Search Results (73)

Rare genetic diseases are often caused by structural variants (SVs), such as insertions, deletions, duplications, inversions, and complex rearrangements. However, due to the technical limitations of short-read sequencing, these variants remain underdiagnosed. Long-read sequencing technologies, including Oxford Nanopore and Pacific Biosciences high-fidelity (HiFi), have recently advanced to the point that they can accurately find SVs throughout the genome, including in previously unreachable areas like repetitive sequences and segmental duplications. This study underscores the transformative role of long-read sequencing in diagnosing rare diseases, emphasizing the bioinformatics tools designed for detecting and interpreting structural variants (SVs). Comprehensive methods are reviewed, including methylation profiling, RNA-seq, phasing analysis, and long-read sequencing. The effectiveness and applications of well-known tools like Sniffles2, SVIM, and cuteSV are also assessed. Case studies illustrate how this technique has revealed new pathogenic pathways and solved cases that were previously undetected. Along with outlining potential future paths like telomere-to-telomere assemblies and pan-genome integration, we also address existing issues, including cost, clinical validation, and computational complexity. For uncommon genetic illnesses, long-read sequencing has the potential to completely change the molecular diagnostic picture as it approaches clinical adoption. Full article

Genomic surveillance of SARS-CoV-2 is crucial for detecting emerging variants and informing public health responses. Various sequencing technologies are used for whole genome sequencing of SARS-CoV-2. This cross-platform benchmark study applied established bioinformatics tools to assess and improve the performance of Illumina NovaSeq, Oxford Nanopore Technologies MinION, and Pacific Biosciences Sequel II sequencing platforms in identifying SARS-CoV-2 variants and lineage assignment. NovaSeq produced the highest number of reads and bases, depth of coverage, completeness of consensus genomes, stable mapping coverage across open reading frames in the genome, and consistent lineage assignments. The long-read sequencing platforms had lower yields, sequencing depth, and mapping coverage, limiting the number of qualified sequences for lineage assignment and variant identification. However, implementing proper quality controls on sequence data overcame these limitations and achieved consistent SARS-CoV-2 lineage assignments across all three sequencing platforms. The advancements in library preparation and technology for long-read sequencing are likely to enhance sequence quality and expand genome coverage, effectively addressing current limitations in genome analysis. By merging the unique advantages of both short- and long-read methods, we can significantly improve SARS-CoV-2 genomic surveillance and provide insights into sequencing strategies for other RNA viruses, pending further validation. This may lead to precise tracking of viral evolution and support public health policy decisions. Full article

This study aims to elucidate the characteristics of the mitogenome of Lysmata lipkei and investigate its phylogenetic relationships. Using both the Illumina NovaSeq 6000 (Illumina, Inc., San Diego, CA, USA) and PacBio Sequel II (Pacific Biosciences of California, Inc., Menlo Park, CA, USA) platforms, the complete mitogenome sequence of L. lipkei was determined. The mitogenome of L. lipkei was annotated, measuring 17,497 bp in length and comprising 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs). The nucleotide composition of the genome exhibited an AT bias of 63.4%. Among the PCGs, the most frequently used codon was UUA. All tRNAs, except for trnD, which lacks the TψC loop, were capable of forming the typical cloverleaf structure. Phylogenetic trees for Caridea were constructed using Bayesian Inference (BI) and Maximum Likelihood (ML) methods based on the nucleotide sequences of the 13 PCGs. Both methods yielded consistent topological structures, with L. lipkei showing the closest phylogenetic relationship to L. kuekenthali. Additionally, Lysmatidae, Thoridae, and Hippolytidae formed a monophyletic clade. This research not only filled the gap in mitogenome data for Lysmatidae but also provided novel molecular insights into Caridean phylogenetics. Full article

