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bioRxiv2022

hibayes: An R Package to Fit Individual-Level, Summary-Level and Single-Step Bayesian Regression Models for Genomic Prediction and Genome-Wide Association Studies

With the rapid development of sequencing technology, the costs of individual genotyping have been reduced dramatically, leading to genomic prediction and genome-wide association studies being widely promoted and used to predict the unknown phenotypes and to locate causal or candidate genes for animal and plant economic traits and, increasingly, for human diseases. Developing newly advanced statistical models to improve accuracy in predicting and locating for the traits with various genetic architectures has always been a hot topic in those two research domains. The Bayesian regression model (BRM) has played a crucial role in the past decade, and it has been used widely in relevant genetic analyses owing to its flexible model assumptions on the unknown genetic architecture of complex traits. To fully utilize the available data from either a self-designed experimental population or a public database, statistical geneticists have constantly extended the fitting capacity of BRM, and a series of new methodologies have been proposed for different application scenarios. Here we introduce hibayes, which is the only one tool that can implement three types of Bayesian regression models. With the richest methods achieved thus far, it covers almost all the functions involved in genetic analyses for genomic prediction and genome-wide association studies, potentially addressing a wide range of research problems, while retaining an easy-to-use and transparent interface. We believe that hibayes will facilitate the researches conducted by human geneticists, as well as plant and animal breeders. The hibayes package is freely available from CRAN at https://cran.r-project.org/package=hibayes.

genetics↗

bioRxiv2023

Pan-genome study underling the extent of genomic variation of invasive Streptococcus pneumoniae in Malawi

AbstractStreptococcus pneumoniae is a common cause of acute bacterial infections in Malawi. Understanding the molecular mechanisms underlying its invasive behavior is crucial for designing new therapeutic strategies. We conducted a pan-genome analysis to identify potential virulence genes in S. pneumoniae by comparing the gene pool of isolates from carriers nasopharyngeal secretions to isolates from the blood and cerebrospinal fluid of patients. Our analysis involved 1,477 pneumococcal isolates from Malawi, comprising 825 samples from carriers (nasopharyngeal swab) and 652 from patients (368 from blood and 284 from cerebrospinal fluid). We identified 56 serotypes in the cohort. While most serotypes exhibited a similar prevalence in both carriage and disease groups, serotypes 1 and 5, the most abundant serotypes in the entire cohort, were significantly more commonly detected in specimens from patients compared to the carriage group. This difference is presumably due to their shorter nasopharyngeal colonization period. Furthermore, these serotypes displayed genetic distinctiveness from other serotypes. A magnificent genetic difference was observed in the absence of genes from the RD8a genomic island in serotypes 1 and 5 compared to significantly prevalent serotypes in the nasopharynx. RD8a genes play pivotal roles in binding to epithelial cells and performing aerobic respiration to synthesize ATP through oxidative phosphorylation. The absence of RD8a from serotypes 1 and 5 may be associated with a shorter duration in the nasopharynx, theoretically due to a reduced capacity to bind to epithelial cells and access free oxygen molecules required for aerobic respiration (essential to maintain the carriage state). Serotypes 1 and 5, significantly harbor operons that encode phosphoenolpyruvate phosphotransferase systems, which might relate to transporting carbohydrates, relying on phosphoenolpyruvate as the energy source instead of ATP. In conclusion, serotypes 1 and 5 as the most prevalent invasive pneumococcal strains in Malawi, displayed considerable genetic divergence from other strains, which may offer insights into their invasiveness and potential avenues for further research. Author summaryDespite introducing the pneumococcal conjugate vaccine in 2011, Streptococcus pneumoniae remains a major cause of bacterial infection in Malawi. Whilst some pneumococcal strains harmlessly colonize the nasopharynx, others find their way into normally sterile sites, such as lungs, blood, and nervous system, resulting in serious illness. Our study identified specific pneumococcal serotypes as the most invasive in Malawi, characterized by a short colonization period and significant genetic distinctiveness from other strains. This genetic divergence notably included the absence of several genes associated with aerobic respiration and the presence of genes facilitating ATP-independent carbohydrate transport. The presence or absence of these genes may underlie their heightened invasiveness and shorter colonization period. This hypothesis positions these genes as potential candidates for future therapeutic research. We propose that the specific gene gain and/or loss in invasive versus other serotypes may be linked to the development of invasive pneumococcal diseases. Impact StatementOur research applied pan-genomics principles to comprehensively assess diversity within the pneumococcus genome, with the primary objective of identifying pneumococcal virulence genes for advancing vaccine design and drug development. Within this study, we identified Serotypes 1 and 5 as the predominant and highly invasive pneumococcal strains in Malawi, characterized by a short nasopharyngeal colonization period, suggesting their potential for rapid infection of sterile sites within the human body such as blood and the central nervous system. These serotypes exhibited significant genetic divergence from other serotypes in Malawi, notably lacking key genes within the RD8a operon while harboring transporters functioning independently of ATP. Its important to note that these findings are based on computational analysis, and further validation through laboratory experiments is essential to confirm their biological significance and potential clinical applications. The implications of our research offer potential avenues for more effective pneumococcal disease prevention and treatment, not only in Malawi but also in regions facing similar challenges.

