Versatile genome assembly evaluation with QUAST-LG

Draft genomes of 10 Vibrio cholerae isolates collected in Sudan in 2019

This report presents the first genomes from positive cases of cholera in Sudan. Genomic analysis of 10 Vibrio cholerae isolates, profiled as serogroup O1, reveals evidence of antimicrobial resistance genes and a 139-kb IncC plasmid with 99.74% identity to the multidrug-resistant plasmid pCNRVC190243 previously reported in Yemen and Lebanon.

An INDEL genomic approach to explore population diversity of phytoplankton

BACKGROUND

Although metabarcoding and metagenomic approaches have generated large datasets on worldwide phytoplankton species diversity, the intraspecific genetic diversity underlying the genetic adaptation of marine phytoplankton to specific environmental niches remains largely unexplored. This is mainly due to the lack of biological resources and tools for monitoring the dynamics of this diversity in space and time.

RESULTS

To gain insight into population diversity, a novel method based on INDEL markers was developed on Bathycoccus prasinos (Mamiellophyceae), an abundant and cosmopolitan species with strong seasonal patterns. Long read sequencing was first used to characterize structural variants among the genomes of six B. prasinos strains sampled from geographically distinct regions in the world ocean. Markers derived from identified insertions/deletions were validated by PCR then used to genotype 55 B. prasinos strains isolated during the winter bloom 2018-2019 in the bay of Banyuls-sur-Mer (Mediterranean Sea, France). This led to their classification into eight multi-loci genotypes and the sequencing of strains representative of local diversity, further improving the available genetic diversity of B. prasinos. Finally, selected markers were directly tracked on environmental DNA sampled during 3 successive blooms from 2018 to 2021, showcasing a fast and cost-effective approach to follow local population dynamics.

CONCLUSIONS

This method, which involves (i) pre-identifying the genetic diversity of B. prasinos in environmental samples by PCR, (ii) isolating cells from selected environmental samples and (iii) identifying genotypes representative of B. prasinos diversity for sequencing, can be used to comprehensively describe the diversity and population dynamics not only in B. prasinos but also potentially in other generalist phytoplankton species.

Longitudinal genomics reveals carbapenem-resistant Acinetobacter baumannii population changes with emergence of highly resistant ST164 clone

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a persistent nosocomial pathogen that poses a significant threat to global public health, particularly in intensive care units (ICUs). Here we report a three-month longitudinal genomic surveillance study conducted in a Hangzhou ICU in 2021. This followed a three-month study conducted in the same ICU in 2019, and infection prevention and control (IPC) interventions targeting patients, staff and the ICU environment. Most A. baumannii isolated in this ICU in 2021 were CRAB (80.9%; 419/518) with higher-level resistance to carbapenems. This was accompanied by the proportion of global clone 2 (GC2) isolates falling from 99.5% in 2019 to 50.8% (213/419) in 2021. The phylogenetic diversity of GC2 increased, apparently driven by regular introductions of distinct clusters in association with patients. The remaining CRAB (40.2%; 206/419) were a highly clonal population of ST164. Isolates of ST164 carried blaNDM-1 and blaOXA-23 carbapenemase genes, and exhibited higher carbapenem MIC50/MIC90 values than GC2. Comparative analysis of publicly available genomes from 26 countries (five continents) revealed that ST164 has evolved towards carbapenem resistance on multiple independent occasions. Its success in this ICU and global capacity for acquiring resistance determinants indicate that ST164 CRAB is an emerging high-risk lineage of global concern.

Lack of wastewater treatment in a small town drives the spread of ESBL-producing Escherichia coli in irrigation waters

Antibiotic resistance (ABR) is a critical and growing global challenge, especially in low- and middle-income countries. Ecuador has made great progress in connecting households to piped water supplies; however, the collection and treatment of domestic wastewater has lagged. This infrastructural gap may be accelerating the spread of ABR into surface waters used downstream for irrigation. We studied the contributions of a small town in Ecuador to the prevalence of extended-spectrum β-lactamase-producing Escherichia coli in a glacial stream used for irrigating crops. The study analyzed water samples upstream (n = 60) and downstream (n = 60) of the town of Píntag as well as 30 lettuce samples irrigated by surface waters downstream of the town. A subset of third generation cephalosporin resistant E. coli (3GCR-EC) isolates (n = 58) were sequenced to characterize antibiotic resistance genes and pathogenic lineages. Our results showed that there was nearly a three-log increase in mean E. coli colony forming units in the downstream samples versus upstream. At the upstream sites above the town of Píntag, 6.7% of water samples were positive for 3GCR-EC compared to 100% of samples collected at the downstream sites. Additionally, 70.1% of sequenced 3GCR-EC isolates collected at downstream sites carried blaCTX-M genes and 3.4% belonged to pandemic lineages ST131 and ST10. As countries develop household piped water infrastructure, attention should focus on how the lack of domestic wastewater collection and treatment may accelerate the spread of ABR in waterways and the food system.

Comparative genomics of zoonotic pathogen Clostridioides difficile of animal origin to understand its diversity

Clostridioides difficile, a zoonotic pathogen causing enteric diseases in different animals and humans. A comprehensive study on the presence of toxin genes and antimicrobial resistance genes based on genome data of C. difficile in animals is scanty. In the present study, a total of 15 C. difficile isolates were recovered from dogs and isolates with toxin genes (D1, CD15 and CD26) along with two other non-toxigenic strains (CD28, CD32) were used for whole genome sequencing and comparative genomics. Sequence type-based clustering was noted in the whole genome phylogeny with 4 known multi-locus sequence typing (MLST) clades namely I, II, IV, and V and a cryptic clade. ST11 and ST54 were reported for the 2nd time worldwide in dogs. Out of 109 genomes used in the study, 29 genomes were predicted with all four toxin genes (toxA, toxB, cdtA, cdtB) while 22 did not have any of the toxin genes. ST11 of MLST clade V had the maximum number of 46 genomes predicted with at least one toxin gene. Among the genomes sequenced in this study, CD26 had a maximum of 5 AMR genes (aac(6')-aph(2″), ant(6)-Ia, catP, erm(B)_18, and tet(M)_11) and CD15 was predicted with 2 AMR genes (aac(6')-aph(2″), erm(B)_18). Tetracycline resistance genes were predicted most in the ST11 genome. Of the 22 non-toxigenic strains, 9 genomes (ST48 = 5, ST3 = 2, ST109 = 1, ST15 = 1) were predicted with a minimum of one AMR gene. Pangenome analysis indicated that the Bpan value is 0.12 showing that C. difficile has an open pangenome structure. This indicates that the organism can evolve by the addition of new genes. This study reports the circulation of clinically important ST11 and multidrug-resistant non-toxigenic strains among animals.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04102-7.

Chromosome-contiguous genome for the Haecon-5 strain of Haemonchus contortus reveals marked genetic variability and enables the discovery of essential gene candidates

Millions of livestock animals worldwide are infected with the haematophagous barber's pole worm, Haemonchus contortus, the aetiological agent of haemonchosis. Despite the major significance of this parasite worldwide and its widespread resistance to current treatments, the lack of a high-quality genome for the well-defined strain of this parasite from Australia, called Haecon-5, has constrained research in a number of areas including host-parasite interactions, drug discovery and population genetics. To enable research in these areas, we report here a chromosome-contiguous genome (∼280 Mb) for Haecon-5 with high-quality models for 19,234 protein-coding genes. Comparative genomic analyses show significant genomic similarity (synteny) with a UK strain of H. contortus, called MHco3(ISE).N1 (abbreviated as "ISE"), but we also discover marked differences in genomic structure/gene arrangements, distribution of nucleotide variability (single nucleotide polymorphisms (SNPs) and indels) and orthology between Haecon-5 and ISE. We used the genome and extensive transcriptomic resources for Haecon-5 to predict a subset of essential single-copy genes employing a "cross-species" machine learning (ML) approach using a range of features from nucleotide/protein sequences, protein orthology, subcellular localisation, single-cell RNA-seq and/or histone methylation data available for the model organisms Caenorhabditis elegans and Drosophila melanogaster. From a set of 1,464 conserved single copy genes, transcribed in key life-cycle stages of H. contortus, we identified 232 genes whose homologs have critical functions in C. elegans and/or D. melanogaster, and prioritised 10 of them for further characterisation; nine of the 10 genes likely play roles in neurophysiological processes, germline, hypodermis and/or respiration, and one is an unknown (orphan) gene for which no detailed functional information exists. Future studies of these genes/gene products are warranted to elucidate their roles in parasite biology, host-parasite interplay and/or disease. Clearly, the present Haecon-5 reference genome and associated resources now underpin a broad range of fundamental investigations of H. contortus and could assist in accelerating the discovery of novel intervention targets and drug candidates to combat haemonchosis.

