The Sequence Alignment/Map format and SAMtools

A high-quality genome assembly of Annona squamosa (custard apple) provides functional insights into an emerging fruit crop

Annona squamosa, also known as custard apple, is an emerging fruit crop with medicinal significance. We constructed a high-quality genome of A. squamosa along with transcriptome data to gain insights into its phylogeny, evolution, and demographic history. The genome has a size of 730.4 Mb with an N50 value of 93.2 Mb assembled into seven pseudochromosomes. The demographic history showed a continuous decline in the effective population size of A. squamosa. Phylogenetic analysis revealed that magnoliids were sister to eudicots. Genome syntenic and Ks distribution analyses confirmed the absence of a recent whole-genome duplication event in the A. squamosa. Gene families related to photosynthesis, oxidative phosphorylation, and plant thermogenesis were found to be highly expanded in the genome. Comparative analysis with other magnoliids revealed the adaptive evolution in the genes of flavonoid biosynthesis pathway, amino sugar, nucleotide sugar and sucrose metabolism, conferring medicinal value, and enhanced hexose sugar accumulation. In addition, we performed genome-wide identification of SWEET genes. Our high-quality genome and evolutionary insights of this emerging fruit crop, thus, serve as a valuable resource for advancing studies in functional genomics, evolutionary biology, and crop improvement.

Revisiting the emergence of the Chikungunya virus in Alagoas, Northeast of Brazil

Chikungunya virus (CHIKV), an Alphavirus, emerged in the Americas in 2013 and was first documented in Brazil in September 2014, in the states of Pará and Bahia. Although Alagoas state officially reported its first case in late 2015, this study investigated potential earlier unreported cases by analyzing samples from a 2013-2014 Orthoflavivirus serological survey. We screened sera from patients with acute febrile illness, initially suspected of dengue but negative in molecular tests for the genus Orthoflavivirus, using ELISA (IgM/IgG), viral isolation, PCR, and next-generation sequencing. Two samples collected in June and August 2014 tested positive for anti-CHIKV IgM, and four additional samples collected between June and September 2014 tested positive for anti-CHIKV IgG antibodies. From one sample IgM-positive (630H) collected in August 2014, we isolated and sequenced a nearly complete genome (95.53% coverage, 2714× depth) classified as the East-Central-South-African (ECSA) genotype. Phylogenetic analyses revealed that the Alagoas-2014 genome formed a distinct, well-supported clade separate from the Bahia 2014 lineage. Temporal inference dated this lineage's origin to October 2013 (90% CI: April 2013-March 2014), suggesting a new introduction of ECSA into Alagoas. This genomic evidence, along with serological data, confirms the undetected early circulation of CHIKV in Alagoas and suggests a possible introduction of ECSA in Brazil in 2014, distinct from the well-documented introduction in Bahia.

Loss of phytochromobilin synthase activity leads to larger seeds with higher protein content in soybean

Seed weight is an important agronomic trait that is related to seed size and determines yield in soybean (Glycine max). We previously identified a spontaneous soybean mutant with light green leaves called ygl2. Here, we cloned YGL2, which encodes a phytochromobilin (PΦB) synthase involved in synthesizing the chromophore of the photoreceptor phytochrome. The lesion in ygl2 is a 10-bp deletion, causing a frameshift mutation and a premature stop codon that truncates the encoded protein. In contrast to the wild type, ygl2 lacks PΦB synthase activity and function. This appears to promote cell expansion, thus increasing seed weight. Surprisingly, the ygl2 mutant also exhibits excellent traits including early maturity and high protein content. Moreover, under the condition of dense planting (3 cm), the yield of YGL2 mutant was significantly increased. Mutants harboring ygl2 mutations that we generated via gene editing had enlarged seeds with high protein content. Moreover, the expression levels of the photoperiod sensitive genes (E1, FT2a, FT5a) were lower in the ygl2 mutant than in the wild type. Mutating the YGL2 gene resulted in increased biliverdin content and decreased heme content. We determined that Lhcb4, a chlorophyll a/b binding protein in photosystem II, interacts with YGL2 but not with the mutant version of the protein. We thus identified a mutation in a PΦB synthase gene that enhances seed weight in soybean, providing a promising breeding target for this important crop.

Rapid reprogramming and stabilization of homoeolog expression bias in hexaploid wheat biparental populations

BACKGROUND

Differences in the relative level of expression of homoeologs, known as homoeolog expression bias, are widely observed in allopolyploids. While the evolution of homoeolog expression bias through hybridization has been characterized, on shorter timescales such as those found in crop breeding programs, the extent to which homoeolog expression bias is preserved or altered between generations remains elusive.

RESULTS

Here we use biparental mapping populations of hexaploid wheat (Triticum aestivum) with a common "Paragon" parent to explore the inheritance of homoeolog expression bias in the F5 generation. We found that homoeolog expression bias is inherited for 26-27% of triads in both populations. Most triads conserved a similar homoeolog expression bias pattern as one or both parents. Inherited patterns were largely driven by changes in the expression of one homoeolog, allowing homoeolog expression bias in subsequent generations to match parental expression. Novel patterns of homoeolog expression bias occurred more frequently in the biparental population from a landrace × elite cross, than in the population with two elite parents.

CONCLUSIONS

These results demonstrate that there is significant reprogramming and stabilization of homoeolog expression bias within a small number of generations that differs significantly based on the parental lines used in the crossing.

Chromosome-level genome assembly of Sambus kanssuensis (Coleoptera: Buprestidae)

Sambus kanssuensis Ganglbauer, 1890 (Coleoptera: Buprestidae), distributed in Gansu and Sichuan Provinces of China, is a phytophagous pest that feeds on the toxic plant Buddleja. However, the genomic resources of this beetle remain unknown, which impedes the understanding of its ecological adaptations. Consequently, this study presents a complete, well-assembled, and annotated genome of S. kanssuensis. The assembled results indicate a genome size of 312.42 Mb, comprising 206 scaffolds, with an N50 of 34.04 Mb; 98.68% of the assembly sequences were anchored to 11 chromosomes, including one sex chromosome. The genome contains 12,723 protein-coding genes, of which 11,977 have been annotated. BUSCO analysis revealed that the completeness of the chromosome-level genome is 97.9%. This chromosome-level genome provides valuable data for further investigations into detoxification mechanisms, ecological adaptations, population genetics, and the evolution of Buprestidae.

Transcriptome analysis of testes gene expression to explore genetic diversity of Mangalica and Camborough boars

The testis, an important reproductive organ, is involved in spermatogenesis and steroid hormone secretion and has been the subject of a wide variety of studies. Pigs are often used as model animals for studies on human physiology and disease, and studies on the testicular development of pigs could shed light on human reproduction. Mangalica, an indigenous Hungarian pig breed, has reproductive traits that are different from those of commercial pig breeds. This specificity could reveal important differences in the cascades and reproductive genes between humans and other animals. In this study, we conducted RNA-sequencing analysis of the testes of 14 days old Mangalica and Camborough boars. We also performed clustering and pathway analysis of differentially expressed genes. These datasets and analyses are expected to provide important gene sets for pig testis development that can be applied in future studies on human reproductive mechanisms.

Whole-blood transcriptomic analysis reveals preoperative complement inhibitor deficiencies linked to postoperative delirium

Postoperative delirium is a type of acute cognitive dysfunction characterized by inattention, disorganized thinking, and altered levels of consciousness that commonly develops after major surgery. Efforts to reduce the incidence of delirium have focused primarily on optimizing perioperative care, however the development of prophylactic interventions have been hindered by a limited understanding of the underlying mechanisms involved in delirium. In this secondary analysis of the Minimizing ICU Neurological Dysfunction with Dexmedetomidine-induced Sleep (MINDDS) trial, a nested case-control study (n = 51) was conducted using total RNA-sequencing analysis of whole-blood to investigate genes associated with delirium risk and development. Transcriptomic analysis revealed significantly lower expression of a key complement pathway inhibitor, C4BPA, in participants who experienced postoperative delirium. This finding was confirmed by quantitative PCR in the MINDDS cohort (n = 319) in adjusted logistic models. Furthermore, complement inhibitor CD55 was also found to be under-expressed in participants who developed delirium. Dexmedetomidine treatment modified associations between C4BPA and CD55 expression and the incidence of postoperative delirium by decreasing incidence in participants with low C4BPA and CD55 expression. This study revealed key complement regulators as risk biomarkers of postoperative delirium. Importantly, our findings suggest postoperative delirium risk is modifiable. Unlike previous research that has mainly focused on proteomics, this study underscores the effectiveness of whole-blood transcriptomics in identifying biomarkers and underlying biological mechanisms of postoperative delirium.