microbiology↗

bioRxiv2023

Differentiated genomic footprints and connections inferred from 440 Hmong-Mien genomes suggest their isolation and long-distance migration

BackgroundThe underrepresentation of Hmong-Mien (HM) people in Asian genomic studies has hindered our comprehensive understanding of population history and human health. South China is an ethnolinguistically diverse region and indigenously settled by ethnolinguistically diverse HM, Austroasiatic (AA), Tai-Kadai (TK), Austronesian (AN), and Sino-Tibetan (ST) people, which is regarded as East Asias initial cradle of biodiversity. However, previous fragmented genetic studies have only presented a fraction of the landscape of genetic diversity in this region, especially the lack of haplotype-based genomic resources. The deep characterization of demographic history and natural-selection-relevant architecture in HM people was necessary. ResultsWe comprehensively reported the population-specific genomic resources and explored the fine-scale genetic structure and adaptative features inferred from the high-density SNP data in 440 individuals from 34 ethnolinguistic populations, including previously unreported She. We identified solid genetic differentiation between inland (Miao/Yao) and coastal (She) southern Chinese HM people, and the latter obtained more gene flow from northern East Asians. Multiple admixture models further confirmed that extensive gene flow from surrounding ST, TK, and AN people entangled in forming the gene pool of coastal southeastern East Asian HM people. Population genetic findings of isolated shared unique ancestral components based on the sharing alleles and haplotypes deconstructed that HM people from Yungui Plateau carried the breadth of genomic diversity and previously unknown genetic features. We identified a direct and recent genetic connection between Chinese and Southeast Asian HM people as they shared the most extended IBD fragments, supporting the long-distance migration hypothesis. Uniparental phylogenetic topology and Network relationship reconstruction found ancient uniparental lineages in southwestern HM people. Finally, the population-specific biological adaptation study identified the shared and differentiated natural-selection signatures among inland and coastal HM people associated with physical features and immune function. The allele frequency spectrum (AFS) of clinical cancer susceptibility alleles and pharmacogenomic genes showed significant differences between HM and northern Chinese people. ConclusionsOur extensive genetic evidence combined with the historic documents supported the view that ancient HM people originated in Yungui regions associated with ancient Three-Miao tribes descended from the ancient Daxi-Qujialing-Shijiahe people. And then, some recently rapidly migrated to Southeast Asia, and some culturally dispersed eastward and mixed respectively with Southeast Asian indigenes, coastal Liangzhu-related ancient populations, and incoming southward Sino-Tibetan people. Generally, complex population migration, admixture, and adaptation history contributed to their specific patterns of non-coding or disease-related genetic variations.

genetics↗

bioRxiv2023

CRISPR-Cas9-mediated genome engineering exaggerates genomic deletion at 10q23.31 including the PTEN gene locus mimicking cancer profiles