Chromosome Structural Rearrangements in Invasive Haplodiploid Ambrosia Beetles Revealed by the Genomes of Euwallacea fornicatus (Eichhoff) and Euwallacea similis (Ferrari) (Coleoptera, Curculionidae, Scolytinae)

Bark and ambrosia beetles are among the most ecologically and economically damaging introduced plant pests worldwide. Life history traits including polyphagy, haplodiploidy, inbreeding polygyny, and symbiosis with fungi contribute to their dispersal and impact. Species vary in their interactions with host trees, with many attacking stressed or recently dead trees, such as the globally distributed Euwallacea similis (Ferrari). Other species, like the Polyphagous Shot Hole Borer Euwallacea fornicatus (Eichhoff), can attack over 680 host plants and is causing considerable economic damage in several countries. Despite their notoriety, publicly accessible genomic resources for Euwallacea Hopkins species are scarce, hampering our understanding of their invasive capabilities as well as modern control measures, surveillance, and management. Using a combination of long and short read sequencing platforms, we assembled and annotated high quality (BUSCO > 98% complete) pseudo-chromosome-level genomes for these species. Comparative macrosynteny analysis identified an increased number of pseudo-chromosome scaffolds in the haplodiploid inbreeding species of Euwallacea compared to diploid outbred species, due to fission events. This suggests that life history traits can impact chromosome structure. Further, the genome of E. fornicatus had a higher relative proportion of repetitive elements, up to 17% more, than E. similis. Metagenomic assembly pipelines identified microbiota associated with both species including Fusarium fungal symbionts and a novel Wolbachia strain. These novel genomes of haplodiploid inbreeding species will contribute to the understanding of how life history traits are related to their evolution and to the management of these invasive pests.

Validation of PCR Diagnostic Assays for Detection and Identification of All Ralstonia solanacearum Sequevars Causing Moko Disease in Banana

Moko disease in banana is a bacterial wilt caused by strains within Ralstonia solanacearum sensu stricto. The disease is endemic to Central and South America but has spread to the Philippines and peninsular Malaysia. Detecting new incursions early in Moko-free banana production regions is of utmost importance for containment and eradication, as Moko management significantly increases costs in banana production. Molecular studies have supported the classification of R. solanacearum sensu stricto into phylotypes IIA, IIB, and IIC, each comprising various sequevars based on nucleotide divergence of a partial sequence within the endoglucanase gene. Moko disease in banana is caused by strains classified as sequevars 6, 24, 41, and 53 within phylotype IIA and sequevars 3, 4, and 25 within phylotype IIB. To ensure accurate diagnostic assays are available to detect all Moko sequevars, we systematically validated previously published assays for Moko diagnostics. To be able to identify all sequevars, including the latest described sequevars, namely IIB-25, IIA-41, and IIA-53, we developed and validated two novel assays using genome-wide association studies on over 100 genomes of R. solanacearum sensu stricto. Validations using 196 bacterial isolates confirmed that a previous multiplex PCR-based assay targeting sequevars IIB-3, IIB-4, IIA-6, and IIA-24 and our two novel assays targeting sequevars IIB-25, IIA-41, and IIA-53 were specific, reproducible, and accurate for Moko diagnostics.

Unravelling the processes involved in biodegradation of chlorinated organic pollutant: From microbial community to isolated organohalide degraders

Hundreds of studies have demonstrated the bioremediation of chlorinated organic pollutants (COPs) in flooded environments. However, the role of specific functional strains in degrading COPs under complex media such as wetlands is still unclear. Here, we focused on the microbial characteristics of COP-polluted sediments, identified the bacteria responsible for degradation and conducted a genomic analysis of these bacteria. Four strains were obtained and identified as Petrimonas sulfuriphila PET, Robertmurraya sp. CYTO, Hungatella sp. CloS1 and Enterococcus avium PseS3, respectively. They were capable of degrading a typical COP, γ-hexachlorocyclohexane (γ-HCH). The residual γ-HCH concentrations were 58.8 % (PET), 45.6 % (CYTO), 60.2 % (CloS1), and 69.3 % (PseS3) of its initial value, respectively. Strain PET, CYTO and CloS1 could degrade γ-HCH to its dehalogenation product chlorobenzene. Each strain harbors genes annotated to the pathway of halogenated organic matter degradation (e.g. 2-haloacid dehalogenase) and cobalamin biosynthesis, which are involved in the degradation of COPs. Comparative genomic analysis of the four strains and other classical organohalide-respiring bacteria (e.g. Dehalococcoides mccartyi and Sulfurospirillum multivorans DSM 12446) showed that they share orthologous clusters related to the cobalamin biosynthetic process (GO:0009236). VB12 was also detected in the culture systems of the four strains, further highlighting the importance of cobalamin in COPs degradation. In the genome of the four strains, some genes were annotated to the halogenated organic matter degradation and cobalamin biosynthesis pathway within horizontal gene transfer (HGT) regions. This further indicated that microorganisms carrying these genes can adapt faster to pollution stress through HGT. Together, these findings revealed the co-evolution mechanism of functional strains and may provide novel insights into improved bioremediation strategies for COP-polluted complex media based on generalist organochlorine-degrading bacteria.

Genomic Features and Antimicrobial Activity of Phaeobacter inhibens Strains from Marine Biofilms

Members of the genus Phaeobacter are widely distributed in the marine environment and are known for their ability to produce tropodithietic acid (TDA). Studies investigating the genomic and metabolic features of Phaeobacter strains from marine biofilms are sparse. Here, we analyze the complete genomes of 18 Phaeobacter strains isolated from biofilms on subtidal stones, with the aim of determining their potential to synthesize secondary metabolites. Based on whole-genome comparison and average nucleotide identity calculation, the isolated bacteria are classified as novel strains of Phaeobacter inhibens. Further analysis reveals a total of 153 biosynthetic gene clusters, which are assigned to 32 gene cluster families with low similarity to previously published ones. Complete TDA clusters are identified in 14 of the 18 strains, while in the other 4 strains the TDA clusters are rather incomplete and scattered across different chromosome and plasmid locations. Phylogenetic analysis suggests that their presence or absence may be potentially attributed to horizontal gene transfer. High-performance liquid chromatography-mass spectrometry analysis demonstrates the production of TDA in all the examined strains. Furthermore, the Phaeobacter strains have strong antibacterial activity against the pathogenic strain Vibrio owensii ems001, which is associated with acute hepatopancreatic necrosis in South American white shrimp. Altogether, this study ameliorates our knowledge of marine biofilm-associated Phaeobacter and offers new avenues for exploiting marine antimicrobial agents.

Large-scale genomic analysis of Elizabethkingia anophelis

The recent emergence of Elizabethkingia anophelis as a human pathogen is a major concern for global public health. This organism has the potential to cause severe infections and has inherent antimicrobial resistance. The potential for widespread outbreaks and rapid global spread highlights the critical importance of understanding the biology and transmission dynamics of this infectious agent. We performed a large-scale analysis of available 540 E. anophelis, including one novel strain isolated from raw milk and sequenced in this study. Pan-genome analysis revealed an open and diverse pan-genome in this species, characterized by the presence of many accessory genes. This suggests that the species has a high level of adaptability and can thrive in a variety of environments. Phylogenetic analysis has also revealed a complex population structure, with limited source-lineage correlation. We identified diverse antimicrobial resistance factors, including core-genome and accessory ones often associated with mobile genetic elements within specific lineages. Mobilome analysis revealed a dynamic landscape primarily composed of genetic islands, integrative and conjugative elements, prophage elements, and small portion of plasmids emphasizing a complex mechanism of horizontal gene transfer. Our study underscores the adaptability of E. anophelis, characterized by a diverse range of antimicrobial resistance genes, putative virulence factors, and genes enhancing fitness. This adaptability is also supported by the organism's ability to acquire genetic material through horizontal gene transfer, primarily facilitated by mobile genetic elements such as integrative and conjugative elements (ICEs). The potential for rapid evolution of this emerging pathogen poses a significant challenge to public health efforts.