The polyadenylase PAPI is required for virulence plasmid maintenance in pathogenic bacteria

Many species of pathogenic bacteria harbor critical plasmid-encoded virulence factors, and yet the regulation of plasmid replication is often poorly understood despite playing a key role in plasmid-encoded gene expression. Human pathogenic Yersinia, including the plague agent Yersinia pestis and its close relative Y. pseudotuberculosis, require the type III secretion system (T3SS) virulence factor to subvert host defense mechanisms and colonize host tissues. The Yersinia T3SS is encoded on the IncFII plasmid for Yersinia virulence (pYV). Several layers of gene regulation enable a large increase in expression of Yersinia T3SS genes at mammalian body temperature. Surprisingly, T3SS expression is also controlled at the level of gene dosage. The number of pYV molecules relative to the number of chromosomes per cell, referred to as plasmid copy number, increases with temperature. The ability to increase and maintain elevated pYV plasmid copy number, and therefore T3SS gene dosage, at 37˚C is important for Yersinia virulence. In addition, pYV is highly stable in Yersinia at all temperatures, despite being dispensable for growth outside the host. Yet how Yersinia reinforces elevated plasmid replication and plasmid stability remains unclear. In this study, we show that the chromosomal gene pcnB encoding the polyadenylase PAP I is required for regulation of pYV plasmid copy number (PCN), maintenance of pYV in the bacterial population outside the host, robust T3SS activity, and Yersinia virulence in a mouse infection model. Likewise, pcnB/PAP I is required for robust expression of the Shigella flexneri T3SS that, similar to Yersinia, is encoded on a virulence plasmid whose replication is regulated by sRNA. Furthermore, Yersinia and Shigella pcnB/PAP I is required for maintaining model antimicrobial resistance (AMR) plasmids whose replication is regulated by sRNA, thereby increasing antibiotic resistance by ten-fold. These data suggest that pcnB/PAP I contributes to the spread and stabilization of sRNA-regulated virulence and AMR plasmids in bacterial pathogens, and is essential in maintaining the gene dosage required to mediate plasmid-encoded traits. Importantly pcnB/PAP I has been bioinformatically identified in many species of bacteria despite being studied in only a few species to date. Our work highlights the potential importance of pcnB/PAP I in antibiotic resistance, and shows for the first time that pcnB/PAP I promotes virulence plasmid stability in natural pathogenic hosts with a direct impact on bacterial virulence.

Identification and Functional Assessment of Candidate Causal Cis-Regulatory Variants Underlying Electrocardiographic QT Interval GWAS Loci

BACKGROUND

Identifying causal variants among tens or hundreds of associated variants at each locus in genome-wide association studies (GWAS) is challenging. As the vast majority of GWAS variants are noncoding, sequence variation at cis-regulatory elements (CREs) affecting transcriptional expression of specific genes is a widely accepted molecular hypothesis. Following this hypothesis, combined with the observation that open chromatin is a universal hallmark of all types of CREs, we aimed to identify candidate causal cis-regulatory variants underlying QT interval GWAS loci.

METHODS

Common variants in high linkage disequilibrium with genome-wide significant variants were identified using variant call format tools. Genome-wide maps of cardiac putative CREs were generated by MACS2-based peak calling in human cardiac left ventricular DNase I sequencing and Assay for Transposase-Accessible Chromatin using sequencing data sets (n=13). Variant-CRE overlap was performed using custom tracks in the Table Browser tool at the UCSC Genome Browser. Luciferase reporter-based enhancer assays for variant-centered test elements were performed in mouse HL1 cardiomyocyte cells. Reporter activities of allelic pairs were compared using a Student t test.

RESULTS

At a dozen GWAS loci, selected for higher effect sizes and better understanding of the likely causal genes, we identified all genome-wide significant variants (n=1401) and included all common variants (minor allele frequency >1%) in high linkage disequilibrium (r2>0.9) with them as candidate variants (n=3482). Candidate variants were filtered for overlap with cardiac left ventricular putative CREs to identify candidate causal cis-regulatory variants (n=476), which were further assessed for being a known cardiac expression quantitative trait locus variant as additional functional evidence (n=243). Functional evaluation of a subset of seven candidate variants by luciferase reporter-based enhancer assays in HL1 cells using variant-centered test elements led to the identification of 6 enhancer variants with significant allelic differences.

CONCLUSIONS

These efforts have generated a comprehensive set of candidate causal variants expected to be enriched for cis-regulatory potential and thereby, explaining the observed genetic associations.

Landscape of the Epstein-Barr virus-host chromatin interactome and gene regulation

The three-dimensional (3D) chromatin structure of Epstein-Barr virus (EBV) within host cells and the underlying mechanisms of chromatin interaction and gene regulation, particularly those involving EBV's noncoding RNAs (ncRNAs), have remained incompletely characterized. In this study, we employed state-of-the-art techniques of 3D genome mapping, including protein-associated chromatin interaction analysis with paired-end tag sequencing (ChIA-PET), RNA-associated chromatin interaction technique (RDD), and super-resolution microscopy, to delineate the spatial architecture of EBV in human lymphoblastoid cells. We systematically analyzed EBV-to-EBV (E-E), EBV-to-host (E-H), and host-to-host (H-H) interactions linked to host proteins and EBV RNAs. Our findings reveal that EBV utilizes host CCCTC-binding factor (CTCF) and RNA polymerase II (RNAPII) to form distinct chromatin contact domains (CCDs) and RNAPII-associated interaction domains (RAIDs). The anchors of these chromatin domains serve as platforms for extensive interactions with host chromatin, thus modulating host gene expression. Notably, EBV ncRNAs, especially Epstein-Barr-encoded RNAs (EBERs), target and interact with less accessible regions of host chromatin to repress a subset of genes via the inhibition of RNAPII-associated chromatin loops. This process involves the cofactor nucleolin (NCL) and its RNA recognition motifs, and depletion of either NCL or EBERs alters expression of genes crucial for host infection control, immune response, and cell cycle regulation. These findings unveil a sophisticated interplay between EBV and host chromatin.

First Mitogenome of the Critically Endangered Arabian Leopard (Panthera pardus nimr)

The Arabian leopard (Panthera pardus nimr), a critically endangered subspecies endemic to the Arabian Peninsula, faces severe threats from habitat loss, prey depletion, and inbreeding, with fewer than 200 individuals remaining. Genomic resources for this subspecies have been scarce, limiting insights into its evolutionary history and conservation needs. Here, we present the first complete mitochondrial DNA (mtDNA) sequence of P. pardus nimr, derived from a wild-born male sampled at the Oman Wildlife Breeding Centre in 2023. Using PacBio HiFi sequencing, we assembled a 16,781 bp mitogenome (GenBank: PQ283265) comprising 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region, with a GC content of 40.94%. Phylogenetic analysis, incorporating 17 Panthera mtDNA sequences, positions P. pardus nimr closest to African leopard populations from South Africa (Panthera pardus), while distinguishing it from Asian subspecies (P. pardus japonensis and P. pardus orientalis). This mitogenome reveals conserved vertebrate mitochondrial structure and provides a critical tool for studying Panthera genus evolution. Moreover, it enhances conservation genetics efforts for P. pardus nimr by enabling population structure analysis and informing breeding strategies to strengthen its survival.

METTL3 inhibits primed-to-naïve transition of pluripotent stem cells through m6A-YTHDF2-pluripotency/Gstp1 mRNA degradation axis

N6-methyladenosine (m6A) plays crucial roles in development and cellular reprogramming. During embryonic development, pluripotency transitions from a naïve to a primed state, and modeling the reverse primed-to-naïve transition (PNT) provides a valuable framework for investigating pluripotency regulation. Here, we show that inhibiting METTL3 significantly promotes PNT in an m6A-dependent manner. Mechanistically, we found that suppressing METTL3 and YTHDF2 prolongs the lifetimes of pluripotency-associated mRNAs, such as Nanog and Sox2, during PNT. In addition, Gstp1 was identified as a downstream target of METTL3 inhibition and YTHDF2 knockout. Gstp1 overexpression enhances PNT, whereas its inhibition impedes the transition. Overall, our findings suggest that YTHDF2 facilitates the removal of pluripotency gene transcripts and Gstp1, thereby promoting PNT reprogramming through m6A-mediated posttranscriptional control.