The CRISPR-Cas9 system is a powerful tool for studying gene functions and has tremendous potential for disease treatment. However, precise genome editing requires thorough assessments to minimize unintended on- and off-target effects. Here, we report an unexpected deletion of a 287 kb region on Chromosome 10 (10q23.31) in chronic myelogenous leukemia HAP1 cells, which are frequently used in CRISPR screens. The deleted region encodes regulatory genes, including PAPSS2, ATAD1, KLLN, and PTEN. We found that this deletion was not a direct consequence of CRISPR-Cas9 off-targeting but rather occurred frequently by the process of generating CRISPR-Cas9-modifed cells. The deletion was associated with global changes in histone acetylation and gene expression, affecting fundamental cellular processes such as cell cycle and DNA replication. We detected this deletion in cancer patient genomes. As in HAP1 cells, the deletion contributed to similar gene expression patterns among cancer patients despite interindividual differences. Overall, our findings suggest that the unintended deletion of 10q23.31 can confound CRISPR-Cas9 studies, highlights the importance of assessing unintended genomic changes in CRISPR-Cas9-modified cells and may have clinical significance in cancer research. HighlightsO_LICRISPR-Cas9-modified HAP1 cells carry an unexpected large genomic deletion at 10q23.31 encompassing four protein-coding genes frequently expressed across various cell types. C_LIO_LIThe 10q23.31 deletion is accompanied by global changes in histone modification and transcriptomes. C_LIO_LIThe generation of CRISPR-Cas9-modified cells rather than Cas9 activity increases the frequencies of the deletion at 10q23.31. C_LIO_LIThe 10q23.31 deletion identified in HAP1 cells resembles a commonly occurring deletion pattern in cancer patients. C_LI

cancer biology↗

bioRxiv2023

Genomic epidemiology and multilevel genome typing of Bordetella pertussis

Bordetella pertussis is responsible for the respiratory infectious disease pertussis (or whooping cough), which causes one of the most severe diseases in infants, although it can be prevented by whole cell and acellular vaccines. The recent resurgence of pertussis is partially due to pathogen adaptation to vaccines as well as resistance to antimicrobials. Surveillance of current circulating and emerging strains is therefore vital to understand the risks they pose to public health. Although there is increased genomics based typing, a genomic nomenclature for this pathogen has not been well established. Here, we implemented the Multilevel Genome Typing (MGT) system for B. pertussis with five levels of resolution, which provide targeted typing of relevant lineages as well as discrimination of closely related strains at the finest scale. The low resolution levels can describe the distribution of alleles of major vaccine antigen genes such as ptxP, fim3, fhaB and prn as well as temporal and spatial trends within the B. pertussis global population. Mid-resolution levels enables typing of antibiotic resistant lineages and Prn deficient lineages within the ptxP3 clade. High resolution levels can capture small-scale epidemiology such as local transmission events and has comparable resolution to existing genomic methods of strain relatedness assessment. The scheme offers stable MGT type assignments aiding harmonisation of typing and communication between laboratories. The scheme is available at www.mgtdb.unsw.edu.au/pertussis/ is regularly updated from global data repositories and accepts public data submissions. The MGT scheme provides a comprehensive, robust, and scalable system for global surveillance of B. pertussis.

microbiology↗

bioRxiv2023

The first two chromosome-scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus

The native, perennial shrub American hazelnut (Corylus americana) is cultivated in the Midwestern U.S. for its significant ecological benefits, as well as its high-value nut crop. Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high-quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome-scale assemblies for this species using the accessions Rush and Winkler. Genomes were assembled using HiFi PacBio reads and Arima Hi-C data, and Oxford Nanopore reads and a high-density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for Rush and Winkler, respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. Rush has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while Winkler had corresponding scores of 96.9 and 96.5, indicating high-quality assemblies. These two independent assemblies enable unbiased assessment of structural variation within C. americana, as well as patterns of syntenic relationships across the Corylus genus. Furthermore, we identified high-density SNP marker sets from genotyping-by-sequencing data using 1,343 C. americana, C. avellana, and C. americana x C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self-incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self-incompatibility in Corylus.

plant biology↗

bioRxiv2023

Genome duplications, genomic conflict, and rapid phenotypic evolution characterize the Cretaceous radiation of Fagales