Examination of venom constituent bioactivities from diverse venomous animals shows certain highly conserved classes, including enzymes (e.g., phospholipases and metalloproteinases) and pore-forming proteins. While antivenoms targeting other unique and lethal venom components have proven to be life-saving, venom-enzyme-driven tissue damage and morbidity persists. Broad-acting enzyme inhibitors demonstrate the potential to augment antivenom approaches. In this study, we investigate the potential utility of certain broad-acting inhibitors in cubozoa for the first time. Fluorogenic assays were used to determine the phospholipase A₂ (PLA₂) and matrix metalloproteinase (MMP) activity of the Hawaiian box jellyfish, Alatina alata, and this was compared to representative elapid, viper, and bee venoms. In vitro, evaluation of selected small-molecule inhibitors demonstrated the ability and feasibility of the broad-acting therapeutic doxycycline, which inhibited the PLA₂ and MMP activity of A. alata (approximately 50% reduction at 0.1 mM (95% CI 0.06–0.15) and 2.1 mM (95% CI 1.4–3.0), respectively), in addition to both snake venoms. Additionally, copper gluconate broadly inhibited the PLA₂ activity of bee, snake, and jellyfish venoms. While all venoms are complex mixtures of bioactive molecules, these studies demonstrate that targeting common class components with broad-acting inhibitors shows promise in clinical and preclinical management. Full article

The discovery of profound differences in the brain microbiota of Alzheimer’s disease (AD) patients and age-matched controls (AMCs) raised questions of postmortem contamination and bacterial transport processes which could be informed by microspatial heterogeneities. We performed semiquantitative species-specific bacterial analyses on multiple micro biopsies from each of the 30 brain specimens (AD and controls). We trimmed ~1 mm of each specimen’s edges for surface contaminants and made multiple sterile biopsy punches of the resultant core of each specimen. To identify species-specific abundances, we used our validated, semiquantitative, full-length 16S rRNA gene pan-domain amplification protocol followed by high-fidelity circular consensus sequencing performed on a Pacific Biosciences Sequel IIe instrument. Statistical analyses showed no significant increase in bacterial abundance on trimmed surfaces compared to core specimens, including C. acnes, the most abundant species previously identified in AD. We did find evidence of substantial bacterial species abundance differences among micro-biopsies obtained from within individual tissue blocks supporting our hypothesis of microspatial heterogeneities. The autopsy brain specimens used in our analyses in this study and our previous publication were not contaminated prior to or postharvesting but we suggest that future microbiological analyses of brain specimens include similar types of edge-core comparison analyses. Further, the species-level bacterial abundance heterogeneities among specimens of the same tissue suggest that multiple symbiotic processes may be occurring. Full article

Hibiscus, which belongs to the Malvaceae family, is primarily distributed in tropical and subtropical regions. Hibiscus species are known for their large, visually striking flowers, which are highly valued for ornamental purposes and are widely admired. Despite this diversity, the mitochondrial DNA of Hibiscus species remains largely unexplored. Here, we assembled chromosome-level mitochondrial genomes (mitogenomes) of H. schizopetalus, H. syriacus, H. hamabo, and Talipariti tiliaceum (Hibiscus tiliaceum) using Illumina short reads (Illumina, Inc., San Diego, CA, USA) and PacBio long reads (Pacific Biosciences of California, Inc., Menlo Park, CA, USA), and conducted comparative genomic analyses. Our findings revealed that the mitogenomes of Hibiscus species exhibited structural complexity, including variable sizes and multi-molecular configurations, while maintaining high conservation in codon usage bias and GC content. Repeat sequence analysis suggested that repeat-mediated homologous recombination played a critical role in frequent recombination events in the mitogenomes. In addition, phylogenetic analysis showed that Hibiscus species did not form a monophyletic clade, and H. hamabo and T. tiliaceum were positioned in sister clades, which was consistent with the results of synteny analysis. To sum up, our study provides valuable resources for phylogenetic research and makes significant contributions to exploring further genetic mechanisms and biodiversity of Hibiscus species. Full article