LIPID RICH 1 modulates allocation of carbon between starch and triacylglycerol in Arabidopsis leaves

Plants accumulate starch and triacylglycerols (TAGs) as carbon sources. Leaves primarily store starch in chloroplasts, with some TAGs stored in lipid droplets, but how carbon resource allocation is regulated in leaves during cellular metabolism is largely unknown. Using a forward genetics approach, we isolated an Arabidopsis thaliana mutant with more lipid droplets in its leaves than the wild type, named lipid rich 1 (liri1). The overaccumulation of lipid droplets was caused by loss of function in the causal gene, encoding an uncharacterized protein. TAG levels were 5-fold higher and starch levels 2-fold lower in the leaves of liri1 than in those of the wild type. LIRI1 localized to the chloroplasts, and contents of chloroplast membrane lipids were 20% higher in liri1 leaves than in wild-type leaves. Co-immunoprecipitation assays revealed that LIRI1 interacts with ACETYL-COENZYME A CARBOXYLASE CARBOXYLTRANSFERASE ALPHA SUBUNIT (an enzyme for fatty acid biosynthesis) and STARCH SYNTHASE 4 (an enzyme for starch biosynthesis). In isotope tracer experiments using [1-13C]sodium acetate, more 13C was incorporated into TAGs in liri1 leaves than in wild-type leaves. Moreover, liri1 plants showed growth defects and irregular chloroplasts. These results indicate that LIRI1 affects the carbon trade-off to inhibit lipid production in leaves.

Limited predictive power of known resistance genes for phenotypic drug resistance in clinical Mycobacterium abscessus complex from Beijing in China

Mycobacterium abscessus complex (MABC) is an emerging pathogen with intrinsic multidrug resistance. Genomic sequencing technology has been widely applied to predict bacterial resistance in other bacteria, but the catalog of known resistance-determining genes to explain phenotypic resistance in the MABC is incomplete for many antibiotics. Eighty-one MABC strains were isolated from sputum samples of patients with pulmonary disease in the Beijing Chest Hospital. All isolates were tested for minimum inhibitory concentrations (MICs) to eight antibiotics and underwent whole-genome sequencing (WGS). Of the total 81 MABC isolates, six strains exhibited clarithromycin (CLM) resistance by day 3 in culture, but only one (16.7%, 1/6) contained a mutation in the rrl gene. All M. abscessus strains contained the erm (41)28T (100.0%, 49/49) polymorphism and exhibited CLM-induced resistance after 14 days in culture. Of the 61 imipenem-resistant strains, 12 (19.7%, 12/61) had mutations in the bla gene. Although there were four (4.9%) amikacin-resistant, nine (11.1%) linezolid-resistant, eight (9.9%) clofazimine-resistant, 23 (28.4%) bedaquiline-resistant, and 27 (33.3%) cefoxitin-resistant strains, no known mutations associated with resistance to these antibiotics were found. These results suggest that the explanatory power of known resistance genes for clinical MABC resistance is limited and that other unidentified genes or novel resistance mechanisms may be involved.

Optical genome mapping reveals novel structural variations in an autism spectrum disorder cohort

Structural variants (SVs) contribute to the genetic architecture of autism spectrum disorder (ASD), but their comprehensive characterization is limited by technological challenges in their detection. Optical genome mapping (OGM) offers a promising alternative, enabling the identification of large-scale SVs that might be overlooked by traditional sequencing methods. This study aimed to use OGM to identify SVs associated with ASD. We generated in-house OGM data from 26 participants diagnosed with ASD, leading to the discovery of 1593 novel SVs. Among them, 114 novel SVs were identified in at least two non-sibling participants, with 57 of them putatively overlapping known gene regions. To validate our findings, two novel SVs were confirmed by Sanger sequencing. The dataset generated in this study can serve as a novel and valuable resource for future research and facilitate the exploration of SVs related to ASD. Our work also underscores the importance of large-scale genomic rearrangements in neurodevelopmental disorders and provides insights into SVs as potential molecular diagnostic and therapeutic targets for ASD.

Genetic surveillance reveals low but sustained malaria transmission with clonal replacement in Sao Tome and Principe

BACKGROUND

Despite efforts to eliminate malaria in Sao Tome and Principe (STP), cases have recently increased. Understanding residual transmission structure is crucial for developing effective elimination strategies.

METHODS

This study collected surveillance data and generated amplicon sequencing data from 980 samples between 2010 and 2016 to examine the genetic structure of the parasite population.

RESULTS

Here we show that the mean multiplicity of infection (MOI) is 1.3, with 11% polyclonal infections, indicating low transmission intensity. Temporal trends of these genetic metrics do not align with incidence rates, suggesting that changes in genetic metrics may not straightforwardly reflect changes in transmission intensity, particularly in low transmission settings where genetic drift and importation have a substantial impact. While 88% of samples are genetically linked, continuous turnover in genetic clusters and changes in drug-resistance haplotypes are observed. Principal component analysis reveals some STP samples are genetically similar to those from Central and West Africa, indicating possible importation.

CONCLUSIONS

These findings highlight the need to prioritize several interventions, such as targeted interventions against transmission hotspots, reactive case detection, and strategies to reduce the introduction of new parasites into this island nation as it approaches elimination. This study also serves as a case study for implementing genetic surveillance in a low transmission setting.

CRAMP1-dependent histone H1 biogenesis is essential for topoisomerase II inhibitor tolerance

Topoisomerase II (TOP2) inhibitors (TOP2i) are mainstay chemotherapeutic agents that undermine genome integrity by stabilizing TOP2-DNA complexes accompanied by DNA damage formation. Here, we reveal the uncharacterized protein CRAMP1 and H1 linker histones as key effectors of TOP2i tolerance in human cells. We demonstrate that CRAMP1 defines a dedicated histone H1 biogenesis factor stimulating transcription of both replicative and non-replicative H1 genes, driven by its concurrent targeting to histone gene loci and H1-specific promoter motifs. CRAMP1 promotes TOP2i tolerance by maintaining H1 supply, involving a novel mechanism uncoupled from TOP2i-induced DNA damage whereby reducing the H1 pool triggers unscheduled TOP2 substrate formation in low-accessibility chromatin states. This amplifies total demand for TOP2 activity, lowering the threshold for TOP2i-mediated exhaustion of TOP2. Our discoveries elucidate the mechanistic basis of histone H1 biogenesis in human cells, opening opportunities for selectively manipulating linker but not core histone supply and targeting cancer-associated H1 deficiency.

TEAL-Seq: targeted expression analysis sequencing

Metagenome sequencing enables the genetic characterization of complex microbial communities. However, determining the activity of isolates within a community presents several challenges, including the wide range of organismal and gene expression abundances, the presence of host RNA, and low microbial biomass at many sites. To address these limitations, we developed "targeted expression analysis sequencing" or TEAL-seq, enabling sensitive species-specific analyses of gene expression using highly multiplexed custom probe pools. For proof of concept, we targeted about 1,700 core and accessory genes of Staphylococcus aureus and S. epidermidis, two key species of the skin microbiome. Two targeting methods were applied to laboratory cultures and human nasal swab specimens. Both methods showed a high degree of specificity, with >90% reads on target, even in the presence of complex microbial or human background DNA/RNA. Targeting using molecular inversion probes demonstrated excellent correlation in inferred expression levels with bulk RNA-seq. Furthermore, we show that a linear pre-amplification step to increase the number of nucleic acids for analysis yielded consistent and predictable results when applied to complex samples and enabled profiling of expression from as little as 1 ng of total RNA. TEAL-seq is much less expensive than bulk metatranscriptomic profiling, enables detection across a greater dynamic range, and uses a strategy that is readily configurable for determining the transcriptional status of organisms in any microbial community.IMPORTANCEThe gene expression patterns of bacteria in microbial communities reflect their activity and interactions with other community members. Measuring gene expression in complex microbiome contexts is challenging, however, due to the large dynamic range of microbial abundances and transcript levels. Here we describe an approach to assessing gene expression for specific species of interest using highly multiplexed pools of targeting probes. We show that an isothermal amplification step enables the profiling of low biomass samples. TEAL-seq should be widely adaptable to the study of microbial activity in natural environments.

Partner dependency alters patterns of coevolutionary selection in mutualisms

Coevolution is a ubiquitous driver of diversification in both mutualistic and antagonistic interactions between species. In mutualisms, coevolution can result in trait complementarity between partners that facilitates their persistence. Despite its importance, most of what we know about coevolution in mutualism comes from obligate interactions, whereas we know comparatively little about facultative interactions, arguably the most common type of mutualism. To evaluate coevolutionary dynamics in facultative mutualism and test how it compares with obligate mutualisms, we used a synthetic yeast mutualism where the partners exchange essential nutrient resources. We manipulated mutualism dependency by controlling the availability of mutualistic resources in the environment and measured coevolution via time-shift assays and tracking the evolution of mutualistic traits over time. In addition, we genotyped the evolved and ancestral mutualists to test for differences in the strength of coevolutionary selection between facultative and obligate mutualisms. We found evidence of coevolution in both facultative and obligate mutualisms, but coevolution was weaker and slower in facultative mutualisms. We also found evidence for evolution of trait complementarity in obligate mutualisms but not in facultative mutualisms. Furthermore, obligate mutualists had more SNPs under positive selection than facultative mutualists. Together, these results provide strong evidence that mutualism dependency impacts both the strength of coevolution and the rate of trait evolution.