Real-time plasmid transmission detection pipeline

The spread of antimicrobial resistance among bacteria by horizontal plasmid transmissions poses a major challenge for clinical microbiology. Here, we evaluate a new real-time plasmid transmission detection pipeline implemented in the SeqSphere+ (Ridom GmbH, Münster, Germany) software. Within the pipeline, a local Mash plasmid database is created, and Mash searches with a distance threshold of 0.001 are used to trigger plasmid transmission early warning alerts (EWAs). Clonal transmissions are detected using core-genome multi-locus sequence typing allelic differences. The tools MOB-suite, NCBI AMRFinderPlus, CGE MobileElementFinder, pyGenomeViz, and MUMmer, integrated in SeqSphere+, are used to characterize plasmids and for visual pairwise plasmid comparisons, respectively. We evaluated the pipeline using published hybrid assemblies (Oxford Nanopore Technology/Illumina) of a surveillance and outbreak data set with plasmid transmissions. To emulate prospective usage, samples were imported in chronological order of sampling date. Different combinations of the user-adjustable parameters sketch size (1,000 vs 10,000) and plasmid size correction were tested, and discrepancies between resulting clusters were analyzed with Quast. When using a sketch size of 1,000 with size correction turned on, the SeqSphere+ pipeline agreed with the published data and produced the same clonal and carbapenemase-carrying plasmid clusters. EWAs were in the correct chronological order. In summary, the developed pipeline presented here is suitable for integration into clinical microbiology settings with limited bioinformatics knowledge due to its automated analyses and alert system, which are combined with the GUI-based SeqSphere+ platform. Thus, with its integrated sample database, (near) real-time plasmid transmission detection is within reach in bacterial routine-diagnostic settings when long-read sequencing is employed.

IMPORTANCE

Plasmid-mediated spread of antimicrobial resistance is a major challenge for clinical microbiology, and monitoring of potential plasmid transmissions is essential to combat further dissemination. Whole-genome sequencing is often used to surveil nosocomial transmissions but usually limited to the detection of clonal transmissions (based on chromosomal markers). Recent advances in long-read sequencing technologies enable full reconstruction of plasmids and the detection of very similar plasmids, but so far, easy-to-use bioinformatic tools for this purpose have been missing. Here, we present an evaluation of an innovative real-time plasmid transmission detection pipeline. It is integrated into the GUI-based SeqSphere+ software, which already offers core-genome multi-locus sequence typing-based pathogen outbreak detection. It requires very limited bioinformatics knowledge, and its database, automated analyses, and alert system make it well suited for prospective clinical application.

Rethinking asexuality: the enigmatic case of functional sexual genes in Lepraria (Stereocaulaceae)

BACKGROUND

The ubiquity of sex across eukaryotes, given its high costs, strongly suggests it is evolutionarily advantageous. Asexual lineages can avoid, for example, the risks and energetic costs of recombination, but suffer short-term reductions in adaptive potential and long-term damage to genome integrity. Despite these costs, lichenized fungi have frequently evolved asexual reproduction, likely because it allows the retention of symbiotic algae across generations. The lichenized fungal genus Lepraria is thought to be exclusively asexual, while its sister genus Stereocaulon completes a sexual reproductive cycle. A comparison of sister sexual and asexual clades should shed light on the evolution of asexuality in lichens in general, as well as the apparent long-term maintenance of asexuality in Lepraria, specifically.

RESULTS

In this study, we assembled and annotated representative long-read genomes from the putatively asexual Lepraria genus and its sexual sister genus Stereocaulon, and added short-read assemblies from an additional 22 individuals across both genera. Comparative genomic analyses revealed that both genera were heterothallic, with intact mating-type loci of both idiomorphs present across each genus. Additionally, we identified and assessed 29 genes involved in meiosis and mitosis and 45 genes that contribute to formation of fungal sexual reproductive structures (ascomata). All genes were present and appeared functional in nearly all Lepraria, and we failed to identify a general pattern of relaxation of selection on these genes across the Lepraria lineage. Together, these results suggest that Lepraria may be capable of sexual reproduction, including mate recognition, meiosis, and production of ascomata.

CONCLUSIONS

Despite apparent maintenance of machinery essential for fungal sex, over 200 years of careful observations by lichenologists have produced no evidence of canonical sexual reproduction in Lepraria. We suggest that Lepraria may have instead evolved a form of parasexual reproduction, perhaps by repurposing MAT and meiosis-specific genes. This may, in turn, allow these lichenized fungi to avoid long-term consequences of asexuality, while maintaining the benefit of an unbroken bond with their algal symbionts.

GTasm: a genome assembly method using graph transformers and HiFi reads

Motivation

Genome assembly aims to reconstruct the whole chromosome-scale genome sequence. Obtaining accurate and complete chromosome-scale genome sequence serve as an indispensable foundation for downstream genomics analyses. Due to the complex repeat regions contained in genome sequence, the assembly results commonly are fragmented. Long reads with high accuracy rate can greatly enhance the integrity of genome assembly results.

Results

Here we introduce GTasm, an assembly method that uses graph transformer network to find optimal assembly results based on assembly graphs. Based on assembly graph, GTasm first extracts features about vertices and edges. Then, GTasm scores the edges by graph transformer model, and adopt a heuristic algorithm to find optimal paths in the assembly graph, each path corresponding to a contig. The graph transformer model is trained using simulated HiFi reads from CHM13, and GTasm is compared with other assembly methods using real HIFI read set. Through experimental result, GTasm can produce well assembly results, and achieve good performance on NA50 and NGA50 evaluation indicators. Applying deep learning models to genome assembly can improve the continuity and accuracy of assembly results. The code is available from https://github.com/chu-xuezhe/GTasm.

Carriage and antimicrobial susceptibility of commensal Neisseria species from the human oropharynx

Commensal Neisseria (Nc) mainly occupy the oropharynx of humans and animals. These organisms do not typically cause disease; however, they can act as a reservoir for antimicrobial resistance genes that can be acquired by pathogenic Neisseria species. This study characterised the carriage and antimicrobial susceptibility profiles of Nc from the oropharynx of 50 participants. Carriage prevalence of Nc species was 86% with 66% of participants colonised with more than one isolate. Isolates were identified by MALDI-ToF and the most common species was N. subflava (61.4%). Minimum inhibitory concentrations (MICs) to penicillin, ceftriaxone, ciprofloxacin, azithromycin, tetracycline, and gentamicin were determined by agar dilution and E-test was used for cefixime. Using Ng CLSI/EUCAST guidelines, Nc resistance rates were above the WHO threshold of 5% resistance in circulating strains for changing the first line treatment empirical antimicrobial: 5% (CLSI) and 13 (EUCAST) for ceftriaxone and 29.3% for azithromycin. Whole genome sequencing of 30 Nc isolates was performed, which identified AMR genes to macrolides and tetracycline. Core gene MLST clustered Nc into three main groups. Gonococcal DNA uptake sequences were identified in two Nc clusters. This suggests that Nc have the potential AMR gene pool and transfer sequences that can result in resistance transfer to pathogenic Neisseria within the nasopharyngeal niche.

Comparative genomics of Fusarium species causing Fusarium ear rot of maize

Fusarium ear rot (FER), caused by the fungal pathogen Fusarium verticillioides, stands as one of the most economically burdensome and pervasive diseases affecting maize worldwide. Its impact on food security is particularly pronounced due to the production of fumonisins, toxic secondary metabolites that pose serious health risks, especially for livestock. FER disease severity is complex and polygenic, with few resistance (R) genes being identified for use in breeding resistant varieties. While FER is the subject of several breeding programs, only a few studies have investigated entire populations of F. verticillioides with corresponding virulence data to better understand and characterize the pathogenomics. Here, we sequenced and compared the genomes of 50 Fusarium isolates (43 F. verticillioides and 7 other Fusarium spp.) that were used to inoculate a diverse maize population. Our objectives were to elucidate the genome size and composition of F. verticillioides, explore the variable relationship between fumonisin production and visual disease severity, and shed light on the phylogenetic relationships among the isolates. Additionally, we conducted a comparative analysis of the nucleotide variants (SNPs) and the isolates' effectoromes to uncover potential genetic determinants of pathogenicity. Our findings revealed several promising leads, notably the association of certain gene groups, such as pectate lyase, with disease severity. These genes should be investigated further as putative alleles for breeding resistant maize varieties. We suggest that, beyond validation of the alleles identified in this study, researchers validate each phenotypic dataset on an individual basis, particularly if considering fumonisin concentrations and when using diverse populations. Our study underscores the importance of genomic analysis in tackling FER and offers insights that could inform the development of resilient maize cultivars. By leveraging advances in genomics and incorporating pathogen populations into breeding programs, resistance to FER can be advanced.

