Genomic Organization Research Articles

The complete mitochondrial genomes of Notropis chlorocephalus and Notropis chiliticus

We present a novel mitogenome assembly of the Redlip Shiner, Notropis chiliticus, and assemblies for the Greenhead Shiner, N. chlorocephalus (Cypriniformes: Leuciscidae). Both are charismatic minnows in the taxonomic group Hydrophlox and are endemic to the eastern United States. The N. chiliticus genome contains 16,711bp and N. chlorocephalus 16,706bp each comprising a total of 13 protein coding genes, 22 tRNAs, two rRNAs, and a control region. Sequence order and genome composition are similar to other Notropis. We provide evidence supporting a monophyletic Hydrophlox, while other phylogenetic relationships within Notropis support convoluted taxonomic revisions throughout the history of the genus.

Randomizing the human genome by engineering recombination between repeat elements.

We lack tools to edit DNA sequences at scales necessary to study 99% of the human genome that is noncoding. To address this gap, we applied CRISPR prime editing to insert recombination handles into repetitive sequences, up to 1697 per cell line, which enables generating large-scale deletions, inversions, translocations, and circular DNA. Recombinase induction produced more than 100 stochastic megabase-sized rearrangements in each cell. We tracked these rearrangements over time to measure selection pressures, finding a preference for shorter variants that avoided essential genes. We characterized 29 clones with multiple rearrangements, finding an impact of deletions on expression of genes in the variant but not on nearby genes. This genome-scrambling strategy enables large deletions, sequence relocations, and the insertion of regulatory elements to explore genome dispensability and organization.

Identification of the shortest species-specific oligonucleotide sequences.

Despite the exponential increase in sequencing information driven by massively parallel DNA sequencing technologies, universal and succinct genomic fingerprints for each organism are still missing. Identifying the shortest species-specific nucleotide sequences offers insights into species evolution and holds potential practical applications in agriculture, wildlife conservation, and healthcare. We propose a new method for sequence analysis termed nucleic "quasi-primes," the shortest occurring sequences in each of 45,076 organismal reference genomes, present in one genome and absent from every other examined genome. In the human genome, we find that the genomic loci of nucleic quasi-primes are most enriched for genes associated with brain development and cognitive function. In a single-cell case study focusing on the human primary motor cortex, nucleic quasi-prime genes account for a significantly larger proportion of the variation based on average gene expression. Nonneuronal cell types, including astrocytes, endothelial cells, microglia perivascular-macrophages, oligodendrocytes, and vascular and leptomeningeal cells, exhibit significant activation of quasi-prime-containing gene associations related to cancer, whereas simultaneously suppressing quasi-prime-containing genes are associated with cognitive, mental, and developmental disorders. We also show that human disease-causing variants, eQTLs, mQTLs, and sQTLs are 4.43-fold, 4.34-fold, 4.29-fold, and 4.21-fold enriched at human quasi-prime loci, respectively. These findings indicate that nucleic quasi-primes are genomic loci linked to the evolution of species-specific traits, and in humans, they provide insights in the development of cognitive traits and human diseases, including neurodevelopmental disorders.

Structural Basis of Differential Gene Expression at eQTLs Loci from High-Resolution Ensemble Models of 3D Single-Cell Chromatin Conformations.