Ancient DNA suggests a historical demographic decline and genetic erosion in the Atlantic bluefin tuna

Overexploitation has depleted fish stocks during the past century; nonetheless, its genomic consequences remain poorly understood for most species. Characterizing the spatiotemporal patterns of these consequences may provide baseline estimates of past diversity and productivity to aid management targets, help predict future dynamics, and facilitate the identification of evolutionary factors limiting fish population recovery. Here, we evaluate human impacts on the evolution of the iconic Atlantic bluefin tuna (Thunnus thynnus), one of the longest and most intensely exploited marine fishes, with a tremendous cultural and economic importance. We sequenced whole genomes from modern (n = 49) and ancient (n = 41) specimens dating up to 5,000 y ago, uncovering several findings. First, we identify temporally stable patterns of population admixture, as bluefin tuna caught off Norway and in the eastern Mediterranean share a greater degree of ancestry with Gulf of Mexico bluefin tuna than western and central Mediterranean bluefin tuna. This suggests that Atlantic spawning areas are important mixing grounds for the genetic diversity of Mediterranean bluefin tuna. We model effective population size to show that Mediterranean bluefin tuna began to undergo a demographic decline by the year 1900 to an extent not observed across the previous millennia. Coinciding with this, we found that heterozygosity and nucleotide diversity were significantly lower in modern (2013 to 2020) than ancient (pre-1941) Mediterranean bluefin tuna, suggesting that bluefin tuna underwent a genetic bottleneck. With this work, we show how ancient DNA provides unique perspectives on ecological complexity with the potential to inform the management and conservation of fishes.

The effect of sample type and location on industrial workplace sink and hand dryer microbiomes

One major issue in tackling antimicrobial resistance (AMR) is the ability to effectively track resistance spread in environments where surveillance is limited. Such environments include those experiencing high volumes of hand washing and drying from multiple users. This study characterised the microbial populations and antimicrobial resistomes of two different sample types from a pharmaceutical industrial site as part of an AMR environmental surveillance programme. Paired samples were collected from hand dryers and adjacent sinks in distinct sampling locations: from toilets adjacent to 'wet' labs, and locations associated with 'dry' activities. Microbial populations in hand dryers were significantly different to those of sinks, whereas there was no significant difference based on sample location. The opposite effect was observed for resistomes, where profiles differed significantly based on sample location, but not sample type. When both sample type and location were considered together, differences in microbiomes were driven primarily by hand dryer profiles from different locations. Analysis of metagenomically-assembled genomes revealed the presence of many poorly characterised organisms, and suggested no specific families predominated in terms of ARG carriage. This study emphasises the impact of human activities in determining the resistome of commonly used appliances, and the need for continued AMR surveillance programmes.

TaRTLEt: Transcriptionally-active Riboswitch Tracer Leveraging Edge deTection

Structured RNAs have emerged as a major component of cellular regulatory systems, but their mechanism of action is often poorly understood. Riboswitches are structured RNAs that allosterically regulate gene expression through any of several different mechanisms. In vitro approaches to characterizing this mechanism are costly, low-throughput, and must be repeated for each individual riboswitch locus of interest. Bioinformatic methods promise higher throughput; despite robust computational identification of riboswitches, however, computational classification of the riboswitch mechanism has so far been both model-bound, relying on identification of sequence motifs known to be required for specific models of riboswitch activity, and empirically untested, with predictions far outpacing biological validation. Here, we introduce TaRTLEt (Transcriptionally-active Riboswitch Tracer Leveraging Edge deTection), a new high-throughput tool that recovers in vivo patterns of riboswitch-mediated transcription termination from paired-end RNA-seq data using edge detection methods. TaRTLEt successfully extracts transcription termination signals despite numerous sources of biological and technical noise. We tested the effectiveness of TaRTLEt on riboswitches identified from a wide range of sequenced bacterial taxa by utilizing publicly available paired-end RNA-seq readsets, finding broad agreement with previously published in vitro characterization results. In addition, we use TaRTLEt to infer the in vivo regulatory mechanism of uncharacterized riboswitch loci from existing public data. TaRTLEt is available on GitHub and can be applied to paired-end RNA-seq datasets from isolates or complex communities.

Predicting high confidence ctDNA somatic variants with ensemble machine learning models

Circulating tumour DNA (ctDNA) is a minimally invasive cancer biomarker that can be used to inform treatment of cancer patients. The utility of ctDNA as a cancer biomarker depends on the ability to accurately detect somatic variants associated with cancer. Accurate somatic variant detection in circulating cell free DNA (cfDNA) NGS data requires filtering strategies to remove germline variants, and NGS artifacts. Rule-based variant filtering methods either remove a substantial number of true positive ctDNA variants along with false variant calls or retain an implausibly large number of total variants. Machine Learning (ML) enables identification of complex patterns which may improve ability to distinguish between real somatic ctDNA variants and false positive calls. We built two Random Forest (RF) models for predicting high confidence somatic ctDNA variants in low and high depth cfDNA NGS data. Low depth models were fitted and evaluated on whole exome sequencing (WES) cfDNA data at depths of approximately 10X while the high depth data was sequenced at approximately 500X. Both models utilise a set of 15 features from variants detected by bcftools, FreeBayes, LoFreq and Mutect2. High confidence ground truth sets were obtained from matched tissue biopsy samples. We benchmarked our models against rule-based filtering with a set of hard, medium, and soft thresholds. Precision-recall curves showed the high depth model outperformed rule-based filtering at all thresholds in Test Data (PR-AUC 0.71). Partial dependence plots showed membership in the COSMIC database, absence from the dbSNP common variants database, and increasing read depth increased mean probability of high confidence somatic variant prediction in both models. Our results demonstrate the utility of supervised ML models for filtering variants in cfDNA data.

Transcriptome-Wide Analysis of Brain Cancer Initiated by Polarity Disruption in Drosophila Type II Neuroblasts

Brain tumors, in particular gliomas and glioblastoma multiforme (GBM), are thought to originate from different cells facing specific founding insults, a feature that partly justifies the complexity and heterogeneity of these severe forms of cancer. However, gliomas and GBM are usually reproduced in animal models by inducing molecular alterations in mature glial cells, which, though being part of the puzzle, do not represent the whole picture. To fill this conceptual gap, we previously developed a neurogenic model of brain cancer in Drosophila, demonstrating that the loss of cell polarity in neural stem cells (called neuroblasts in the fruit fly) is sufficient to promote the formation of malignant masses that continue to grow in the adult, displaying several phenotypic traits typical of human GBM. Here, we expand on previous work by restricting polarity disruption to Drosophila type II neuroblasts, whose self-renewal is comparable to that of mammalian neural progenitors, with the aim to capture the molecular signature of the resulting cancers in a specific and reproducible context. A comparison of the most deregulated transcripts with those found in human primary GBMs confirmed that our model can be proficiently used to delve into the roots of human brain tumorigenesis.

Population genomics uncovers loci for trait improvement in the indigenous African cereal tef (Eragrostis tef)

Tef (Eragrostis tef) is an indigenous African cereal that is gaining global attention as a gluten-free "superfood" with high protein, mineral, and fibre contents. However, tef yields are limited by lodging and by losses during harvest owing to its small grain size (150× lighter than wheat). Breeders must also consider a strong cultural preference for white-grained over brown-grained varieties. Tef is relatively understudied with limited "omics" resources. Here, we resequence 220 tef accessions from an Ethiopian diversity collection and also perform multi-locational phenotyping for 25 agronomic and grain traits. Grain metabolome profiling reveals differential accumulation of fatty acids and flavonoids between white and brown grains. k-mer and SNP-based genome-wide association uncover important marker-trait associations, including a significant 70 kb peak for panicle morphology containing the tef orthologue of rice qSH1-a transcription factor regulating inflorescence morphology in cereals. We also observe a previously unknown relationship between grain size, colour, and fatty acids. These traits are highly associated with retrotransposon insertions in homoeologues of TRANSPARENT TESTA 2, a known regulator of grain colour. Our study provides valuable resources for tef research and breeding, facilitating the development of improved cultivars with desirable agronomic and nutritional properties.