O_LIFlowering plant lineages display remarkable diversity in life history and morphological form. However our understanding of how this phenotypic diversity or disparity, arises and what, if any, relation there is to processes such as gene and genome duplication remains unlcear. C_LIO_LIHere we investigate the relationship between phenotypic and genomic evolution in the angiosperm order Fagales, a lineage of woody plants that has been a dominant component of temperate and subtropical forests since the Late Cretaceous. To this end, we examine newly generated trait and transcriptomic datasets spanning the phylogenetic breadth of the order, including most extant genera as well as a rich diversity of Cretaceous fossil representatives. C_LIO_LIOur phylogenomic analyses resolved the location of an ancient polyploidization event in Juglandaceae and identified hotspots of gene-duplication and genomic conflict across the order. Examinations of phenotypic evolution (including morphospace occupancy and rate shifts) show that the morphospace occupied by Fagales was filled by the early Cenozoic and rates of evolution were highest during the early radiation of the Fagales crown and its major families. Many instances of phenotypic rates also correspond to hotspots of gene duplication. C_LIO_LIOur results show that Fagales conform to an "early burst" model of phenotypic diversification, with morphospace being filled early in the groups evolutionary history. Our study is consistent with others showing a decoupling of species diversification with other biological processes (e.g., phenotypic and genomic evolution), underscoring the complexity of understanding the major drivers of plant evolution over broad timescales. C_LI

evolutionary biology↗

bioRxiv2023

Natural genomic variation in rice blast genomes is associated with specific heterochromatinmodifications

Genome organization in eukaryotes exhibits non-random patterns tied to transcription, replication, and chromatin. However, the driving forces across these processes, and their impacts on genome evolution remain unclear. To address this, we analyzed sequence data from 86 Magnaporthe oryzae isolates, a globally important plant pathogenic fungus, alongside new reference genomes, to investigate DNA sequence variation and the epigenome. Histone modification profiles were obtained through genome-wide chromatin immunoprecipitation-sequencing of the four new reference strains, which revealed that repressive histone marks (H3K27me3, H3K9me3) were associated with SNP and INDEL frequency. Densely grouped SNPs were found to reside in heterochromatin, often outside transposable elements, highlighting the link between heterochromatin and DNA variation. Even when controlling for selection, silent SNP frequency/kb was higher in H3K27me3-associated genes. Effector genes, key to pathogenicity, also displayed this trend. Comparing the reference strains, euchromatic regions were often syntenic, while heterochromatic regions trended towards non-syntenic. Heterochromatin emerged as a major factor associated with diverse DNA variations in M. oryzae populations, even when accounting for selective pressure. This underscores heterochromatins pivotal role in shaping genetic diversity in these mainly asexually reproducing fungi.

evolutionary biology↗

bioRxiv2024

Comprehensive Analysis of Nascent Transcriptome Reveals Diverse Transcriptional Profiles Across the Trypanosoma cruzi Genome Underlining the Regulatory Role of Genome Organization, Chromatin Status, and Cis-Acting Elements

Trypanosomatids are eukaryotic parasites exhibiting polycistronic transcription and trans-splicing. Post-transcriptional mechanisms are acknowledged as pivotal in gene expression regulation of their protein-coding genes. To comprehensively investigate the impact of transcription on gene expression in Trypanosoma cruzi and the association with the epigenetic landscape, we conducted a genome-wide nascent transcriptomic analysis. Our findings reveal significant asymmetrical transcriptional abundance across the genome, notably between polycistronic transcription units (PTUs) enriched in conserved genes (core PTUs) and those containing virulence genes (disruptive PTUs). We found that trypanosomes exploit linear genome organization to regulate transcription abundance by embedding virulence genes into highly transcribed core-enriched PTUs, by positioning PTUs near non-coding regions of small non-coding RNAs (e.g., tRNAs, snoRNAs), and by placing core CDSs in PTUs of various sizes. Additionally, we found correlations between open chromatin status and nascent transcript levels, both globally and particularly at transcription starting regions (divergent strand switch regions - dSSRs), indicating a crucial role for chromatin architecture in transcriptional regulation. While both core and disruptive dSSRs exhibit similar levels of some epigenetic marks (H2B.V deposition and 5mC), disruptive dSSRs display significantly higher 5hmC content and nucleosome occupancy compared to core dSSRs. Furthermore, we identified distinct conserved motifs within dSSRs of core and disruptive PTUs. These findings challenge the notion of constitutive and uniform transcription in T. cruzi, underscoring the paramount importance of linear genome organization, cis-acting motifs, and chromatin landscape in transcriptional regulation.