Techniques such as high-throughput chromosome conformation capture (Hi-C) have provided a wealth of information on nucleus organization and genome important for understanding gene expression regulation. Genome-Wide Association Studies (GWASs) have identified numerous loci associated with complex traits. Expression quantitative trait loci (eQTL) studies have further linked the genetic variants to alteration in expression levels of associated target genes across individuals. However, the functional roles of many eQTLs in non-coding regions remain unclear. Current joint analyses of Hi-C and eQTLs data lack advanced computational tools, limiting what can be learned from these data. We developed a computational method for simultaneous analysis of Hi-C and eQTL data, capable of identifying a small set of non-random interactions from all Hi-C interactions. Using these non-random interactions, we reconstructed large ensembles (×105) of high-resolution single-cell 3D chromatin conformations with thorough sampling, accurately replicating Hi-C measurements. Our results revealed many-body interactions in chromatin conformation at the single-cell level within eQTL loci, providing a detailed view of how 3D chromatin structures form the physical foundation for gene regulation, including how genetic variants of eQTLs affect the expression of associated eGenes. Furthermore, our method can deconvolve chromatin heterogeneity and investigate the spatial associations of eQTLs and eGenes at subpopulation level, revealing their regulatory impacts on gene expression. Together, ensemble modeling of thoroughly sampled single-cell chromatin conformations combined with eQTL data, helps decipher how 3D chromatin structures provide the physical basis for gene regulation, expression control, and aid in understanding the overall structure-function relationships of genome organization. It is available at https://github.com/uic-liang-lab/3DChromFolding-eQTL-Loci. Supplementary data are available at Bioinformatics online.

Chromosome distribution of four LTR retrotransposons and 18 S rDNA in coffea eugenioides

Repetitive sequences are recognized for their roles in plant genome organization and function. Mobile elements are notable repeatome sequences due to their intrinsic mutagenic potential, which is related to the origin of adaptive novelties. Understanding the genomic organization and dynamics of the repeatome is fundamental to enlighten their role in plant genome evolution. We aimed to map and assemble the first karyogram for a Coffea species with a closer look at mobile elements. Four LTR-retrotransposons (LTR-RTs) and the 18S rDNA of Coffea eugenioides, a diploid progenitor of the allotetraploid Coffea arabica, were unprecedently mapped in prometaphase/metaphase chromosomes and interphase nuclei. The LTR-RTs included three Ty1/Copia (Bianca, TAR and Tork) and one Ty3/Gypsy (Athila) identified based on homology searches. The four LTR-RTs were mainly distributed in a clustered pattern throughout different portions of the 2n = 22 chromosomes. Athila showed the most intense fluorescence signals and co-located with the secondary constriction of chromosome 3. In addition, the 18S rDNA was mapped in the distal portions of the short arms of chromosome pairs 3 and 5. The obstacles related to obtaining high-quality chromosomes from Coffea species have long been hampering the cytogenomics, which associates in silico analysis with the in situ mapping. Thus, we hope that the results presented here enlighten not only the composition, but also the distribution of mobile elements in the C. eugenioides genome, providing background for further cytogenomic investigations regarding Coffea repeatome.

Some novel field isolates belonging to lineage-1 of the genotype GI-avian infectious bronchitis virus (AIBV) show strong evidence of recombination with field/vaccinal strains.

Avian infectious bronchitis virus (AIBV) infection remains one of the significant challenges for the poultry industry due to the high rates of morbidity, mortality, and poor production performance. The AIBV genome is prone to frequent changes due to the possibility of drift and recombination between various genotypes. Despite the massive administration of several types of vaccines, many outbreaks of AIBV continue to be reported worldwide. One of the major goals of this study was to monitor genetic changes in the viral genomes of some recent field isolates of the AIBV from broiler chickens. To achieve these goals, we tested several pools of tissue specimens (trachea and kidneys) from some suspected AIBV outbreaks in broiler chickens by quantitative real-time PCR (q-RT-PCR). We selected two samples, one from the trachea (IBV-4) and one from the kidney (AIBV-6), for the next-generation sequencing (NGS). The full-length genomes of these two isolates were deposited in the GenBank (Accession Numbers: PQ468962 and PQ468963). The viral genome size of AIBV-4 and AIBV-6 was 27,475 and 27,469 nucleotides in length. AIBV-4 have typical AIBV genome organization (5'UTR, ORF1a, ORF1b, S, 3a, 3b, E, M, 4b, 5a, 5b, N, and 3'UTR), while AIBV-6 lack 5b. These two AIBV isolates belong to sublineage-1 of the genotype GI-1 based on the phylogenetic using the full-length, the S, and the N protein sequences. The S1/S2 cleavage sites show polybasic amino acid sequences (RR-F-RR) as direct evidence of virulence of these isolates. The analysis shows multiple recombination events of these isolates with some natural and vaccine strains. The potential major parent for both AIBV-4 and AIBV-6 was AIBV Beaudette. Active and vigilant monitoring of the AIBV sequences of the currently circulating strains in chickens is highly encouraged to help develop novel vaccines and diagnostic assays that match the field circulating strains.