Duplication of the autism-related gene Chd8 leads to behavioral hyperactivity and neurodevelopmental defects in mice

Mutations in the gene encoding chromodomain helicase DNA-binding protein 8 (CHD8) are strongly associated with autism spectrum disorder (ASD). Although duplications of the chromosomal locus including CHD8 have also been detected in individuals with neurodevelopmental disorders, the contribution of CHD8 duplication to clinical phenotypes and the underlying mechanisms have remained unknown. Here we show that Chd8 knock-in (KI) mice that overexpress CHD8 as a model of human CHD8 duplication manifest growth retardation, microcephaly, impaired neuronal differentiation, and behavioral abnormalities including hyperactivity and reduced anxiety-like behavior. Chd8 overexpression affects the transcription and chromatin accessibility of genes related to neurogenesis, with these changes being associated with aberrant binding of CHD8 to enhancer regions. Furthermore, pharmacological intervention partially ameliorates the hyperactivity of Chd8 KI mice. Our results thus indicate that Chd8 KI mice recapitulate key features of CHD8 duplication syndrome in humans, providing insight into pathogenic mechanisms underlying neurodevelopmental disorders.

Comparing Genome Sequencing Methods to Reconstruct the Spread of Piscine Myocarditis Virus in Ireland

Piscine myocarditis virus (PMCV), a double-stranded RNA virus, is the causative agent of cardiomyopathy syndrome (CMS) in Atlantic salmon Salmo salar, which was first reported in Ireland in 2012. PMCV continues to be a disease threat to Atlantic salmon aquaculture in Ireland, and as such, it is of growing importance to understand how the virus spreads. Genetic sequences allow for transmission pathways to be examined, with whole genomes providing the most accurate information. In this study, whole genome sequencing has been applied to Irish strains of PMCV, in doing so revealing how > 80% of the genetic diversity of the virus lies outside the commonly sequenced open reading frames (ORFs). Second, this paper examines the effectiveness of incorporating a MinION sequencing approach into routine diagnostics by comparing a MinION generated genome to the corresponding sequence generated via Illumina MiSeq. The results showed the MinION genome shared 99.59% identity with the Illumina genome, and while this accuracy may be sufficient for studies such as pathogen identification and deeper evolutionary questions, it was shown to be insufficient for accurately tracking viral transmission pathways. Finally, comparing Irish and Faroese sequences reveals that some strains of PMCV in Ireland may originate from wild fish.

A GDSL esterase/lipase gene GbGELP identified from a fiber micronaire QTL qMIC-A11 modulates cell elongation and fiber development

KEY MESSAGE

A fiber micronaire QTL qMIC-A11 was fine-mapped, and the GDSL esterase/lipase gene GbGELP was identified as the causal gene of the QTL. GbGELP modulates cell elongation and cotton fiber development. Fine mapping and map-based cloning of fiber micronaire (MIC)-related quantitative trait loci (QTL) have not been reported to date. Here, we utilized a G. hirsutum (Gh) acc. TM-1-G. barbadense (Gb) acc. Hai7124 introgression line CSSL47, which exhibits a significant decrease in MIC compared to TM-1, to cross with TM-1 and develop the F2 and F2:3 secondary segregating populations. Further, a stable MIC QTL qMIC-A11 was simultaneously detected in the F2 and F2:3 populations and anchored within a 407 kb region. Among them, GB_A11G1593 encoding a GDSL esterase/lipase, exhibited substantially higher expression levels at fiber elongation period in CSSL47 compared to TM-1, which was temporally identified as the causal gene for qMIC-A11 and named as GbGELP. The heterologous expression of GbGELP in Arabidopsis showed increased root length, root cell length, rosette leaf growth, and trichome density. However, knockdown of GbGELP homologs in CSSL47 significantly decreased the fiber length. Further investigation found that there was an A/T single-nucleotide polymorphism variation (SNP) in the promoter of GELP orthologs between CSSL47 and TM-1, which results in a differential CATTAAATT/CATTTAATT HAHR1-box cis-acting element, a binding site for the homeodomain-leucine zipper IV (HD-ZIP IV). GbGELP was regulated by a HD-ZIP IV transcription factor GhHDG2 via binding to the CATTAAATT element in the GbGELP promoter, while GhGELP could be activated due to GhHDG2 unable to bind the CATTTAATT element in the GhGELP promoter. The fine-mapped MIC QTL qMIC-A11, along with the causal gene GbGELP, will be utilized to improve the fiber quality in cotton breeding.

Precise measurement of molecular phenotypes with barcode-based CRISPRi systems

Genome-wide CRISPR-Cas9 screens have untangled regulatory networks driving diverse biological processes. Their success relies on interrogating specific molecular phenotypes and distinguishing key regulators from background effects. Here, we realize these goals by optimizing CRISPR interference with barcoded expression reporter sequencing (CiBER-seq) to dramatically improve the sensitivity and scope of genome-wide screens. We systematically address technical factors that distort phenotypic measurements by normalizing expression reporters against closely matched promoters. We use our improved CiBER-seq to accurately capture known components of well-studied RNA and protein quality control systems. These results demonstrate the precision and versatility of CiBER-seq for dissecting cellular pathways.

Shaking culture attenuates circadian rhythms in induced pluripotent stem cells during osteogenic differentiation through the TEAD-Fbxl3-CRY axis

Circadian rhythms, which synchronize cellular and organismal activities with the Earth's 24-hour light-dark cycle, are controlled by clock genes. These genes not only regulate metabolic and physiological processes but also influence osteogenesis. Despite extensive research on the genetic control of circadian rhythms, little is known about the mechanisms by which mechanical factors in the extracellular environment affect these rhythms during the osteogenic differentiation of induced pluripotent stem cells (iPSCs). Shaking culture, which promotes the formation of three-dimensional organoid-like constructs from iPSC embryoid bodies (iPSC-EBs), introduces distinct biomechanical forces compared with static adherent culture. This raises the question of how these forces affect the circadian gene expression during osteogenic differentiation. In this study, we investigated the effects of shaking cultures on the circadian rhythm of key clock genes (Clock, Bmal1, and Npas2) in iPSC-EBs. In the adherent culture, iPSC-EBs displayed rhythmic oscillations of the clock genes, which were attenuated in the shaking culture. RNA-seq analysis revealed that the yes-associated protein (YAP)-transcriptional enhanced associate domain (TEAD) transcriptional cascade was activated in the shaking culture. Further investigations using assay for transposase-accessible chromatin with sequencing and chromatin immunoprecipitation assays identified Fbxl3 as a direct target of this transcriptional cascade. Fbxl3 upregulation in the shaking culture enhanced the degradation of CRY proteins, which are essential components of the circadian feedback loop, thereby suppressing clock gene oscillations. In addition, treatment with verteporfin, a YAP-TEAD inhibitor, restored circadian gene oscillations and increased the expression of osteogenic markers in shaking culture. These findings highlight a novel mechanistic link between biomechanical cues and circadian regulation and offer potential insights for optimizing tissue engineering strategies in regenerative medicine.

IncRNA-ZFAS1, an Emerging Gate-Keeper in DNA Damage-Dependent Transcriptional Regulation

Numerous long noncoding RNAs (lncRNAs) are generated in response to external stimuli, but the scope and functions of such activity are not known. Here, this study provides insight into how the transcription of lncRNAs is connected to DNA damage response by identifying the lncRNA ZFAS1, which is required for cell cycle arrest, transcription regulation, and DNA repair. Mechanistically, ZFAS1 facilitates dynamic changes in hyperphosphorylated forms of the large subunit of RNA polymerase II (RNAPII) around transcription initiation sites by directly targeting the regulated genes. It is shown that extensive transcription shutdown and concomitant stimulated engagement of RNAPII-Ser2P are crucial for repair and cell survival upon genotoxic stress. Finally, ZFAS1 knockout in mice dampened nucleotide excision repair (NER) and led to kidney dysplasia. Overall, the findings extend the understanding of lncRNAs in DNA damage repair (DDR) and imply a protective role of lncRNA against DDR-deficient developmental disorders.

Perfluoroalkyl substance pollutants disrupt microglia function and trigger transcriptional and epigenomic changes

Per- and polyfluoroalkyl substances (PFAS), commonly referred to as "forever chemicals", are widely utilized in various industries and consumer products worldwide. Their exposure has been associated with numerous diseases and malignancies, including neurodevelopmental and neurodegenerative disorders. However, the molecular mechanisms underlying PFAS-induced adverse effects on the central nervous system (CNS) remain poorly understood. In this study, we investigated the transcriptomic and epigenetic changes in microglia exposed to perfluorooctane sulfonate (PFOS), a prevalent PFAS compound. Our findings demonstrate that 24-hour PFOS exposure (25 and 50 µM) disrupts the microglial transcriptome and compromises their homeostatic state, marked by increased inflammation and impaired actin cytoskeleton remodeling. Comparative analysis with in vivo transcriptional states revealed that PFOS-exposed microglia exhibit gene expression profiles resembling those of aged microglia. Additionally, profiling of active chromatin regions uncovered significant alterations in the H3K27ac landscape in PFOS-exposed microglia. Notably, these epigenetic disruptions persisted even after PFOS withdrawal, with a subset of H3K27ac-enriched regions remaining altered, suggesting the presence of lasting epigenetic scars. Furthermore, transcription factor analysis implicated the AP-1 and TEAD families as potential upstream regulators connecting the altered chromatin landscape to transcriptomic changes. Collectively, these findings provide mechanistic insights into how PFOS exposure disrupts microglial function and highlight its potential role in exacerbating neurodegenerative processes.