The Chinese sturgeon (Acipenser sinensis) is an ancient, complex autooctoploid fish species that is currently facing conservation challenges throughout its distribution. To comprehensively characterize the expression profiles of genes and their associated biological functions across different tissues, we performed a transcriptome-scale gene expression analysis, focusing on housekeeping genes (HKGs), tissue-specific genes (TSGs), and co-expressed gene modules in various tissues. We collected eleven tissues to establish a transcriptomic repository, including data from Pacific Biosciences isoform sequencing (PacBio Iso-seq) and RNA sequencing (RNA-seq), and then obtained 25,434 full-length transcripts, with lengths from 307 to 9515 bp and an N50 of 3195 bp. Additionally, 20,887 transcripts were effectively identified and classified as known homologous genes. We also identified 787 HKGs, and the number of TSGs varied from 25 in the liver to 2073 in the brain. TSG functions were mainly enriched in certain signaling pathways involved in specific physiological processes, such as voltage-gated potassium channel activity, nervous system development, glial cell differentiation in the brain, and leukocyte transendothelial migration in the spleen and pronephros. Meanwhile, HKGs were highly enriched in some pathways involved in ribosome biogenesis, proteasome core complex, spliceosome activation, elongation factor activity, and translation initiation factor activity, which have been strongly implicated in fundamental biological tissue functions. We also predicted five modules, with eight hub genes in the brown module, most of which (such as rps3a, rps7, rps23, rpl11, rpl17, rpl27, and rpl28) were linked to ribosome biogenesis. Our results offer insights into ribosomal proteins that are indispensable in ribosome biogenesis and protein synthesis, which are crucial in various cell developmental processes and neural development of Chinese sturgeon. Overall, these findings will not only advance the understanding of fundamental biological functions in Chinese sturgeon but also supply a valuable genetic resource for characterizing this extremely important species. Full article

Advancements in genomics and machine learning have significantly enhanced the study of Salmonella epidemiology. Whole-genome sequencing has revolutionized bacterial genomics, allowing for detailed analysis of genetic variation and aiding in outbreak investigations and source tracking. Short-read sequencing technologies, such as those provided by Illumina, have been instrumental in generating draft genomes that facilitate serotyping and the detection of antimicrobial resistance. Long-read sequencing technologies, including those from Pacific Biosciences and Oxford Nanopore Technologies, offer the potential for more complete genome assemblies and better insights into genetic diversity. In addition to these sequencing approaches, machine learning techniques like decision trees and random forests provide powerful tools for pattern recognition and predictive modeling. Importantly, the study of bacteriophages, which interact with Salmonella, offers additional layers of understanding. Phages can impact Salmonella population dynamics and evolution, and their integration into Salmonella genomics research holds promise for novel insights into pathogen control and epidemiology. This review revisits the history of Salmonella and its pathogenesis and highlights the integration of these modern methodologies in advancing our understanding of Salmonella. Full article

(1) Background: Chitons (Mollusca, Polyplacophora) are relatively primitive species in Mollusca that allow the study of biomineralization. Although mitochondrial genomes have been isolated from Polyplacophora, there is no genomic information at the chromosomal level; (2) Methods: Here we report a chromosome-level genome assembly for Acanthochiton rubrolineatus using PacBio (Pacific Biosciences, United States) reads and high-throughput chromosome conformation capture (Hi-C) data; (3) Results: The assembly spans 1.08 Gb with a contig N50 of 3.63 Mb and 99.97% of the genome assigned to eight chromosomes. Among the 32,291 predicted genes, 76.32% had functional predictions. The divergence time of Brachiopoda and Mollusca was ~550.8 Mya (million years ago), and that of A. rubrolineatus and other mollusks was ~548.5 Mya; (4) Conclusions: This study not only offers high-quality reference sequences for the Acanthochiton rubrolineatus genome, but also establishes groundwork for investigating the mechanisms of Polyplacophora biomineralization and its evolutionary history. This research will aid in uncovering the genetic foundations of molluscan adaptations across diverse environments. Full article