Metagenomic assemblies tend to break around antibiotic resistance genes

BACKGROUND

Assembly of metagenomic samples can provide essential information about the mobility potential and taxonomic origin of antibiotic resistance genes (ARGs) and inform interventions to prevent further spread of resistant bacteria. However, similar to other conserved regions, such as ribosomal RNA genes and mobile genetic elements, almost identical ARGs typically occur in multiple genomic contexts across different species, representing a considerable challenge for the assembly process. Usually, this results in many fragmented contigs of unclear origin, complicating the risk assessment of ARG detections. To systematically investigate the impact of this issue on detection, quantification and contextualization of ARGs, we evaluated the performance of different assembly approaches, including genomic-, metagenomic- and transcriptomic-specialized assemblers. We quantified recovery and accuracy rates of each tool for ARGs both from in silico spiked metagenomic samples as well as real samples sequenced using both long- and short-read sequencing technologies.

RESULTS

The results revealed that none of the investigated tools can accurately capture genomic contexts present in samples of high complexity. The transcriptomic assembler Trinity showed a better performance in terms of reconstructing longer and fewer contigs matching unique genomic contexts, which can be beneficial for deciphering the taxonomic origin of ARGs. The currently commonly used metagenomic assembly tools metaSPAdes and MEGAHIT were able to identify the ARG repertoire but failed to fully recover the diversity of genomic contexts present in a sample. On top of that, in a complex scenario MEGAHIT produced very short contigs, which can lead to considerable underestimation of the resistome in a given sample.

CONCLUSIONS

Our study shows that metaSPAdes and Trinity would be the preferable tools in terms of accuracy to recover correct genomic contexts around ARGs in metagenomic samples characterized by uneven coverages. Overall, the inability of assemblers to reconstruct long ARG-containing contigs has impacts on ARG quantification, suggesting that directly mapping reads to an ARG database should be performed as a complementary strategy to get accurate ARG abundance and diversity measures.

Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil

Circular extrachromosomal DNA (ecDNA) is a form of oncogene amplification found across cancer types and associated with poor outcome in patients. ecDNA can be structurally complex and can contain rearranged DNA sequences derived from multiple chromosome locations. As the structure of ecDNA can impact oncogene regulation and may indicate mechanisms of its formation, disentangling it at high resolution from sequencing data is essential. Even though methods have been developed to identify and reconstruct ecDNA in cancer genome sequencing, it remains challenging to resolve complex ecDNA structures, in particular amplicons with shared genomic footprints. We here introduce Decoil, a computational method that combines a breakpoint-graph approach with LASSO regression to reconstruct complex ecDNA and deconvolve co-occurring ecDNA elements with overlapping genomic footprints from long-read nanopore sequencing. Decoil outperforms de novo assembly and alignment-based methods in simulated long-read sequencing data for both simple and complex ecDNAs. Applying Decoil on whole-genome sequencing data uncovered different ecDNA topologies and explored ecDNA structure heterogeneity in neuroblastoma tumors and cell lines, indicating that this method may improve ecDNA structural analyses in cancer.

Absence of the dolichol synthesis gene DHRSX leads to N-glycosylation defects in Lec5 and Lec9 Chinese hamster ovary cells

Glycosylation-deficient Chinese hamster ovary cell lines have been instrumental in the discovery of N-glycosylation machinery. Yet, the molecular causes of the glycosylation defects in the Lec5 and Lec9 mutants have been elusive, even though for both cell lines a defect in dolichol formation from polyprenol was previously established. We recently found that dolichol synthesis from polyprenol occurs in three steps consisting of the conversion of polyprenol to polyprenal by DHRSX, the reduction of polyprenal to dolichal by SRD5A3, and the reduction of dolichal to dolichol, again by DHRSX. This led us to investigate defective dolichol synthesis in Lec5 and Lec9 cells. Both cell lines showed increased levels of polyprenol and its derivatives, concomitant with decreased levels of dolichol and derivatives, but no change in polyprenal levels, suggesting DHRSX deficiency. Accordingly, N-glycan synthesis and changes in polyisoprenoid levels were corrected by complementation with human DHRSX but not with SRD5A3. Furthermore, the typical polyprenol dehydrogenase and dolichal reductase activities of DHRSX were absent in membrane preparations derived from Lec5 and Lec9 cells, while the reduction of polyprenal to dolichal, catalyzed by SRD5A3, was unaffected. Long-read whole genome sequencing of Lec5 and Lec9 cells did not reveal mutations in the ORF of SRD5A3, but the genomic region containing DHRSX was absent. Lastly, we established the sequence of Chinese hamster DHRSX and validated that this protein has similar kinetic properties to the human enzyme. Our work therefore identifies the basis of the dolichol synthesis defect in Chinese hamster ovary Lec5 and Lec9 cells.

Genomic sequences and annotations of two Pseudomonas species isolated from marine and terrestrial habitats

Here, we present the complete genome sequences and annotations of two species of the Pseudomonas genus isolated from marine and terrestrial environments. Both genomes and their annotations are available on BacBrowse (https://BacBrowse.univ-nantes.fr). This study will contribute to a better understanding of the diversity present within the Pseudomonas genus.

Complete genome sequence of Deinococcus sonorensis type strain KR-87: a rare biofilm-producing representative of the genus Deinococcus

Here, we present a complete genome of Deinococcus sonorensis KR-87T, a biofilm-producing mesophile from the Arizonan Sonoran Desert. The sequence, assembled using Oxford Nanopore Technologies' long-read sequencing platform, predicts a genome size of 4.78 Mbp, with 6 replicons, 4,361 protein-coding genes, and a G+C content of 69.0%.

Draft genome of Thermoanaerobacter thermohydrosulfuricus strain AK152, a novel thermophilic and anaerobic bacterium isolated from a hot spring in Iceland

We present the draft genome of the bacterium Thermoanaerobacter thermohydrosulfuricus strain AK152, a thermophilic, endospore-spore-forming, anaerobe isolated from a hot spring in Grensdalur, in Southwestern Iceland. This assembled genome will lay the foundation for identifying the carboxylic and amino acid fermentation pathways, suggesting biotechnological applications for this strain.

Draft genome sequence of a spa non-typeable Staphylococcus aureus USA300 isolate causing complicated bacteremia

Spa-typing is a major genetic tool used to distinguish between Staphylococcus aureus strains. Interestingly, although rare, ~1%-2 of isolates are considered Spa-non-typeable . Herein, we present the draft genome sequence of just such a strain, S. aureus TGH1097, a USA300 isolate from a complex bacteremia infection.

Genome report: First whole genome sequence of Triatoma sanguisuga (Le Conte, 1855), vector of Chagas disease

Triatoma sanguisuga is the most widespread triatomine bug species in the United States (US). The species vectors the human parasite Trypanosoma cruzi, which causes Chagas disease. Vector-borne Chagas disease is rarely diagnosed in the US, but T. sanguisuga has been implicated in a handful of cases. Despite its public health importance, little is known about the genomics or population genetics of T. sanguisuga. Here, we used long-read sequencing to assemble the first whole genome sequence for T. sanguisuga using DNA extracted from one adult specimen from Delaware. The final size of the genome was 1.162 Gbp with 77.7x coverage. The assembly consisted of 183 contigs with an N50 size of 94.97 Kb. The Benchmarking Universal Single-Copy Ortholog (BUSCO) complete score was 99.1%, suggesting a very complete assembly. Genome-wide GC level was 33.56%, and DNA methylation was 18.84%. The genome consists of 61.4% repetitive DNA and 17,799 predicted coding genes. The assembled T. sanguisuga genome was slightly larger than that of Triatominae species Triatoma infestans and Rhodnius prolixus (949 Mbp with 90.4% BUSCO score and 706 Mbp with 96.5% BUSCO score, respectively). The T. sanguisuga genome is the first North American triatomine species genome to be sequenced, and it is the most complete genome yet for any Triatominae species. The T. sanguisuga genome will allow for deeper investigations into epidemiologically relevant aspects of this important vector species, including blood feeding, host seeking, and parasite competence, thus providing potential vector-borne disease management targets and strengthening public health preparedness.