POCALI: Prediction and Insight on CAncer LncRNAs by Integrating Multi-Omics Data with Machine Learning

Long non-coding RNAs (lncRNAs) are receiving increasing attention as biomarkers for cancer diagnosis and therapy. Although there are many computational methods to identify cancer lncRNAs, they do not comprehensively integrate multi-omics features for predictions or systematically evaluate the contribution of each omics to the multifaceted landscape of cancer lncRNAs. In this study, an algorithm, POCALI, is developed to identify cancer lncRNAs by integrating 44 omics features across six categories. The contributions of different omics are explored to identifying cancer lncRNAs and, more specifically, how each feature contributes to a single prediction. The model is evaluated and benchmarked POCALI with existing methods. Finally, the cancer phenotype and genomics characteristics of the predicted novel cancer lncRNAs are validated. POCALI identifies secondary structure and gene expression-related features as strong predictors of cancer lncRNAs, and epigenomic features as moderate predictors. POCALI performed better than other methods, especially in terms of sensitivity, and predicted more candidates. Novel POCALI-predicted cancer lncRNAs have strong relationships with cancer phenotypes, similar to known cancer lncRNAs. Overall, this study facilitates the identification of previously undetected cancer lncRNAs and the comprehensive exploration of the multifaceted feature contributions to cancer lncRNA prediction.

Small intestinal neuroendocrine tumors lack early genomic drivers, acquire DNA repair defects and harbor hallmarks of low REST expression

The tumorigenesis of small intestinal neuroendocrine tumors (siNETs) is not understood and comprehensive genomic and transcriptomic data sets are limited. Therefore, we performed whole genome and transcriptome analysis of 39 well differentiated siNET samples. Our genomic data revealed a lack of recurrent driver mutations and demonstrated that multifocal siNETs from individual patients can arise genetically independently. We detected germline mutations in Fanconi anemia DNA repair pathway (FANC) genes, involved in homologous recombination (HR) DNA repair, in 9% of patients and found mutational signatures of defective HR DNA repair in late-stage tumor evolution. Furthermore, transcriptomic analysis revealed low expression of the transcriptional repressor REST. Summarizing, we identify a novel common transcriptomic signature of siNETs and demonstrate that genomic alterations alone do not explain initial tumor formation, while impaired DNA repair likely contributes to tumor evolution and represents a potential pharmaceutical target in a subset of patients.

Genome-wide analyses of cell-free DNA for therapeutic monitoring of patients with pancreatic cancer

Determining response to therapy for patients with pancreatic cancer can be challenging. We evaluated methods for assessing therapeutic response using cell-free DNA (cfDNA) in plasma from patients with metastatic pancreatic cancer in the CheckPAC trial (NCT02866383). Patients were evaluated before and after initiation of therapy using tumor-informed plasma whole-genome sequencing (WGMAF) and tumor-independent genome-wide cfDNA fragmentation profiles and repeat landscapes (ARTEMIS-DELFI). Using WGMAF, molecular responders had a median overall survival (OS) of 319 days compared to 126 days for nonresponders [hazard ratio (HR) = 0.29, 95% confidence interval (CI) = 0.11-0.79, P = 0.011]. For ARTEMIS-DELFI, patients with low scores after therapy initiation had longer median OS than patients with high scores (233 versus 172 days, HR = 0.12, 95% CI = 0.046-0.31, P < 0.0001). We validated ARTEMIS-DELFI in patients with pancreatic cancer in the PACTO trial (NCT02767557). These analyses suggest that noninvasive mutation and fragmentation-based cfDNA approaches can identify therapeutic response of individuals with pancreatic cancer.

Genomic and chromosomal architectures underlying fertility maintenance in the testes of intergeneric homoploid hybrids

The remarkable diversity of the Cyprinidae family highlights the importance of hybridization and gene flow in generating genetic variation, adaptation, and even speciation. However, why do cyprinid fish frequently overcome postzygotic reproductive isolation, a mechanism that normally prevents successful reproduction after fertilization? To address this gap in knowledge, we conducted comparative studies using reciprocal F1 hybrid lineages derived from intergeneric hybridization between the cyprinid species Megalobrama amblycephala and Culter alburnus. Utilizing long-read genome sequencing, ATAC-seq, Hi-C, and mRNA-seq technologies, we identified rapid genomic variations, chromatin remodeling, and gene expression changes in the testicular cells of F1 hybrid individuals. By analyzing the distribution of these alterations across three gene categories (allelic genes, orphan genes, and testis-specific genes), we found that changes were less pronounced in allelic and testis-specific genes but significantly more pronounced in orphan genes. Furthermore, we hypothesize that rnf212b is a crucial testis-specific gene that regulates spermatogenesis. Our findings suggest that allelic and testis-specific genes potentially mitigate "genomic shock" on reproductive function following hybridization. This research offers potential insights into the formation mechanisms of homoploid hybridization by demonstrating the coordinated interplay of genomic variations, chromatin remodeling, and gene expression changes during testicular development and spermatogenesis.

Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity

High-throughput massively parallel reporter assays (MPRAs) and phenotype-rich in vivo transgenic mouse assays are two potentially complementary ways to study the impact of noncoding variants associated with psychiatric diseases. Here, we investigate the utility of combining these assays. Specifically, we carry out an MPRA in induced human neurons on over 50,000 sequences derived from fetal neuronal ATAC-seq datasets and enhancers validated in mouse assays. We also test the impact of over 20,000 variants, including synthetic mutations and 167 common variants associated with psychiatric disorders. We find a strong and specific correlation between MPRA and mouse neuronal enhancer activity. Four out of five tested variants with significant MPRA effects affected neuronal enhancer activity in mouse embryos. Mouse assays also reveal pleiotropic variant effects that could not be observed in MPRA. Our work provides a catalog of functional neuronal enhancers and variant effects and highlights the effectiveness of combining MPRAs and mouse transgenic assays.

Development and application of sex-specific indel markers for Hippophae salicifolia based on third-generation sequencing

Hippophae salicifolia, a dioecious shrub endemic to the Himalayan region, holds substantial ecological and economic value. The lack of pre-flowering morphological traits for sex identification has long impeded efficient germplasm management and breeding efforts. In this study, we utilized third-generation sequencing technology to conduct whole-genome comparative analysis of known-sex individuals, identifying insertion/deletion loci significantly associated with sex. Based on these loci, we designed a specific primer pair, Hsa09. PCR amplification results demonstrated 100% accuracy in sex differentiation, with female individuals showing a single band and male individuals exhibiting a double-band pattern. Cross-species validation revealed limited applicability of Hsa09 in closely related Hippophae species, suggesting notable divergence in sex determination mechanisms within the genus. This study establishes the first molecular tool for early sex identification in H. salicifolia, overcoming the dependence on reproductive organ development in traditional methods. It provides essential technical support for understanding the evolutionary pathways of sex chromosomes and advancing sex-regulated breeding strategies within the Hippophae genus.

Novel microsatellite instability test of sebaceous tumours to facilitate low-cost universal screening for Lynch syndrome

BACKGROUND

One in five patients with sebaceous tumours (STs) may have Lynch syndrome (LS), an inherited disorder that increases the risk of developing cancer. Patients with LS benefit from cancer surveillance and prevention programmes and immunotherapy. While universal tumour mismatch repair (MMR) deficiency testing is recommended in colorectal and endometrial cancers to screen for LS, there is no consensus screening strategy for STs, leading to low testing rates and inequity of care.

OBJECTIVES

To assess a low-cost and scalable sequencing-based microsatellite instability (MSI) assay, previously shown to enhance LS screening of colorectal cancers, for MMR deficiency detection in STs against the current clinical standard of immunohistochemistry (IHC).

METHODS

Consecutive ST cases (n = 107) were identified from the records of a single pathology department. MMR protein IHC staining was interpreted by a consultant histopathologist. MSI analysis used amplicon sequencing of 14 microsatellites and a naive Bayesian classifier to calculate the sample MSI score.