P-1829. Genomic Characterization of Clinically Significant Isolates and Its Effects on Clinical Outcomes, 2022 to 2024

Abstract Background Antimicrobial resistance has evolved into a complex global issue involving many clinically relevant organisms. Among these pathogens, carbapenem-resistant organisms (CROs) are of particular concern due to their limited treatment options and high mortality rates. In collaboration with Solu, whole-genome sequencing (WGS) was performed on clinical isolates recovered from our patient population to gain a better insight into resistance mechanisms present and their direct effect on clinical outcomes. Methods For genomic characterization (WGS), a total of 109 carbapenem resistant isolates across three clinically relevant bacterial groups (Enterobacterales, Pseudomonas aeruginosa and Acinetobacter baumannii complex) were sequenced. Solu utilized a hybrid assembly approach utilizing both long reads generated with Oxford Nanopore Technologies (ONT) complemented by Illumina short reads for the reconstruction of bacterial genomes. Results Multilocus sequence typing (MLST) revealed genetic diversity among all three groups of bacterial isolates. Among members of the family Enterobacterales, there were eight distinct sequence types: ST-131, ST-1431, ST-167, ST-2155, ST-361, ST-410, ST-685 and ST-405. A. baumannii complex strains mostly comprised of ST-2 and ST-1022. The presence of numerous sequence types was observed with the P. aeruginosa isolates, highlighting the biocomplexity within our patient population. Furthermore, genomic analysis of these isolates disclosed a broad range of antimicrobial resistance genes that span across several classes of antibiotics. Isolates across all genera harbored plasmid-mediated carbapenemase genes bla-NDM-5, bla-NDM1, bla-OXA-48 and bla-OXA23. Interestingly, cefiderocol resistance was primarily associated with the Escherichia coli ST-405 strain containing AMR gene bla-NDM5. Patients associated with a carbapenemase-producing strain were observed to have higher mortality rates (12.8%) and longer length of hospital stay (25.6%). Conclusion By having a comprehensive insight into the genomic composition of isolates that make up our patient population, we can provide a more targeted medical treatment approach and investigate and better prevent transmission events. Disclosures All Authors: No reported disclosures

Metagenomics and Metagenome-Assembled Genomes: Analysis of Cupei from Sichuan Baoning Vinegar, One of the Four Traditional Renowned Vinegars in China

The microbial community in vinegar has primarily been investigated by analyzing short reads to determine operational taxonomic units, but it is also crucial to identify metagenome-assembled genomes (MAGs). In this study, the microbial diversity and functionality in Sichuan Baoning vinegar were examined through deep metagenomic sequencing and metagenomic binning. Results revealed that the most prevalent phylum was Firmicutes, followed by Proteobacteria and unclassified Bacteria. The most abundant bacterial species was Acetilactobacillus jinshanensis, while Saccharomyces cerevisiae was the most prevalent fungal species. The predominant viral species were Hopescreekvirus LfeInf, Myoviridae sp., and Siphoviridae sp. A total of 1395 MAGs were reconstructed, with 660 of them annotated. The majority of MAGs resolved at the species level were attributed to Firmicutes (n = 308), with Acetilactobacillus jinshanensis being the most abundant. According to the average nucleotide identity values, 223 out of the 660 MAGs might represent novel species. The recovered MAGs exhibited biomarker genes indicative of the genetic potential to encode several important secondary metabolites. This study helps to uncover the microbial composition and functional potential of microbial genomes in Sichuan Baoning vinegar.

Rewiring cancer: 3D genome determinants of cancer hallmarks.