A hybrid genome assembly of the endangered aye-aye (Daubentonia madagascariensis)

The aye-aye (Daubentonia madagascariensis) is the only extant member of the Daubentoniidae primate family. Although several reference genomes exist for this endangered strepsirrhine primate, the predominant usage of short-read sequencing has resulted in limited assembly contiguity and completeness, and no protein-coding gene annotations have yet been released. Here, we present a novel, fully annotated, chromosome-level hybrid de novo assembly for the species based on a combination of Oxford Nanopore Technologies long reads and Illumina short reads and scaffolded using genome-wide chromatin interaction data-a community resource that will improve future conservation efforts as well as primate comparative analyses.

HyLight: Strain aware assembly of low coverage metagenomes

Different strains of identical species can vary substantially in terms of their spectrum of biomedically relevant phenotypes. Reconstructing the genomes of microbial communities at the level of their strains poses significant challenges, because sequencing errors can obscure strain-specific variants. Next-generation sequencing (NGS) reads are too short to resolve complex genomic regions. Third-generation sequencing (TGS) reads, although longer, are prone to higher error rates or substantially more expensive. Limiting TGS coverage to reduce costs compromises the accuracy of the assemblies. This explains why prior approaches agree on losses in strain awareness, accuracy, tendentially excessive costs, or combinations thereof. We introduce HyLight, a metagenome assembly approach that addresses these challenges by implementing the complementary strengths of TGS and NGS data. HyLight employs strain-resolved overlap graphs (OG) to accurately reconstruct individual strains within microbial communities. Our experiments demonstrate that HyLight produces strain-aware and contiguous assemblies at minimal error content, while significantly reducing costs because utilizing low-coverage TGS data. HyLight achieves an average improvement of 19.05% in preserving strain identity and demonstrates near-complete strain awareness across diverse datasets. In summary, HyLight offers considerable advances in metagenome assembly, insofar as it delivers significantly enhanced strain awareness, contiguity, and accuracy without the typical compromises observed in existing approaches.

Chromosome-level genome assembly of the sacoglossan sea slug Elysia timida (Risso, 1818)

BACKGROUND

Sequencing and annotating genomes of non-model organisms helps to understand genome architecture, the genetic processes underlying species traits, and how these genes have evolved in closely-related taxa, among many other biological processes. However, many metazoan groups, such as the extremely diverse molluscs, are still underrepresented in the number of sequenced and annotated genomes. Although sequencing techniques have recently improved in quality and quantity, molluscs are still neglected due to difficulties in applying standardized protocols for obtaining genomic data.

RESULTS

In this study, we present the chromosome-level genome assembly and annotation of the sacoglossan sea slug species Elysia timida, known for its ability to store the chloroplasts of its food algae. In particular, by optimizing the long-read and chromosome conformation capture library preparations, the genome assembly was performed using PacBio HiFi and Arima HiC data. The scaffold and contig N50s, at 41.8 Mb and 1.92 Mb, respectively, are approximately 30-fold and fourfold higher compared to other published sacoglossan genome assemblies. Structural annotation resulted in 19,904 protein-coding genes, which are more contiguous and complete compared to publicly available annotations of Sacoglossa with respect to metazoan BUSCOs. We found no evidence for horizontal gene transfer (HGT), i.e. no photosynthetic genes encoded in the sacoglossan nucleus genome. However, we detected genes encoding polyketide synthases in E. timida, indicating that polypropionates are produced. HPLC-MS/MS analysis confirmed the presence of a large number of polypropionates, including known and yet uncharacterised compounds.

CONCLUSIONS

We can show that our methodological approach helps to obtain a high-quality genome assembly even for a "difficult-to-sequence" organism, which may facilitate genome sequencing in molluscs. This will enable a better understanding of complex biological processes in molluscs, such as functional kleptoplasty in Sacoglossa, by significantly improving the quality of genome assemblies and annotations.

Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew

Plant pathogens adapt at speeds that challenge contemporary disease management strategies like the deployment of disease resistance genes. The strong evolutionary pressure to adapt, shapes pathogens' genomes, and comparative genomics has been instrumental in characterizing this process. With the aim to capture genomic variation at high resolution and study the processes contributing to adaptation, we here leverage an innovative, multi-genome method to construct and annotate the first pangenome graph of an oomycete plant pathogen. We expand on this approach by analysing the graph and creating synteny based single-copy orthogroups for all genes. We generated telomere-to-telomere genome assemblies of six genetically diverse isolates of the oomycete pathogen Peronospora effusa, the economically most important disease in cultivated spinach worldwide. The pangenome graph demonstrates that P. effusa genomes are highly conserved, both in chromosomal structure and gene content, and revealed the continued activity of transposable elements which are directly responsible for 80% of the observed variation between the isolates. While most genes are generally conserved, virulence related genes are highly variable between the isolates. Most of the variation is found in large gene clusters resulting from extensive copy-number expansion. Pangenome graph-based discovery can thus be effectively used to capture genomic variation at exceptional resolution, thereby providing a framework to study the biology and evolution of plant pathogens.

Specific amino acid changes correlate with pathogenic flavobacteria

Flavobacterium is a genus of microorganisms living in a variety of hosts and habitats across the globe. Some species are found in fish organs, and only a few, such as Flavobacterium psychrophilum and Flavobacterium columnare, cause severe disease and losses in fish farms. The evolution of flavobacteria that are pathogenic to fish is unknown, and the protein changes accountable for the selection of their colonization to fish have yet to be determined. A phylogenetic tree was constructed with the complete genomic sequences of 208 species of the Flavobacterium genus using 861 softcore genes. This phylogenetic analysis revealed clade CII comprising nine species, including five pathogenic species, and containing the most species that colonize fish. Thirteen specific amino acid changes were found to be conserved across 11 proteins within the CII clade compared with other clades, and these proteins were enriched in functions related to replication, recombination, and repair. Several of these proteins are known to be involved in pathogenicity and fitness adaptation in other bacteria. Some of the observed amino acid changes can be explained by preferential selection for certain codons and tRNA frequency. These results could help explain how species belonging to the CII clade adapt to fish environments.

De Novo Assembly and Annotation of the Siganus fuscescens (Houttuyn, 1782) Genome: Marking a Pioneering Advance for the Siganidae Family

This study presents the first draft genome of Siganus fuscescens, and thereby establishes the first whole-genome sequence for a species in the Siganidae family. Leveraging both long and short read sequencing technologies, i.e., Oxford Nanopore and Illumina sequencing, we successfully assembled a mitogenome spanning 16.494 Kb and a first haploid genome encompassing 498 Mb. The assembled genome accounted for a 99.6% of the estimated genome size and was organized into 164 contigs with an N50 of 7.2 Mb. This genome assembly showed a GC content of 42.9% and a high Benchmarking Universal Single-Copy Orthologue (BUSCO) completeness score of 99.5% using actinopterygii_odb10 lineage, thereby meeting stringent quality standards. In addition to its structural aspects, our study also examined the functional genomics of this species, including the intricate capacity to biosynthesize long-chain polyunsaturated fatty acids (LC-PUFAs) and secrete venom. Notably, our analyses revealed various repeats elements, which collectively constituted 17.43% of the genome. Moreover, annotation of 28,351 genes uncovered both shared genetic signatures and those that are unique to S. fuscescens. Our assembled genome also displayed a moderate prevalence of gene duplication compared to other fish species, which suggests that this species has a distinctive evolutionary trajectory and potentially unique functional constraints. Taken altogether, this genomic resource establishes a robust foundation for future research on the biology, evolution, and the aquaculture potential of S. fuscescens.

Parallel loss of sexual reproduction in field populations of a brown alga sheds light on the mechanisms underlying the emergence of asexuality

Sexual reproduction is widespread, but asexual lineages have repeatedly arisen from sexual ancestors across a wide range of eukaryotic taxa. The molecular changes underpinning the switch to asexuality remain elusive, particularly in organisms with haploid sexual systems. Here we explore independent events of loss of sex in the brown alga Scytosiphon, examine the proximate and evolutionary mechanisms involved, and test the importance of sexual conflict on gene expression changes following loss of sex. We find that asexual females ('Amazons') lose ability to produce sex pheromone and, consequently, are incapable of attracting males, whereas they gain rapid parthenogenic development from large, unfertilized eggs. These phenotypic changes are accompanied by convergent changes in gene expression. Decay of female functions, rather than relaxation of sexual antagonism, may be a dominant force at play during the emergence of asexuality in haploid sexual systems. Moreover, we show that haploid purifying selection plays a key role in limiting the accumulation of deleterious alleles in Amazons, and we identify an autosomal locus associated with the Amazon phenotype. The sex chromosome, together with this autosomal locus, may underlie the switch to obligate asexuality in the Amazon populations.