molecular biology↗

bioRxiv2024

CRISPR-Cas9/Cas12a Systems for efficient genome editing and large genomic fragment deletions in Aspergillus niger

CRISPR technology has revolutionized fungal genetic engineering by accelerating the pace and expanding the feasible scope of experiments in this field. Among various CRISPR-Cas systems, Cas9 and Cas12a are widely used in genetic and metabolic engineering. In filamentous fungi, both Cas9 and Cas12a have been utilized as CRISPR nucleases. In this work we first compared efficacies and types of genetic edits for CRISPR-Cas9 and -Cas12a systems at the polyketide synthase (albA) gene locus in Aspergillus niger. By employing a tRNA-based gRNA polycistronic cassette, both Cas9 and Cas12a have demonstrated remarkable editing efficacy. Cas12a demonstrated superiority over Cas9 protein when one gRNA was used for targeting, achieving an editing efficiency of 89.5% compared to 15% for Cas9. Moreover, when employing two gRNAs for targeting, both systems achieved up to 100% editing efficiency for single gene editing. In addition, the CRISPR-Cas9 system has been reported to induce large genomic deletions in various species. However, its use for engineering large chromosomal segments deletions in filamentous fungi still requires optimization. Here, we engineered Cas9 and - Cas12a-induced large genomic fragment deletions by targeting various genomic regions of A. niger ranging from 3.5 kb to 40 kb. Our findings demonstrate that targeted engineering of large chromosomal segments can be achieved, with deletions of up to 66.7% efficiency. Furthermore, by targeting a secondary metabolite gene cluster, we show that fragments over 100 kb can be efficiently and specifically deleted using the CRISPR-Cas9 or -Cas12a system. Overall, in this paper, we present an efficient multi-gRNA genome editing system utilizing Cas9 or Cas12a that enables highly efficient targeted editing of genes and large chromosomal regions in A. niger.

microbiology↗

bioRxiv2024

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes

Here, we present CompareM2, a genomes-to-report pipeline for comparative analysis of bacterial and archaeal genomes derived from isolates and metagenomic assemblies. CompareM2 is easy to install and operate, and integrates community-adopted tools to perform genome quality control and annotation, taxonomic and functional predictions, as well as comparative analyses of core- and pan-genome partitions and phylogenetic relations. The central results generated via the CompareM2 workflow are emphasized in a portable dynamic report document. CompareM2 is free software and welcomes modifications and pull requests from the community on its Git repository at https://github.com/cmkobel/comparem2.

bioinformatics↗

bioRxiv2024

Inferring demographic and selective histories from population genomic data using a two-step approach in species with coding-sparse genomes: an application to human data

The demographic history of a population, and the distribution of fitness effects (DFE) of newly arising mutations in functional genomic regions, are fundamental factors dictating both genetic variation and evolutionary trajectories. Although both demographic and DFE inference has been performed extensively in humans, these approaches have generally either been limited to simple demographic models involving a single population, or, where a complex population history has been inferred, without accounting for the potentially confounding effects of selection at linked sites. Taking advantage of the coding-sparse nature of the genome, we propose a 2-step approach in which coalescent simulations are first used to infer a complex multi-population demographic model, utilizing large non-functional regions that are likely free from the effects of background selection. We then use forward-in-time simulations to perform DFE inference in functional regions, conditional on the complex demography inferred and utilizing expected background selection effects in the estimation procedure. Throughout, recombination and mutation rate maps were used to account for the underlying empirical rate heterogeneity across the human genome. Importantly, within this framework it is possible to utilize and fit multiple aspects of the data, and this inference scheme represents a generalized approach for such large-scale inference in species with coding-sparse genomes.

genetics↗

bioRxiv2025

Accurate and Reproducible Whole-Genome Genotyping for Bacterial Genomic Surveillance with Nanopore Sequencing Data