In modern cancer biology, Hanahan and Weinberg's classic depiction of the Hallmarks of Cancer serves as a heuristic for understanding malignant phenotypes [1]. Genetic determinants of these phenotypes promote cancer induction and progression, and these mutations drive current approaches to understanding and treating cancer. Meanwhile, for over a century, pathologists have noted that profound alterations of nuclear structure accompany transformation, integrating these changes into diagnostic classifications (Figure 1). Nevertheless, the relationship of nuclear organization to malignant phenotypes has lagged. Recent advances yield profound insight into the 3D genome's relationship with cancer phenotypes, suggesting that spatial genome organization influences many, if not all, of these malignant features. Here, we highlight recent discoveries elucidating connections between 3D genome organization and cancer phenotypes.

ParSite is a multicolor DNA labeling system that allows for simultaneous imaging of triple genomic loci in living cells.

The organization of the human genome in space and time is critical for transcriptional regulation and cell fate determination. However, robust methods for tracking genome organization or genomic interactions over time in living cells are lacking. Here, we developed a multicolor DNA labeling system, ParSite, to simultaneously track triple genomic loci in the U2OS cells. The tricolor ParSite system is derived from the T. thermophilus ParB/ParSc (TtParB/ParSc) system by rational design. We mutated the interface between TtParB and ParSc and generated a new pair of TtParBm and ParSm for genomic DNA labeling. The insertions of 16 base-pair palindromic ParSc and ParSm into genomic loci allow dual-color DNA imaging in living cells. A pair of genomic loci labeled by ParSite could be colocalized with p53-binding protein 1 (53BP1) in response to CRISPR/Cas9-mediated double-strand breaks (DSBs). The ParSite permits tracking promoter and terminator dynamics of the APP gene, which spans 290 kilobases in length. Intriguingly, the hybrid ParS (ParSh) of half-ParSc and half-ParSm enables for the visualization of a third locus independent of ParSc or ParSm. We simultaneously labeled 3 loci with a genomic distance of 36, 89, and 352 kilobases downstream the C3 repeat locus, respectively. In sum, the ParSite is a robust DNA labeling system for tracking multiple genomic loci in space and time in living cells.

High-throughput sequencing: a breakthrough in molecular diagnosis for precision medicine.

High-resolution insights into the nucleotide arrangement within an organism's genome are pivotal for deciphering its genetic composition, function, and evolutionary trajectory. Over the years, nucleic acid sequencing has been instrumental in driving significant advancements in genomics and molecular biology. The advent of high-throughput or next-generation sequencing (NGS) technologies has revolutionized whole genome sequencing, revealing novel and intriguing features of genomes, such as single nucleotide polymorphisms and lethal mutations in both coding and non-coding regions. These platforms provide a practical approach to comprehensively identifying and analyzing whole genomes with remarkable throughput, accuracy, and scalability within a short time frame. The resulting data holds immense potential for enhancing healthcare systems, developing novel and personalized therapies, and preparing for future pandemics and outbreaks. Given the wide array of available high-throughput sequencing platforms, selecting the appropriate technology based on specific needs is crucial. However, there is limited information regarding sample preparation, sequencing principles, and output data to facilitate a comparative evaluation of these platforms. This review details various NGS technologies and approaches, examining their advantages, limitations, and future potential. Despite being in their early stages and facing challenges, ongoing advancements in NGS are expected to yield significant future benefits.

HiCForecast: Dynamic Network Optical Flow Estimation Algorithm for Spatiotemporal Hi-C Data Forecasting.

The exploration of the 3D organization of DNA within the nucleus in relation to various stages of cellular development has led to experiments generating spatiotemporal Hi-C data. However, there is limited spatiotemporal Hi-C data for many organisms, impeding the study of 3D genome dynamics. To overcome this limitation and advance our understanding of genome organization, it is crucial to develop methods for forecasting Hi-C data at future time points from existing time-series Hi-C data. In this work, we designed a novel framework named HiCForecast, adopting a dynamic voxel flow algorithm to forecast future spatiotemporal Hi-C data. We evaluated how well our method generalizes forecasting data across different species and systems, ensuring performance in homogeneous, heterogeneous, and general contexts. Using both computational and biological evaluation metrics, our results show that HiCForecast outperforms the current state-of-the-art algorithm, emerging as an efficient and powerful tool for forecasting future spatiotemporal Hi-C datasets. HiCForecast is publicly available at https://github.com/OluwadareLab/HiCForecast. Supplementary data are available at Bioinformatics online.