Within the phylum Cnidaria, sea anemones (class Anthozoa) express a rich diversity of ion-channel peptide modulators with biomedical applications, but corollary discoveries from jellyfish (subphylum Medusozoa) are lacking. To bridge this gap, bioactivities of previously unexplored proteinaceous and small molecular weight (~15 kDa to 5 kDa) venom components were assessed in a mouse dorsal root ganglia (DRG) high-content calcium-imaging assay, known as constellation pharmacology. While the addition of crude venom led to nonspecific cell death and Fura-2 signal leakage due to pore-forming activity, purified small molecular weight fractions of venom demonstrated three main, concentration-dependent and reversible effects on defined heterogeneous cell types found in the primary cultures of mouse DRG. These three phenotypic responses are herein referred to as phenotype A, B and C: excitatory amplification (A) or inhibition (B) of KCl-induced calcium signals, and test compound-induced disturbances to baseline calcium levels (C). Most notably, certain Alatina alata venom fractions showed phenotype A effects in all DRG neurons; Physalia physalis and Chironex fleckeri fractions predominantly showed phenotype B effects in small- and medium-diameter neurons. Finally, specific Physalia physalis and Alatina alata venom components induced direct excitatory responses (phenotype C) in glial cells. These findings demonstrate a diversity of neuroactive compounds in jellyfish venom potentially targeting a constellation of ion channels and ligand-gated receptors with broad physiological implications. Full article

The pale chub Zacco platypus (Cypriniformes; Xenocyprididae; Jordan & Evermann, 1902) is widely distributed across freshwater ecosystems in East Asia and has been recognized as a potential model fish species for ecotoxicology and environmental monitoring. Here, a high-quality de novo genome assembly of Z. platypus was constructed through the integration of a combination of long-read Pacific Bioscience (PacBio) sequencing, short-read Illumina sequencing, and Hi-C sequencing technologies. Z. platypus has the smallest genome size compared to other species belonging to the order Cypriniformes. The assembled genome encompasses 41.45% repeat sequences. As shown in other fish, a positive correlation was observed between genome size and the composition of transposable elements (TE) in the genome. Among TEs, a relatively higher rate of DNA transposon was observed, which is a common pattern in the members of the order Cypriniformes. Functional annotation was processed using four representative databases, identifying a core set of 12,907 genes shared among them. Orthologous gene family analysis revealed that Z. platypus has experienced more gene family contraction rather than expansion compared to other Cypriniformes species. Among the uniquely expanded gene families in Z. platypus, detoxification and stress-related gene families were identified, suggesting that this species could represent a promising model for ecotoxicology and environmental monitoring. Taken together, the Z. platypus genome assembly will provide valuable data for omics-based health assessments in aquatic ecosystems, offering further insights into the environmental and ecological facets within this species. Full article

Cancer is a multifaceted disease arising from numerous genomic aberrations that have been identified as a result of advancements in sequencing technologies. While next-generation sequencing (NGS), which uses short reads, has transformed cancer research and diagnostics, it is limited by read length. Third-generation sequencing (TGS), led by the Pacific Biosciences and Oxford Nanopore Technologies platforms, employs long-read sequences, which have marked a paradigm shift in cancer research. Cancer genomes often harbour complex events, and TGS, with its ability to span large genomic regions, has facilitated their characterisation, providing a better understanding of how complex rearrangements affect cancer initiation and progression. TGS has also characterised the entire transcriptome of various cancers, revealing cancer-associated isoforms that could serve as biomarkers or therapeutic targets. Furthermore, TGS has advanced cancer research by improving genome assemblies, detecting complex variants, and providing a more complete picture of transcriptomes and epigenomes. This review focuses on TGS and its growing role in cancer research. We investigate its advantages and limitations, providing a rigorous scientific analysis of its use in detecting previously hidden aberrations missed by NGS. This promising technology holds immense potential for both research and clinical applications, with far-reaching implications for cancer diagnosis and treatment. Full article