RESULTS

Loss of MMR protein expression was observed in 49/104 STs with interpretable IHC [47.1%, 95% confidence interval (CI) 37.3-57.2]. MMR deficiency was less frequent in carcinoma than in adenoma and sebaceoma (P = 4.74 × 10-3). The majority of MMR-deficient STs had concurrent loss of MSH2 and MSH6 expression. The MSI score achieved a receiver operator characteristic area under curve of 0.944 relative to IHC. Lower MSI scores were associated with MSH6 deficiency.

CONCLUSIONS

These data support MSI testing as an adjunct or alternative to MMR IHC in STs. Integration of STs into established LS screening pathways using this high-throughput methodology could increase testing and reduce costs.

Genome-Wide Identification, Phylogeny, and Abiotic Stress Response Analysis of OSCA Family Genes in the Alpine Medicinal Herb Notopterygium franchetii

Hyperosmolality-gated calcium-permeable cation channel protein denoted as OSCA, which are mechanosensitive pore-forming ion channels, play a pivotal role in plants' responses to abiotic stressors. Notopterygium franchetii, an endemic perennial plant species distributed in the Qinghai-Tibetan Plateau and its adjacent high-altitude regions, is likely to have undergone adaptive evolution in response to extreme abiotic stress conditions. The current study was conducted to characterize the genome-wide characteristics and phylogenetic evolution of the OSCA gene family in N. franchetii and identify its response patterns to drought and high-temperature stresses. We examined the gene family's structural features, phylogenetic relationships, and response to abiotic stresses. The N. franchetii genome had 29 OSCA gene family members on 11 chromosomes. Subcellular localization showed they were mainly in the cell membrane, and a promoter cis-acting element study found that the OSCA gene family contained methyl jasmonate, abscisic acid, and various adversity and hormone response components. Under drought stress, most of the NofOSCAs genes showed a tendency to increase over time in the roots of N. franchetii, while in the aboveground parts, most of the NofOSCAs genes showed a tendency to increase and then decrease. The expression of different NofOSCAs genes in N. franchetii also showed alternating changes under high-temperature stress. Nine members of NofOSCAs were found to be linked to the PPI network, and these members were involved in membrane structure, transmembrane transport, and ion channel function. Our analysis of differential expression revealed that the expression of OSCA genes differed among the different N. franchetii tissues, with the roots exhibiting the highest average expression level, and many genes displayed tissue-specific high expression patterns. These results provided novel insights into the phylogenetic evolution and abiotic stress response mechanisms in the high-altitude medicinal herb N. franchetii.

Low Efficiency of Homology-Independent Targeted Integration for CRISPR/Cas9 Correction in the Vicinity of the SLC26A4 c.919-2A>G Variant

Recessive variants of SLC26A4 are a common cause of hereditary hearing impairment and are responsible for non-syndromic enlarged vestibular aqueducts and Pendred syndrome. Patients with bi-allelic SLC26A4 variants often suffer from fluctuating hearing loss and recurrent vertigo, ultimately leading to severe to profound hearing impairment. However, there are currently no satisfactory prevention or treatment options for this condition. The CRISPR/Cas9 genome-editing technique is a well-known tool for correcting point mutations or manipulating genes and shows potential therapeutic applications for hereditary disorders. In this study, we used the homology-independent targeted integration (HITI) strategy to correct the SLC26A4 c.919-2A>G variant, the most common SLC26A4 variant in the Han Chinese population. Next-generation sequencing was performed to evaluate the editing efficiency of the HITI strategy. The results showed that only 0.15% of the reads successfully exhibited HITI integration, indicating that the c.919-2 region may not be a suitable region for HITI selection. This suggests that other site selection or insertion strategies may be needed to improve the efficiency of correcting the SLC26A4 c.919-2A>G variant. This experience may serve as a valuable reference for other researchers considering CRISPR target design in this region.

Landscape of essential growth and fluconazole-resistance genes in the human fungal pathogen Cryptococcus neoformans

Fungi can cause devastating invasive infections, typically in immunocompromised patients. Treatment is complicated both by the evolutionary similarity between humans and fungi and by the frequent emergence of drug resistance. Studies in fungal pathogens have long been slowed by a lack of high-throughput tools and community resources that are common in model organisms. Here we demonstrate a high-throughput transposon mutagenesis and sequencing (TN-seq) system in Cryptococcus neoformans that enables genome-wide determination of gene essentiality. We employed a random forest machine learning approach to classify the C. neoformans genome as essential or nonessential, predicting 1,465 essential genes, including 302 that lack human orthologs. These genes are ideal targets for new antifungal drug development. TN-seq also enables genome-wide measurement of the fitness contribution of genes to phenotypes of interest. As proof of principle, we demonstrate the genome-wide contribution of genes to growth in fluconazole, a clinically used antifungal. We show a novel role for the well-studied RIM101 pathway in fluconazole susceptibility. We also show that insertions of transposons into the 5' upstream region can drive sensitization of essential genes, enabling screenlike assays of both essential and nonessential components of the genome. Using this approach, we demonstrate a role for mitochondrial function in fluconazole sensitivity, such that tuning down many essential mitochondrial genes via 5' insertions can drive resistance to fluconazole. Our assay system will be valuable in future studies of C. neoformans, particularly in examining the consequences of genotypic diversity.

3D genome organization shapes DNA damage susceptibility to platinum-based drugs

Platinum (Pt) drugs are widely utilized in cancer chemotherapy. Although cytotoxic and resistance mechanisms of Pt drugs have been thoroughly explored, it remains elusive what factors affect the receptiveness of DNA to drug-induced damage in nuclei. Here, we demonstrate that nuclear locations of chromatin play a key role in Pt drug-induced DNA damage susceptibility in vivo. By integrating data from damage-seq experiments with 3D genome structure information, we show that nuclear locations of chromatin relative to specific nuclear bodies and compartments explain patterns of cisplatin DNA damage susceptibility. This aligns with observations of cisplatin enrichment in biomolecular condensates at certain nuclear bodies. Finally, 3D structure mapping of DNA damage reveals characteristic differences between nuclear distributions of oxaliplatin-induced DNA damage in drug resistant versus sensitive cells. DNA damage increases in gene-poor chromatin at the nuclear periphery, while it decreases in gene-rich regions located at nuclear speckles. This suggests a strategic redistribution of Pt drug-induced damage in nuclei during chemoresistance development.

HPV-associated squamous cell carcinoma and adenocarcinoma in distinct cervical sites: a case report

BACKGROUND

The synchronous occurrence of adenocarcinoma and squamous cell carcinoma in distinct cervical regions is exceptionally rare. This report highlights a case of HPV-associated adenocarcinoma and squamous cell carcinoma at distinct sites in a patient with primary stage IA1 cervical cancer.

CASE PRESENTATION

A 54-year-old female tested HPV type 18 positive in a routine physical exam. Cervical Liquid - based Cytology Test (LCT) showed Atypical Squamous Cells of Undetermined Significance (ASCUS). Colposcopy-directed biopsies revealed moderately differentiated squamous cell carcinoma at multiple sites (3, 6, 9, 12 o'clock positions and the ECC), with a clinical diagnosis of stage IA1. Preoperative abdominal MRI (including contrast enhancement) showed no lymph node enlargement, and urinary CT urography was normal. Squamous cell carcinoma antigen levels were within the normal range.

Evaluation of the role of whiB6 and kdpDE in the dominant multidrug-resistant clone Mycobacterium tuberculosis B0/W148

Multidrug-resistant (MDR) strains of Mycobacterium tuberculosis represent an obstacle to eradicating tuberculosis (TB) due to the low treatment success rate of MDR TB. Among them, the MDR B0/W148 clone has recently evolved from the M. tuberculosis Beijing lineage 2 and is widely disseminated in Russia and Europe. To get more insights into the genetic factors underlying the evolutionary success of the MDR M. tuberculosis B0/W148 clone in addition to environmental and patient-related features, we focused on two mutations specific to this clone that are found in the transcriptional regulators WhiB6 and KdpDE and investigated in a H37Rv strain background the transcriptional profile associated with these mutations and their impact on the in vitro and in vivo growth characteristics. Through the construction and use of H37Rv∆whiB6, H37Rv∆kdpDE, and complemented strains, neither mutation impaired the in vitro growth of M. tuberculosis in standard mycobacterial growth media. The mutation T51P in whiB6 prevented the upregulation of 9 genes in the esx-1 core region and 44 genes elsewhere in the genome, while the deletion of two nucleotides in kdpD leads to a fusion protein of KdpD with KdpE that inhibits the transcriptional activity of KdpE. Neither mutation led to hypervirulence in a mouse infection model. These results point to the role of other MDR B0/W148 specific mutations in the wide geographic diffusion of this clone and/or put in question a hypothesized hypervirulence as a driving factor for this large dissemination.