Long-read sequencing and genome assembly of natural history collection samples and challenging specimens

Museum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protocols can yield contiguous genome assemblies. Additionally, using a modified amplification-based protocol, employing an alternative polymerase to overcome PCR bias, we assembled the 3.1 Gb maned sloth genome, surpassing the previous 500 Mb protocol size limit. Our protocol also improves assemblies of other difficult-to-sequence molluscs and arthropods, including millimeter-sized organisms. By highlighting collections as valuable sample resources and facilitating genome assembly of tiny and challenging organisms, our study advances efforts to obtain reference genomes of all eukaryotes.

A new high-quality genome assembly and annotation for the threatened Florida Scrub-Jay (Aphelocoma coerulescens)

The Florida Scrub-Jay (Aphelocoma coerulescens), a Federally Threatened, cooperatively-breeding bird, is an emerging model system in evolutionary biology and ecology. Extensive individual-based monitoring and genetic sampling for decades has yielded a wealth of data, allowing for the detailed study of social behavior, demography, and population genetics of this natural population. Here, we report a linkage map and a chromosome-level genome assembly and annotation for a female Florida Scrub-Jay made with long-read sequencing technology, chromatin conformation data, and the linkage map. We constructed a linkage map comprising 4,468 SNPs that had 34 linkage groups and a total sex-averaged autosomal genetic map length of 2446.78 cM. The new genome assembly is 1.33 Gb in length, consisting of 33 complete or near-complete autosomes and the sex chromosomes (ZW). This highly contiguous assembly has an NG50 of 68 Mb and a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 97.1% with respect to the Aves database. The annotated gene set has a BUSCO transcriptome completeness score of 95.5% and 17,964 identified protein-coding genes, 92.5% of which have associated functional annotations. This new, high-quality genome assembly and linkage map of the Florida Scrub-Jay provides valuable tools for future research into the evolutionary dynamics of small, natural populations of conservation concern.

De Novo Genome Assembly and Phylogenetic Analysis of Cirsium nipponicum

Background: Cirsium nipponicum, a pharmaceutically valuable plant from the Asteraceae family, has been utilized for over 2000 years. Unlike other thistles, it is native to East Asia and found exclusively on Ulleung Island on the Korea Peninsula. Despite its significance, the genome information of C. nipponicum has remained unclear. Methods: In this study, we assembled the genome of C. nipponicum using both short reads from Illumina sequencing and long reads from Nanopore sequencing. Results: The assembled genome is 929.4 Mb in size with an N50 length of 0.7 Mb, covering 95.1% of BUSCO core groups listed in edicots_odb10. Repeat sequences accounted for 70.94% of the assembled genome. We curated 31,263 protein-coding genes, of which 28,752 were functionally annotated using public databases. Phylogenetic analysis of 11 plant species using single-copy orthologs revealed that C. nipponicum diverged from Cynara cardunculus approximately 15.9 million years ago. Gene family evolutionary analysis revealed significant expansion and contraction in genes involved in abscisic acid biosynthesis, late endosome to vacuole transport, response to nitrate, and abaxial cell fate specification. Conclusions: This study provides a reference genome of C. nipponicum, enhancing our understanding of its genetic background and facilitating an exploration of genetic resources for beneficial phytochemicals.

SpLitteR: diploid genome assembly using TELL-Seq linked-reads and assembly graphs

Background

Recent advances in long-read sequencing technologies enabled accurate and contiguous de novo assemblies of large genomes and metagenomes. However, even long and accurate high-fidelity (HiFi) reads do not resolve repeats that are longer than the read lengths. This limitation negatively affects the contiguity of diploid genome assemblies since two haplomes share many long identical regions. To generate the telomere-to-telomere assemblies of diploid genomes, biologists now construct their HiFi-based phased assemblies and use additional experimental technologies to transform them into more contiguous diploid assemblies. The barcoded linked-reads, generated using an inexpensive TELL-Seq technology, provide an attractive way to bridge unresolved repeats in phased assemblies of diploid genomes.

Results

We developed the SpLitteR tool for diploid genome assembly using linked-reads and assembly graphs and benchmarked it against state-of-the-art linked-read scaffolders ARKS and SLR-superscaffolder using human HG002 genome and sheep gut microbiome datasets. The benchmark showed that SpLitteR scaffolding results in 1.5-fold increase in NGA50 compared to the baseline LJA assembly and other scaffolders while introducing no additional misassemblies on the human dataset.

Conclusion

We developed the SpLitteR tool for assembly graph phasing and scaffolding using barcoded linked-reads. We benchmarked SpLitteR on assembly graphs produced by various long-read assemblers and have demonstrated that TELL-Seq reads facilitate phasing and scaffolding in these graphs. This benchmarking demonstrates that SpLitteR improves upon the state-of-the-art linked-read scaffolders in the accuracy and contiguity metrics. SpLitteR is implemented in C++ as a part of the freely available SPAdes package and is available at https://github.com/ablab/spades/releases/tag/splitter-preprint.

Molecular epidemiology of extended-spectrum beta-lactamase-producing-Klebsiella species in East Tennessee dairy cattle farms

Introduction

The rising prevalence of Extended-Spectrum Beta-Lactamase (ESBL)-producing Klebsiella species (spp.) poses a significant threat to human and animal health and environmental safety. To address this pressing issue, a comprehensive study was undertaken to elucidate the burden and dissemination mechanisms of ESBL-Klebsiella spp. in dairy cattle farms.

Methods

Fifty-seven Klebsiella species were isolated on CHROMagar™ ESBL plates and confirmed with MADLI-TOF MS and whole genome sequenced from 14 dairy farms.

Results and discussion

Six families of beta-lactamase (bla) (bla CTX-M, bla SHV, bla TEM, bla OXY, bla OXA, and bla SED) were detected in ESBL-Klebsiella spp. genomes. Most (73%) of isolates had the first three types of beta-lactamase genes, with bla SHV being the most frequent, followed by bla CTX-M. Most (93%) isolates harbored two or more bla genes. The isolates were genotypically MDR, with 26 distinct types of antibiotic resistance genes (ARGs) and point mutations in gyrA, gyrB, and parC genes. The genomes also harbored 22 different plasmid replicon types, including three novel IncFII. The IncFII and Col440I plasmids were the most frequent and were associated with bla CTXM-27 and qnrB19 genes, respectively. Eighteen distinct sequence types (STs), including eight isolates with novel STs of K. pneumoniae, were detected. The most frequently occurring STs were ST353 (n = 8), ST469 (n = 6), and the novel ST7501 (n = 6). Clusters of ESBL-Klebsiella strains with identical STs, plasmids, and ARGs were detected in multiple farms, suggesting possible clonal expansion. The same ESBL variant was linked to identical plasmids in different Klebsiella STs in some farms, suggesting horizontal spread of the resistance gene. The high burden and dual spread mechanism of ESBL genes in Klebsiella species, combined with the emergence of novel sequence types, could swiftly increase the prevalence of ESBL-Klebsiella spp., posing significant risks to human, animal, and environmental health. Immediate action is needed to implement rigorous surveillance and control measures to mitigate this risk.

Genetic Profile and Toxigenic Potential of Bacillus cereus Isolates from a Norwegian Ice Cream Production Plant

Members of the B. cereus group are spore-forming organisms commonly associated with spoilage of milk and dairy products. We have determined the genetic identity and growth characteristics of 57 B. cereus isolates collected from a Norwegian ice cream production plant. Our findings revealed persistence of B. cereus spp. strains for up to 19 months, suggesting the plant's susceptibility to long-term colonization. One of the mesophilic isolates, NVH-YM303, carried a complete cereulide synthetase operon. To assess the potential food poisoning risk associated with the presence of cereulide-producing strains in the production line, we examined the production of cereulide in ice cream and milk at different temperatures by NVH-YM303 and by the emetic psychrotrophic B. weihenstephanensis strain BtB2-4. Our findings revealed that NVH-YM303 produced higher levels of cereulide in ice cream as compared to milk. Furthermore, it was observed that NVH-YM303 produced more cereulide in ice cream at 25 °C compared to 15 °C. Conversely, BtB2-4 produced more cereulide in ice cream at 15 °C than at 25 °C. The results obtained in this study contribute to knowledge important for risk assessment of the potential hazards posed by the presence of B. cereus within ice cream production facilities.