Despite recent advances in error rate reduction, until recently Oxford Nanopore Technology (ONT) sequences lacked the accuracy required for fine scale bacterial genomic analysis. Here, recent software improvements of ONT and the ONT-cgMLST-Polisher within the SeqSphere+ software were evaluated. We used short-(Illumina) and long-read ONT sequences of 80 multidrug-resistant bacteria (MDROs) for benchmarking. Illumina reads were de-novo-assembled using SKESA. For ONT, Dorado super accurate (SUP) model 4.3 or 5.0 basecalled reads were assembled with Flye and then polished with Medaka v1.12 m4.3 or Medaka v2.0 bacterial methylation model. In addition, the ONT-cgMLST-Polisher was run over all assemblies. The ground truth (GT) hybrid assemblies were created using Hybracter v0.10.0. Sixteen isolates from four species out of the original 80 isolates were sent to six laboratories for a ring trial. The 80 MDROs basecalled with SUP m4.3 had an average cgMLST allele distance (AD) to the GT of 4.94 with Medaka v1.12 and 1.78 with Medaka v2.0, respectively. After further polishing the Medaka v2.0 data with the ONT-cgMLST-Polisher, the AD dropped to 0.09. Using data basecalled with SUP m5.0 with Medaka v2.0 further reduced the AD significantly to 0.04. While the ring trial data basecalled with Dorado SUP m4.3 showed more variability and insufficient results for some samples, model 5.0 data resulted in average ADs of 0.36 and 0.17 without and with the ONT-cgMLST-Polisher, respectively. In conclusion, recent ONT Dorado and Medaka models combined with the ONT-cgMLST-Polisher improved ONT sequencing accuracy and made it sufficiently reproducible for genomic surveillance of bacteria. Importance Oxford Nanopore Technologies (ONT) sequencing methodology is especially attractive for small and medium-sized laboratories due to its relatively low capital investment and price per sample consumable costs. However, until recently it lacked accuracy and reproducibility for bacterial genomic genotyping. Here, we present an evaluation of the most recent ONT bioinformatic (basecalling and polishing of consensus) improvements and a new ONT-cgMLST-Polisher tool. We demonstrate that by applying those procedures ONT whole-genome genotyping-based surveillance of bacteria is finally accurate and reproducible enough for routine application even in small laboratories

bioinformatics↗

bioRxiv2025

Pre-training Genomic Language Model with Variants for Better Modeling Functional Genomics

Sequence-to-function models can predict gene expression from sequence data and be used to link genetic information with transcriptomics data to understand regulatory processes and their effects on complex phenotypes. The genomic language models are pre-trained with large-scale DNA sequences and can generate robust representations of these sequences by learning the genomic context. How-ever, few studies can estimate the predictability of gene expression levels and bridge these two classes of models together to explore individualized gene expression prediction. In this manuscript, we propose UKBioBERT as a DNA language model pre-trained with genetic variants from UK BioBank. We demonstrate that UKBioBERT generates informative embeddings capable of identifying gene functions, and improving gene expression prediction in cell lines, thereby enhancing our understanding of gene expression predictability. Building upon these embeddings, we combine UKBioBERT with state-of-the-art sequence-to-function architectures, Enformer and Borzoi, to create UKBioFormer and UKBioZoi. These models exhibit better performance in predicting highly predictable gene expression levels and can be generalized across different cohorts. Furthermore, UKBioFormer effectively captures the relationship between genetic variants and expression variations, enabling in-silico mutation analyses and eQTL identification. Collectively, our findings underscore the value of integrating genomic language models and sequence-to-function approaches for advancing functional genomics research.

bioinformatics↗

bioRxiv2025

GENOMIC LANGUAGE MODELS (GLMS) DECODE BACTERIAL GENOMES FOR IMPROVED GENE PREDICTION AND TRANSLATION INITIATION SITE IDENTIFICATION

Accurate bacterial gene prediction is essential for understanding microbial functions and advancing biotechnology. Traditional methods based on sequence homology and statistical models often struggle with complex genetic variations and novel sequences due to their limited ability to interpret the "language of genes." To overcome these challenges, we explore Genomic Language Models (gLMs) --inspired by Large Language Models in Natural Language Processing-- to enhance bacterial gene prediction. These models learn patterns and contextual dependencies within genetic sequences, similar to how LLMs process human language. We employ transformers, specifically DNABERT, for bacterial gene prediction using a two-stage framework: first, identifying Coding Sequence (CDS) regions, and then refining predictions by identifying the correct Translation Initiation Sites (TIS). DNABERT is fine-tuned on a curated set of NCBI complete bacterial genomes using a k-mer tokenizer for sequence processing. Our results show that GeneLM significantly improves gene prediction accuracy. Compared to Prodigal, a leading prokaryotic gene finder, GeneLM reduces missed CDS predictions while increasing matched annotations. More notably, our TIS predictions surpass traditional methods when tested against experimentally verified sites. GeneLM demonstrates the power of gLMs in decoding genetic information, achieving state-of-the-art performance in bacterial genome analysis. This advancement highlights the potential of language models to revolutionize genome annotation, outperforming conventional tools and enabling more precise genetic insights.