De novo genome assembly and annotations of Bombus lapidarius and Bombus niveatus provide insights into the environmental adaptability

Bumblebees are ubiquitous, cold-adapted, primitively eusocial bees and important pollinators for crops and vegetation. However, many species are declining worldwide due to multiple factors, including human-induced habitat loss, agricultural chemicals, global warming, and climate change. In particular, future climate scenarios predict a shift in the spatial distribution of bumblebees under global warming, with some species declining and others potentially expanding. Here, we report a de novo genome assembly and annotation for Bombus lapidarius and Bombus niveatus to decipher species-specific potential genomic capacity against such environmental stressors. With harboring more than 23,000 protein-coding genes, the assembled genomes of B. lapidarius and B. niveatus are 244.44 Mb (scaffold N50 of 9.45 Mb) and 259.84 Mb (scaffold N50 of 10.94 Mb), respectively, which exhibit similar trends in terms of genome size and composition with other bumblebees. Gene family analysis reveals differences in species-specific expanded gene families. B. lapidarius exhibits expanded genes related to pre/postsynaptic organization, while B. niveatus shows a distinct expansion in gene families regulating cellular growth, aging, and responses to abiotic and biotic stressors, such as those containing SCAN domains, WD-repeats, and Ras-related proteins. Our genome-wide screens revealed positive selection on environmental stress-responsive genes such as dip2, yme1l, and spg7 in B. lapidarius, whereas positive selection signatures were found in genes such as myd88, mybbp1A, and rhau, which are involved in environmental stress resistance for B. niveatus. These high-quality genome assemblies and comparative genome analysis unveil potential drivers that underlie genome evolution in bumblebees, offering valuable insights into environmental adaptation and conservation efforts.

Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics

Single-cell three-dimensional (3D) genome techniques have advanced our understanding of cell-type-specific chromatin structures in complex tissues, yet current methodologies are limited in cell throughput. Here we introduce a high-throughput single-cell Hi-C (dscHi-C) approach and its transcriptome co-assay (dscHi-C-multiome) using droplet microfluidics. Using dscHi-C, we investigate chromatin structural changes during mouse brain aging by profiling 32,777 single cells across three developmental stages (3 months, 12 months, and 23 months), yielding a median of 78,220 unique contacts. Our results show that genes with significant structural changes are enriched in pathways related to metabolic process and morphology change in neurons, and innate immune response in glial cells, highlighting the role of 3D genome organization in physiological brain aging. Furthermore, our multi-omics joint assay, dscHi-C-multiome, enables precise cell type identification in the adult mouse brain and uncovers the intricate relationship between genome architecture and gene expression. Collectively, we developed the sensitive, high-throughput dscHi-C and its multi-omics derivative, dscHi-C-multiome, demonstrating their potential for large-scale cell atlas studies in development and disease.

Molecular Characterization of Yellow Mosaic Disease Causing Begomoviruses in Pigeonpea (Cajanus cajan L.) from Three Agro-ecological Zones of India.