Diarrheagenic Escherichia coli in Stool Specimens Collected from Patients Attending Primary Healthcare Facilities in Ethiopia: Whole-Genome Sequencing-Based Molecular Characterization

The diarrheagenic Escherichia coli (DEC) is the major cause of diarrheal diseases in Africa, including Ethiopia. However, the genetic diversity of E. coli pathotypes found in Ethiopia has not been studied well. This study aimed to characterize potential DEC belonging to enteropathogenic (EPEC), Shiga toxin-producing (STEC), enteroaggregative (EAEC), enterotoxigenic (ETEC), and enteroinvasive (EIEC) E. coli pathotypes from stool specimens of patients attending primary healthcare units (n = 260) in Addis Ababa and Hossana using whole-genome sequencing. Real-time PCR assays were used to identify DEC isolates belonging to EPEC, STEC, EAEC, ETEC, and EIEC pathotypes, which were then subjected to whole-genome sequencing on the Illumina platform. Twenty-four whole-genome nucleotide sequences of DEC strains with good enough quality were analyzed for virulence-associated genes (VAGs), antibiotic resistance genes (ARGs), phylogenetic groups, serogroups, and sequence types. The majority (62.5%) of DEC isolates belonged to the phylogenetic group B1. The identified DEC isolates belonged to 21 different serogroups and 17 different sequence types. All tested DEC isolates carried multiple VAGs and ARGs. The findings highlight the high diversity in the population structure of the studied DEC isolates, which is important for designing targeted interventions to reduce the diarrheal burden in Ethiopia.

Long-read de novo genome assembly of Gulf toadfish (Opsanus beta)

BACKGROUND

The family Batrachoididae are a group of ecologically important teleost fishes with unique life histories, behavior, and physiology that has made them popular model organisms. Batrachoididae remain understudied in the realm of genomics, with only four reference genome assemblies available for the family, with three being highly fragmented and not up to current assembly standards. Among these is the Gulf toadfish, Opsanus beta, a model organism for serotonin physiology which has recently been bred in captivity.

RESULTS

Here we present a new, de novo genome and transcriptome assemblies for the Gulf toadfish using PacBio long read technology. The genome size of the final assembly is 2.1 gigabases, which is among the largest teleost genomes. This new assembly improves significantly upon the currently available reference for Opsanus beta with a final scaffold count of 62, of which 23 are chromosome scale, an N50 of 98,402,768, and a BUSCO completeness score of 97.3%. Annotation with ab initio and transcriptome-based methods generated 41,076 gene models. The genome is highly repetitive, with ~ 70% of the genome composed of simple repeats and transposable elements. Satellite DNA analysis identified potential telomeric and centromeric regions.

CONCLUSIONS

This improved assembly represents a valuable resource for future research using this important model organism and to teleost genomics more broadly.

Complete Genome of Achromobacter xylosoxidans, a Nitrogen-Fixing Bacteria from the Rhizosphere of Cowpea (Vigna unguiculata [L.] Walp) Tolerant to Cucumber Mosaic Virus Infection

Achromobacter xylosoxidans is one of the nitrogen-fixing bacteria associated with cowpea rhizosphere across Africa. Although its role in improving soil fertility and inducing systemic resistance in plants against pathogens has been documented, there is limited information on its complete genomic characteristics from cowpea roots. Here, we report the complete genome sequence of A. xylosoxidans strain DDA01 isolated from the topsoil of a field where cowpea plants tolerant to cucumber mosaic virus (CMV) were grown in Ibadan, Nigeria. The genome of DDA01 was sequenced via Illumina MiSeq and contained 6,930,067 nucleotides with 67.55% G + C content, 73 RNAs, 59 tRNAs, and 6421 protein-coding genes, including those associated with nitrogen fixation, phosphate solubilization, Indole3-acetic acid production, and siderophore activity. Eleven genetic clusters for secondary metabolites, including alcaligin, were identified. The potential of DDA01 as a plant growth-promoting bacteria with genetic capabilities to enhance soil fertility for resilience against CMV infection in cowpea is discussed. To our knowledge, this is the first complete genome of diazotrophic bacteria obtained from cowpea rhizosphere in sub-Saharan Africa, with potential implications for improved soil fertility, plant disease resistance, and food security.

Holistic understanding of trimethoprim resistance in Streptococcus pneumoniae using an integrative approach of genome-wide association study, resistance reconstruction, and machine learning

Antimicrobial resistance (AMR) is a public health threat worldwide. Next-generation sequencing (NGS) has opened unprecedented opportunities to accelerate AMR mechanism discovery and diagnostics. Here, we present an integrative approach to investigate trimethoprim (TMP) resistance in the key pathogen Streptococcus pneumoniae. We explored a collection of 662 S. pneumoniae genomes by conducting a genome-wide association study (GWAS), followed by functional validation using resistance reconstruction experiments, combined with machine learning (ML) approaches to predict TMP minimum inhibitory concentration (MIC). Our study showed that multiple additive mutations in the folA and sulA loci are responsible for TMP non-susceptibility in S. pneumoniae and can be used as key features to build ML models for digital MIC prediction, reaching an average accuracy within ±1 twofold dilution factor of 86.3%. Our roadmap of in silico analysis-wet-lab validation-diagnostic tool building could be adapted to explore AMR in other combinations of bacteria-antibiotic.

IMPORTANCE

In the age of next-generation sequencing (NGS), while data-driven methods such as genome-wide association study (GWAS) and machine learning (ML) excel at finding patterns, functional validation can be challenging due to the high numbers of candidate variants. We designed an integrative approach combining a GWAS on S. pneumoniae clinical isolates, followed by whole-genome transformation coupled with NGS to functionally characterize a large set of GWAS candidates. Our study validated several phenotypic folA mutations beyond the standard Ile100Leu mutation, and showed that the overexpression of the sulA locus produces trimethoprim (TMP) resistance in Streptococcus pneumoniae. These validated loci, when used to build ML models, were found to be the best inputs for predicting TMP minimal inhibitory concentrations. Integrative approaches can bridge the genotype-phenotype gap by biological insights that can be incorporated in ML models for accurate prediction of drug susceptibility.

Complete genome sequence of Pigmentibacter ruber isolated from a human patient in Japan

Pigmentibacter ruber is a newly described bacterium belonging to the Silvanigrellaceae family that was isolated from human blood in 2021. We report the complete genome sequence of a clinical isolate of P. ruber (GTC16762) obtained from a human patient in Japan. Its genome contains a 3.6-Mb chromosome and three circular plasmids.

Genome sequences of Clostridium perfringens isolated from diseased dogs

Two Clostridium perfringens isolates originating from two Norwegian dogs with acute hemorrhagic diarrhea were sequenced. Based on Illumina and Oxford Nanopore Technology sequencing, hybrid assemblies were generated, and one of the genomes was completed and closed. For both isolates, virulence genes and their genomic location have been identified.

Complete genome sequence of Pseudomonas aeruginosa Y010, a taro rhizosphere strain producing potent antimicrobial agents

Pseudomonas aeruginosa Y010, isolated from the taro rhizosphere, exhibits great antagonistic abilities against Dickeya strains that cause soft-rot and blackleg diseases of plants by producing potent antimicrobial agents. The complete genome of Y010 was sequenced and annotated, which is 6,415,628 bp in length with 66.39% GC content.