IMPORTANCE

Human tuberculosis (TB), caused by the bacterium Mycobacterium tuberculosis, remains a global public health issue estimated to have been responsible for 1.25 million deaths in 2023. Multidrug-resistant (MDR) strains of M. tuberculosis, resistant to rifampicin and isoniazid, lead to lower treatment success. Among them, the MDR B0/W148 clone has widely disseminated in Russia and Europe. To get more insights into the genetic factors underlying the evolutionary success of this clone, we investigated two strain-specific mutations found in the transcriptional regulators WhiB6 and KdpDE. By constructing and analyzing laboratory M. tuberculosis strains carrying these specific mutations, we found numerous changes in their transcriptional profiles, whereas we observed only a little impact of these mutations on the virulence of M. tuberculosis in a mouse infection model. Our study provides new insights into the transcriptional landscape of the selected MDR strains, although no direct connection to virulence could be established.

DNMT3A-dependent DNA methylation shapes the endothelial enhancer landscape

DNA methylation plays a fundamental role in regulating transcription during development and differentiation. However, its functional role in the regulation of endothelial cell (EC) transcription during state transition, meaning the switch from an angiogenic to a quiescent cell state, has not been systematically studied. Here, we report the longitudinal changes of the DNA methylome over the lifetime of the murine pulmonary vasculature. We identified prominent alterations in hyper- and hypomethylation during the transition from angiogenic to quiescent ECs. Once a quiescent state was established, DNA methylation marks remained stable throughout EC aging. These longitudinal differentially methylated regions correlated with endothelial gene expression and highlighted the recruitment of de novo DNA methyltransferase 3a (DNMT3A), evidenced by its motif enrichment at transcriptional start sites of genes with methylation-dependent expression patterns. Loss-of-function studies in mice revealed that the absence of DNMT3A-dependent DNA methylation led to the loss of active enhancers, resulting in mild transcriptional changes, likely due to loss of active enhancer integrity. These results underline the importance of DNA methylation as a key epigenetic mechanism of EC function during state transition. Furthermore, we show that DNMT3A-dependent DNA methylation appears to be involved in establishing the histone landscape required for accurate transcriptome regulation.

Nuclear m6A modification regulates satellite transcription and chromosome segregation

The precise location and functions of N6-methyladenosine (m6A) modification on mammalian nuclear noncoding RNA remain largely unknown. Here we developed nuclear-m6A-label-seq to directly map human and mouse cell nuclear RNA m6A methylome at single-base resolution. Specifically, m6A modifications have been identified on abundant human γ satellite DNA II (GSATII) RNA transcripts, a type of repeat RNA, transcribed from SST1-TAR1-GSATII satellite arrays in the pericentromeric region of chromosome 9. GSATII RNA m6A positively regulates the transcription of GSATII-located satellite arrays as well as trans-associated peri/centromeric satellites, typically chromosome 3 centromeric higher-order repeat α satellite. Dysregulation of this circuit renders a phenotype of abnormal chromosome segregation. Mechanistic study reveals that YTHDC1 reads GSATII RNA m6A marks and recruits bromodomain protein 4 (BRD4) to promote transcriptions of the associated satellites via an m6A-YTHDC1-BRD4-H3K27ac axis. These results uncover a mechanism governing the transcription of cis- and trans-associated pericentromeric and centromeric satellites via cross-talk between epitranscriptomic and epigenomic marks.

Phylogenetic relationships and the identification of allopolyploidy in circumpolar Silene sect. Physolychnis

PREMISE

Species complexes are groups of closely related species with ambiguous delimitation, often composed of recently diverged lineages. Polyploidization and uniparental reproduction (i.e., selfing and apomixis) can play important roles in the origin of species complexes. These complexes pose challenges for species-based scientific questions, such as the estimation of species richness or conservation prioritization.

METHODS

We determined the potential of resolving taxonomically complex groups using target enrichment in the circumpolar Silene uralensis complex (Caryophyllaceae). We proposed a metric using genetic distances between phased alleles to distinguish diploids from allopolyploids.

RESULTS

Our results identified geographic structure of populations, with the northern American and Greenlandic samples having a common ancestor. We found little phylogenetic support for the most recent taxonomic treatment of the Silene uralensis complex.

CONCLUSIONS

The study highlights the use of target enrichment in testing taxonomic hypotheses in diploids and the challenges of studying recently diverged lineages.

Defining the networks that connect RNase III and RNase J-mediated regulation of primary and specialized metabolism in Streptomyces venezuelae

RNA metabolism involves coordinating RNA synthesis with RNA processing and degradation. Ribonucleases play fundamental roles within the cell, contributing to the cleavage, modification, and degradation of RNA molecules, with these actions ensuring appropriate gene regulation and cellular homeostasis. Here, we employed RNA sequencing to explore the impact of RNase III and RNase J on the transcriptome of Streptomyces venezuelae. Differential expression analysis comparing wild-type and RNase mutant strains at distinct developmental stages revealed significant changes in transcript abundance, particularly in pathways related to multicellular development, nutrient acquisition, and specialized metabolism. Both RNase mutants exhibited dysregulation of the BldD regulon, including altered expression of many cyclic-di-GMP-associated enzymes. We also observed precocious chloramphenicol production in these RNase mutants and found that in the RNase III mutant, this was associated with PhoP-mediated regulation. We further found that RNase III directly targeted members of the PhoP regulon, suggesting a link between RNA metabolism and a regulator that bridges primary and specialized metabolism. We connected RNase J function with translation through the observation that RNase J directly targets multiple ribosomal protein transcripts for degradation. These findings establish distinct but complementary roles for RNase III and RNase J in coordinating the gene expression dynamics critical for S. venezuelae development and specialized metabolism.

IMPORTANCE

RNA processing and metabolism are mediated by ribonucleases and are fundamental processes in all cells. In the morphologically complex and metabolically sophisticated Streptomyces bacteria, RNase III and RNase J influence both development and metabolism through poorly understood mechanisms. Here, we show that both ribonucleases are required for the proper expression of the BldD developmental pathway and contribute to the control of chloramphenicol production, with an interesting connection to phosphate regulation for RNase III. Additionally, we show that both RNases have the potential to impact translation through distinct mechanisms and can function cooperatively in degrading specific transcripts. This study advances our understanding of RNases in Streptomyces biology by providing insight into distinct contributions made by these enzymes and the intriguing interplay between them.

The TetR-like regulator Sco4385 and Crp-like regulator Sco3571 modulate heterologous production of antibiotics in Streptomyces coelicolor M512

Heterologous expression in well-studied model strains is a routinely applied method to investigate biosynthetic pathways. Here, we pursue a comparative approach of large-scale DNA-affinity-capturing assays (DACAs) coupled with semi-quantitative mass spectrometry (MS) to identify putative regulatory proteins from Streptomyces coelicolor M512, which bind to the heterologously expressed biosynthetic gene clusters (BGCs) of the liponucleoside antibiotics caprazamycin and liposidomycin. Both gene clusters share an almost identical genetic arrangement, including the location of promoter regions, as detected by RNA sequencing. A total of 2,214 proteins were trapped at the predicted promoter regions, with only three binding to corresponding promoters in both gene clusters. Among these, the overexpression of a yet uncharacterized TetR-family regulator (TFR), Sco4385, increased caprazamycin but not liposidomycin production. Protein-DNA interaction experiments using biolayer interferometry confirmed the binding of Sco4385 to Pcpz10 and PlpmH at different locations within both promoter regions, which might explain its functional variance. Sequence alignment allowed the determination of a consensus sequence present in both promoter regions, to which Sco4385 was experimentally shown to bind. Furthermore, we found that the overexpression of the Crp regulator, Sco3571, leads to a threefold increase in caprazamycin and liposidomycin production yields, possibly due to an increased expression of a precursor pathway.IMPORTANCEStreptomycetes are well-studied model organisms for the biosynthesis of pharmaceutically, industrially, and biotechnologically valuable metabolites. Their naturally broad repertoire of natural products can be further exploited by heterologous expression of biosynthetic gene clusters (BGCs) in non-native host strains. This approach forces the host to adapt to a new regulatory and metabolic environment. In our study, we demonstrate that a host regulator not only interacts with newly incorporated gene clusters but also regulates precursor supply for the produced compounds. We present a comprehensive study of regulatory proteins that interact with two genetically similar gene clusters for the biosynthesis of liponucleoside antibiotics. Thereby, we identified regulators of the heterologous host that influence the production of the corresponding antibiotic. Surprisingly, the regulatory interaction is highly specific for each biosynthetic gene cluster, even though they encode largely structurally similar metabolites.