Pigeonpea (Cajanus cajan L.) plants exhibiting symptoms of yellow mosaic disease (YMD) were collected in winter 2023 from multiple agricultural fields of Kanpur, Sehore, and Madhubani, representing three different agro-ecological zones in India. The recorded disease incidence ranged from 3 to 5%, 1 to 4%, and 12 to 20% in these zones, respectively. This study aimed to identify and characterize the causal agent, suspected to be a begomovirus, an emerging plant pathogen of pigeonpea causing YMD. Total DNA was extracted from 28 YMD-affected leaf samples and subjected to rolling circle amplification for PCR-based virus detection. Of all the tested samples, one tested positive for mungbean yellow mosaic virus (MYMV), while the remaining tested positive for mungbean yellow mosaic India virus (MYMIV). Subsequently, PCR-based amplification and sequencing of the full-length DNA-A and DNA-B components were conducted. BLASTn analysis revealed that the assembled sequences of the DNA-A and DNA-B components had the highest nucleotide identity with MYMIV (DNA-A: 97-99%, DNA-B: 95-97%) and MYMV (DNA-A: 99%, DNA-B: 98%). Phylogenetic analysis supported these findings. Additionally, the DNA-A and DNA-B components obtained from each sample were found to be cognate, with over 92% similarity in their common region. Thus, the cognate DNA components constituted the isolates of MYMIV and MYMV identified from pigeonpea. The identified isolates exhibited the typical genome organization of an Old World bipartite begomovirus, with no recombination events detected. This study reports, for the first time, the complete annotated genomes of MYMIV from Sehore and Madhubani, as well as MYMIV and MYMV from Kanpur, infecting pigeonpea.

Prevalent integration of genomic repetitive and regulatory elements and donor sequences at CRISPR-Cas9-induced breaks

CRISPR-Cas9 genome editing has been extensively applied in both academia and clinical settings, but its genotoxic risks, including large insertions (LgIns), remain poorly studied due to methodological limitations. This study presents the first detailed report of unintended LgIns consistently induced by different Cas9 editing regimes using various types of donors across multiple gene loci. Among these insertions, retrotransposable elements (REs) and host genomic coding and regulatory sequences are prevalent. RE frequencies and 3D genome organization analysis suggest LgIns originate from randomly acquired genomic fragments by DNA repair mechanisms. Additionally, significant unintended full-length and concatemeric double-stranded DNA (dsDNA) donor integrations occur when donor DNA is present. We further demonstrate that phosphorylated dsDNA donors consistently reduce large insertions and deletions by almost two-fold without compromising homology-directed repair (HDR) efficiency. Taken together, our study addresses a ubiquitous and overlooked risk of unintended LgIns in Cas9 editing, contributing valuable insights for the safe use of Cas9 editing tools.

Comprehensive analysis of 111 Pleuronectiformes mitochondrial genomes: insights into structure, conservation, variation and evolution

BackgroundPleuronectiformes, also known as flatfish, are important model and economic animals. However, a comprehensive genome survey of their important organelles, mitochondria, has been limited. Therefore, we aim to analyze the genomic structure, codon preference, nucleotide diversity, selective pressure and repeat sequences, as well as reconstruct the phylogenetic relationship using the mitochondrial genomes of 111 flatfish species.ResultsOur analysis revealed a conserved gene content of protein-coding genes and rRNA genes, but varying numbers of tRNA genes and control regions across species. Various gene rearrangements were found in flatfish species, especially for the rearrangement of nad5-nad6-cytb block in Samaridae family, the swapping rearrangement of nad6 and cytb gene in Bothidae family, as well as the control region translocation and tRNA-Gln gene inversion in the subfamily Cynoglossinae, suggesting their unique evolutionary history and/or functional benefit. Codon usage showed obvious biases, with adenine being the most frequent nucleotide at the third codon position. Nucleotide diversity and selective pressure analysis suggested that different protein-coding genes underwent varying degrees of evolutionary pressure, with cytb and cox genes being the most conserved ones. Phylogenetic analysis using both whole mitogenome information and concatenated independently aligned protein-coding genes largely mirrored the taxonomic classification of the species, but showed different phylogeny. The identification of simple sequence repeats and various long repetitive sequences provided additional complexity of genome organization and offered markers for evolutionary studies and breeding practices.ConclusionsThis study represents a significant step forward in our comprehension of the flatfish mitochondrial genomes, providing valuable insights into the structure, conservation and variation within flatfish mitogenomes, with implications for understanding their evolutionary history, functional genomics and fisheries management. Future research can delve deeper into conservation biology, evolutionary biology and functional usages of variations.