Halotolerant Endophytic Bacteria Priestia flexa 7BS3110 with Hg2+ Tolerance Isolated from Avicennia germinans in a Caribbean Mangrove from Colombia

The mangrove ecosystems of the Department of Atlántico (Colombian Caribbean) are seriously threatened by problems of hypersalinization and contamination, especially by heavy metals from the Magdalena River. The mangrove plants have developed various mechanisms to adapt to these stressful conditions, as well as the associated microbial populations that favor their growth. In the present work, the tolerance and detoxification capacity to heavy metals, especially to mercury, of a halotolerant endophytic bacterium isolated from the species Avicennia germinans located in the Balboa Swamp in the Department of Atlántico was characterized. Diverse microorganisms were isolated from superficially sterilized A. germinans leaves. Tolerance to NaCl was evaluated for each of the obtained isolates, and the most resistant was selected to assess its tolerance to Pb2+, Cu2+, Hg2+, Cr3+, Co2+, Ni2+, Zn2+, and Cd2+, many of which have been detected in high concentrations in the area of study. According to the ANI and AAI percentages, the most halotolerant strain was identified as Priestia flexa, named P. flexa 7BS3110, which was able to tolerate up to 12.5% (w/v) NaCl and presented a minimum inhibitory concentrations (MICs) of 0.25 mM for Hg, 10 mM for Pb, and 15 mM for Cr3+. The annotation of the P. flexa 7BS3110 genome revealed the presence of protein sequences associated with exopolysaccharide (EPS) production, thiol biosynthesis, specific proteins for chrome efflux, non-specific proteins for lead efflux, and processes associated with sulfur and iron homeostasis. Scanning electron microscopy (SEM) analysis showed morphological cellular changes and the transmission electron microscopy (TEM) showed an electrodense extracellular layer when exposed to 0.25 mM Hg2+. Due to the high tolerance of P. flexa 7BS3110 to Hg2+ and NaCl, its ability to grow when exposed to both stressors was tested, and it was able to thrive in the presence of 5% (w/v) NaCl and 0.25 mM of Hg2+. In addition, it was able to remove 98% of Hg2+ from the medium when exposed to a concentration of 14 mg/L of this metalloid. P. flexa 7BS3110 has the potential to bioremediate Hg2+ halophilic contaminated ecosystems.

Chamaeleo calyptratus (veiled chameleon) chromosome-scale genome assembly and annotation provides insights into the evolution of reptiles and developmental mechanisms

The family Chamaeleonidae comprises 228 species, boasting an extensive geographic spread and an array of evolutionary novelties and adaptations, but a paucity of genetic and molecular analyses. Veiled chameleon (Chamaeleo calyptratus) has emerged as a tractable research organism for the study of squamate early development and evolution. Here we report a chromosomal-level assembly and annotation of the veiled chameleon genome. We note a remarkable chromosomal conservation across squamates, but comparisons to more distant genomes reveal GC peaks correlating with ancestral chromosome fusion events. We subsequently identified the XX/XY region on chromosome 5, confirming environmental-independent sex determination in veiled chameleons. Furthermore, our analysis of the Hox gene family indicates that veiled chameleons possess the most complete set of 41 Hox genes, retained from an amniote ancestor. Lastly, the veiled chameleon genome has retained both ancestral paralogs of the Nodal gene, but is missing Dand5 and several other genes, recently associated with the loss of motile cilia during the establishment of left-right patterning. Thus, a complete veiled chameleon genome provides opportunities for novel insights into the evolution of reptilian genomes and the molecular mechanisms driving phenotypic variation and ecological adaptation.

A chromosome-level genome assembly of Drosophila madeirensis, a fruit fly species endemic to the island of Madeira

Drosophila subobscura is distributed across Europe, the Near East, and the Americas, while its sister species, Drosophila madeirensis, is endemic to the island of Madeira in the Atlantic Ocean. D. subobscura is known for its strict light-dependence in mating and its unique courtship displays, including nuptial gift-giving. D. subobscura has also attracted the interest of researchers because of its abundant variations in chromosomal polymorphisms correlated to the latitude and season, which have been used as a tool to track global climate warming. Although D. madeirensis can be an important resource for understanding the evolutionary underpinning of these genetic characteristics of D. subobscura, little work has been done on the biology of this species. Here, we used a HiFi long-read sequencing data set to produce a de novo genome assembly for D. madeirensis. This assembly comprises a total of 111 contigs spanning 135.5 Mb and has an N50 of 24.2 Mb and a BUSCO completeness score of 98.6%. Each of the 6 chromosomes of D. madeirensis consisted of a single contig except for some centromeric regions. Breakpoints of the chromosomal inversions between D. subobscura and D. madeirensis were characterized using this genome assembly, updating some of the previously identified locations.

The draft genomes of Crassostrea gasar and Crassostrea rhizophorae: key resources for leveraging oyster cultivation in the Southwest Atlantic

OBJECTIVES

The two oyster species studied hold considerable economic importance for artisanal harvest (Crassostrea rhizophorae) and aquaculture (Crassostrea gasar). Their draft genomes will play an important role in the application of genomic methods such as RNAseq, population-based genomic scans aiming at addressing expression responses to pollution stress, adaptation to salinity and temperature variation, and will also permit investigating the genetic bases and enable marker-assisted selection of economically important traits like shell and mantle coloration and resistance to temperature and disease.

DATA DESCRIPTION

The draft assembly size of Crassostrea gasar is 506 Mbp, and of Crassostrea rhizophorae is 584 Mbp with scaffolds N50 of 11,3 Mbp and 4,9 Mbp, respectively. The general masked bases by RepeatMasker in both genomes were highly similar using different datasets. The masked bases varied from 9.41% in C. gasar to 10.05% in C. rhizophorae and 42.85% in C. gasar to 44.44% in C. rhizophorae using Dfam and RepeatModeler datasets, respectively. Functional annotation with eggNog resulted in 34,693 annotated proteins in C. rhizophorae and 26,328 in C. gasar. BUSCO analysis shows that almost 99% of genes (5,295) are complete in relation to the mollusk orthologous genes dataset (mollusca_odb10).

Wolbachia strain diversity in a complex group of sympatric cryptic parasitoid wasp species

BACKGROUND

Maternally-inherited symbionts can induce pre-mating and/or post-mating reproductive isolation between sympatric host lineages, and speciation, by modifying host reproductive phenotypes. The large parasitoid wasp genus Cotesia (Braconidae) includes a diversity of cryptic species, each specialized in parasitizing one to few related Lepidoptera host species. Here, we characterized the infection status of an assemblage of 21 Cotesia species from 15 countries by several microbial symbionts, as a first step toward investigating whether symbionts may provide a barrier to gene flow between these parasitoid host lineages.

RESULTS

The symbiotic microbes Arsenophonus, Cardinium, Microsporidium and Spiroplasma were not detected in the Cotesia wasps. However, the endosymbiotic bacterium Wolbachia was present in at least eight Cotesia species, and hence we concentrated on it upon screening additional DNA extracts and SRAs from NCBI. Some of the closely related Cotesia species carry similar Wolbachia strains, but most Wolbachia strains showed patterns of horizontal transfer between phylogenetically distant host lineages.

CONCLUSIONS

The lack of co-phylogenetic signal between Wolbachia and Cotesia suggests that the symbiont and hosts have not coevolved to an extent that would drive species divergence between the Cotesia host lineages. However, as the most common facultative symbiont of Cotesia species, Wolbachia may still function as a key-player in the biology of the parasitoid wasps. Its precise role in the evolution of this complex clade of cryptic species remains to be experimentally investigated.

Sampling fish gut microbiota - A genome-resolved metagenomic approach

Despite a surge in microbiota-focused studies in teleosts, few have reported functional data on whole metagenomes as it has proven difficult to extract high biomass microbial DNA from fish intestinal samples. The zebrafish is a promising model organism in functional microbiota research, yet studies on the functional landscape of the zebrafish gut microbiota through shotgun based metagenomics remain scarce. Thus, a consensus on an appropriate sampling method accurately representing the zebrafish gut microbiota, or any fish species is lacking. Addressing this, we systematically tested four methods of sampling the zebrafish gut microbiota: collection of faeces from the tank, the whole gut, intestinal content, and the application of ventral pressure to facilitate extrusion of gut material. Additionally, we included water samples as an environmental control to address the potential influence of the environmental microbiota on each sample type. To compare these sampling methods, we employed a combination of genome-resolved metagenomics and 16S metabarcoding techniques. We observed differences among sample types on all levels including sampling, bioinformatic processing, metagenome co-assemblies, generation of metagenome-assembled genomes (MAGs), functional potential, MAG coverage, and population level microdiversity. Comparison to the environmental control highlighted the potential impact of the environmental contamination on data interpretation. While all sample types tested are informative about the zebrafish gut microbiota, the results show that optimal sample type for studying fish microbiomes depends on the specific objectives of the study, and here we provide a guide on what factors to consider for designing functional metagenome-based studies on teleost microbiomes.