functional potential, including N2 fixation, methylotrophy, and denitrification. Our findings demonstrate that host identity outweighs ecosystem age in structuring foliar endophyte communities and that stochastic processes play a central role in community assembly. The coexistence of stable dominant taxa and a dynamic rare biosphere may enhance plant responsiveness to environmental changes, while the functional potential of endophytes may remain largely consistent across seasons and successional stages.

The combination of gas-phase infrared (IR) spectroscopy with ion mobility spectrometry and mass spectrometry provides detailed, multidimensional structural information that facilitates the identification of unknown analytes. The instrumentation for performing these measurements is typically home-built and requires substantial expertise to operate. Here, we demonstrate messenger-tagging IR spectroscopy on a modified Synapt G2-S ion mobility-mass spectrometer (IM-MS). Messenger-tagging is performed in a commercially available cryogenic ion trap inserted between the exit of the transfer cell and the TOF pusher assembly, and tagged ions are excited by IR light before MS measurement. We report the adjustments to the timing cycle and voltage gradient in the Synapt G2-S necessary for efficient trapping and messenger-tagging in the cryogenic trap. The capabilities of this instrument are demonstrated by measuring IM-MS-IR data for leucine enkephalin, a benchmark standard in mass spectrometry. The ability to selectively transmit ions of specific mobility enables the separation and subsequent IR spectroscopy of the isomeric trisaccharides cellotriose and melezitose. These data demonstrate the first implementation of messenger-tagging IR spectroscopy in a widely used, commercially available IM-MS system. The user-friendly implementation of these techniques overcomes a significant barrier to the widespread incorporation of orthogonal IR spectroscopy measurements in existing IM-MS workflows and will aid in distinguishing unknown molecules in untargeted -omics measurements.

The effective capture of radioactive CH3I under high-temperature and low-concentration conditions remains a critical challenge in nuclear waste management. Herein, we report a supramolecular strategy that combines intramolecular hydrogen bond-directed ligand preorganization with metal-coordination assembly to construct a nitrogen-enriched metal-organic cage for CH3I capture. Accordingly, a hydrogen-bonded triazole ligand selectively assembles with Pd(II) to form a discrete Pd3L6 cage featuring a large, accessible cavity arrayed with inwardly oriented triazole nitrogen atoms, thereby creating a confined nucleophile-rich microenvironment for CH3I adsorption. The cage captures CH3I through a chemisorption-driven pathway involving nucleophilic alkylation of the triazole nitrogen atoms to generate N-methylated triazolium sites, which further promote additional noncovalent uptake within the cavity. The assembled cage exhibits an excellent CH3I adsorption capacity (1.69 g g-1, 48.7 mol mol-1) and rapid uptake kinetics (0.17 g g-1 h-1) under static conditions. More importantly, it represents the first cage adsorbent shown to capture CH3I under simulated nuclear off-gas conditions, achieving a dynamic adsorption capacity of 0.13 g g-1 at 150 °C and a CH3I flow rate of 0.8 mg min-1. This work establishes hydrogen bond-directed foldamer preorganization as a supramolecular strategy for constructing metal-organic cages with confined reactive cavities for challenging molecule capture.

Mutations that arise in the shoot apical meristems can become fixed, but typically only in one of the meristem layers. Therefore, in long-lived, clonally propagated species, polymorphic genomes coexist in the form of periclinal chimeras. Given their evolutionary and economic impact, it is critical to understand the dynamics and phenotypic implications of layer-specific variation. Here, we γ-irradiated axillary buds from an elite peppermint clone and obtained 261 independent mutants carrying large indels. We produced a haplotype-aware, high-continuity assembly of this sterile allohexaploid and, using short-read sequencing, detected, on average, six large indels per mutant. Importantly, most of these mutants were periclinal chimeras: comparison of mutation frequency in root (derived solely from the L2/3 layer) and leaves (which contain cells from all three layers) demonstrated that the indels are confined to either the outer, L1-derived layer, or the inner L2/3 layers. We observed that the L1 layer was more often mutated, confirming that mutation rate in the shoot apical meristem is potentially optimized to each meristematic layer. To assess whether deletion of a single haplotype in a single meristematic layer could affect plant function, we characterized mutants under field conditions, detecting variation in secondary metabolite production. Two mutants produced an oil with very low (-)-menthol levels, associated with the loss of a single haplotype of the menthone-menthol reductase gene in the epidermal layer. These results highlight the evolutionary relevance of layer-specific genetic variation and present opportunities for improvement of clonally propagated crops that suffer from genetic diversity bottlenecks.