SMC translocation is unaffected by an excess of nucleoid associated proteins in vivo

Genome organization is important for DNA replication, gene expression, and chromosome segregation. In bacteria, two large families of proteins, nucleoid-associated proteins (NAPs) and SMC complexes, play important roles in organizing the genome. NAPs are highly abundant DNA-binding proteins that can bend, wrap, bridge, and compact DNA, while SMC complexes load onto the chromosome, translocate on the DNA, and extrude DNA loops. Although SMC complexes are capable of traversing the entire chromosome bound by various NAPs in vivo, it is unclear whether SMC translocation is influenced by NAPs. In this study, using Bacillus subtilis as a model system, we expressed a collection of representative bacterial and archaeal DNA-binding proteins that introduce distinct DNA structures and potentially pose different challenges for SMC movement. By fluorescence microscopy and chromatin immunoprecipitation, we observed that these proteins bound to the genome in characteristic manners. Using genome-wide chromosome conformation capture (Hi-C) assays, we found that the SMC complex traversed these DNA-binding proteins without slowing down. Our findings revealed that the DNA-loop-extruding activity of the SMC complex is unaffected by exogenously expressed DNA-binding proteins, which highlights the robustness of SMC motors on the busy chromatin.

Sequence analysis and genome organization of a new marafivirus from Leptochloa chinensis.

High-throughput sequencing was used to identify and characterize a novel marafivirus from the weed Leptochloa chinensis, which was tentatively named "Leptochloa chinensis marafivirus" (LcMV). The complete genome of the virus consists of 6,178 base pairs, and its nucleotide sequence is 73.82% identical to that of Sorghum almum marafivirus, which is a member of the genus Marafivirus within the family Tymoviridae. The LcMV genome contains a relatively large open reading frame (ORF) encoding a single polyprotein (220.6 kDa) with five functional domains (methyltransferase, papain-like protease, helicase, RNA-dependent RNA polymerase, and coat proteins), which is a characteristic of members of this genus. Furthermore, a 16-nucleotide conserved marafibox sequence was identified at nucleotide positions 5341-5356. The coat protein of LcMV is 68.02% identical to that of Sorghum almum marafivirus. Phylogenetic analysis based on nucleotide and polyprotein sequences showed that LcMV is closely related to members of the genus Marafivirus. Our findings support the classification of LcMV as a member of a new species within this genus. This is the first report of a marafivirus infecting Leptochloa chinensis, a very important weed of rice.

A Review of the Molecular Understanding of the Mpox Virus (MPXV): Genomics, Immune Evasion, and Therapeutic Targets

The Mpox virus (MPXV), a zoonotic pathogen from the Orthopoxvirus genus, has emerged as a significant global public health concern, especially after the unprecedented outbreak in 2022. This review synthesizes the MPXV’s molecular features, focusing on its genomic structure, replication mechanisms, immune evasion strategies, and implications for diagnostics and therapeutics. The study examines the virus’s genomic organization utilizing recent peer-reviewed literature, highlighting essential genes like OPG027 and D1L, which contribute to host adaptation, increased transmissibility, and immune evasion. Advances in molecular diagnostics, including real-time PCR and genome sequencing, are reviewed, emphasizing their critical role in outbreak monitoring and control. However, challenges persist, such as diagnostic limitations in resource-constrained settings and the lack of targeted vaccines and antivirals. This review discusses new antiviral candidates, confirmed through computational and in vitro techniques, identifying thymidine kinase and VP39 as key therapeutic targets. Emphasizing the need for genomic surveillance to track adaptive evolution, results show that particular mutations, such as in the OPG027 and D1L genes, increase the transmissibility and immune evasion of the MPXV. These molecular revelations highlight the urgent necessity for better diagnostics catered towards addressing present constraints and developing focused treatments that reduce the effect of the virus. This study emphasizes how these results underscore the need for combined public health plans to handle the changing MPXV epidemiology properly.