bioinformatics↗

bioRxiv2025

Single cell multi-omic whole genome sequencing and chromatin accessibility profiling reveals genome-epigenome coevolution in colorectal cancer

Epigenetic alterations co-evolve with genetic mutations to drive carcinogenesis and treatment response. Resolving genome-epigenome coevolution requires accurate multi-omic single cell measurement. Here we develop a new technology called "double ATAC" (dATAC) for high-throughput, high-quality, concurrent whole genome sequencing and chromatin accessibility profiling of individual somatic cells. dATAC is a "one pot" method that uses two rounds of tagmentation to sequentially label open chromatin regions and then the whole genome, and produces data of the same quality as current leading single-omic methods. Using colorectal cancer as a model system, we apply dATAC to reveal convergent reorganisation of the epigenome across expanding drug-resistant clones during 5-FU chemotherapy exposure, remarkable stoichiometry of chromatin accessibility at somatic copy number alterations, and the clonal expansion of copy-number altered T cells in the stroma of metastatic disease. dATAC is a robust single cell technology to accurately profile genome-epigenome coevolution across tissues, diseases and species.

molecular biology↗

bioRxiv2025

Unveiling Genomic Rearrangements in Engineered iPSC Lines by Optical Genome Mapping

We demonstrate here the use of optical genome mapping (OGM) to detect genetic alterations arising from gene editing by various technologies in human induced pluripotent stem cells (iPSCs). OGM enables an unbiased and comprehensive analysis of the entire genome, allowing the detection of genomic structural variants (SVs) of all classes with a quantitative variant allele frequency (VAF) sensitivity of 5%. In this pilot study, we conducted a comparative dual analysis between the parental iPSCs and the derived cells that had undergone gene editing using various techniques, including transposons, lentiviral transduction, and CRISPR-Cas9-mediated safe harbor locus insertion at the adeno-associated virus integration site 1 (AAVS1). These analyses demonstrated that iPSCs that had been edited using transposons or lentiviral transduction resulted in a high number of transgene insertions in the genome. In contrast, CRISPR-Cas9 technology resulted in a more precise and limited transgene insertion, with only a single target sequence observed at the intended locus. These studies demonstrate the value of OGM to detect genetic alterations in engineered cell products and suggests that OGM, together with DNA sequencing, could be a valuable tool when evaluating genetically modified iPSCs for research and therapeutic purposes.

molecular biology↗

bioRxiv2025

Geographic distribution of genetic diversity of Heterocephalus glaber analyzed using whole genome sequencing and a chromosome-scale genome assembly

Naked mole-rats (Heterocephalus glaber) are a species of rodent endemic to the Horn of Africa, notable among mammals for their long lifespans, resistances to a variety of stresses, and eusocial mating behavior. Though their natural range extends across large portions of Kenya, Ethiopia, Somalia, and Djibouti, the large majority of genetic and genomic analyses focus on Kenyan specimens. Here, we constructed a chromosome-scale reference genome assembly for H.glaber, along with new reference assemblies of both the Damaraland mole-rat (Fukomys damarensis) and guinea pig (Cavia porcellus) genomes to aid annotation. We leveraged our H.glaber assembly, along with modern whole-genome sequencing, to characterize the genetic diversity of specimens deriving from Kenya, southern Ethiopia, and eastern Ethiopia. We found the Kenyan and southern Ethiopian specimens to be closely related to each other and highly diverged from eastern Ethiopian specimens. We also found specimens collected from nearby locations in southern Ethiopia to be more closely related to Kenyan specimens than to each other. This unexpected distribution of shared genetic diversity highlights the importance of local migration barriers to gene flow in wild H.glaber populations.

ecology↗