Background: Menstrual blood (MB) is a convenient specimen type that can be self-collected easily and non-invasively by women. This study assessed the potential application of MB as a diagnostic specimen to detect genital tract infections (GTIs) and human papillomavirus (HPV) infections in women. Method: Genomic DNA was extracted from MB samples. Pacific Bioscience (Pacbio) 16S ribosomal DNA (rDNA) high-fidelity (HiFi) long-read sequencing and HPV PCR were performed. Results: MB samples were collected from women with a pathological diagnosis of CIN1, CIN2, CIN3 or HPV infection. The sensitivity and positive predictive value (PPV) of high-risk HPV detection using MB were found to be 66.7%. A shift in vaginal flora and a significant depletion in Lactobacillus spp. in the vaginal microbiota communities were observed in the MB samples using 16S rDNA sequencing. Conclusions: In this study, we demonstrated that MB is a proper diagnostic specimen of consideration for non-invasive detection of HPV DNA and genotyping using PCR and the diagnosis of GTIs using metagenomic next-generation sequencing (mNGS). MB testing is suitable for all women who menstruate and this study has opened up the possibility of the use of MB as a diagnostic specimen to maintain women’s health. Full article

The sea star Patiria pectinifera (Asteroidea; Asterinidae; homotypic synonym: Asterina pectinifera; Muller & Troschel, 1842) is widely distributed in the coastal regions of the Seas of East Asia and the northern Pacific Ocean. Here, a de novo genome sequence of P. pectinifera as a reference for fundamental and applied research was constructed by employing a combination of long-read Oxford Nanopore Technology (ONT) PromethION, short-read Illumina platforms, and 10 × Genomics. The draft genome of P. pectinifera, containing 13,848,344 and 156,878,348 contigs from ONT and Illumina platforms, respectively, was obtained. Assembly with CANU resulted in 2262 contigs with an N50 length of 367 kb. Finally, ARCS + LINKS assembly combined these contigs into 328 scaffolds, totaling 499 Mb with an N50 length of 2 Mbp. The estimated genome size by GenomeScope analysis was 461 Mb. BUSCO analysis indicated that 930 (97.5%) of the expected genes were found in the assembly, with 889 (93.2%) being single-copy and 41 (4.3%) duplicated after searching against the metazoan database. Annotation, utilizing sequences obtained from Illumina RNA-Seq and Pacific Biosciences Iso-Seq, led to the identification of 22,367 protein-coding genes. When examining the orthologous relationship of P. pectinifera against the scaffolds of the common sea star Patiria miniata, high contiguity was observed. Annotation of repeat elements highlighted an enrichment of 1,121,079 transposable elements, constituting 47% of the genome, suggesting their potential role in shaping the genome structure of P. pectinifera. This de novo genome assembly is expected to be a valuable resource for future studies, providing insight into the developmental, environmental, and ecological aspects of P. pectinifera biology. Full article

The Chinese soft-shelled turtle (Pelodiscus sinensis), an economically important aquatic species in China, displays considerable sexual dimorphism: the male P. sinensis is larger and, thus, more popular in the market. In this study, we obtained the full-length (FL) transcriptome data of P. sinensis by using Pacific Biosciences (PacBio)’s isoform sequencing and analyzed the transcriptome structure. In total, 1,536,849 high-quality FL transcripts were obtained through single-molecule real-time (SMRT) sequencing, which were then corrected using Illumina sequencing data. Next, 89,666 nonredundant FL transcripts were generated after mapping to the reference genome of P. sinensis; 291 fusion genes and 17,366 novel isoforms were successfully annotated using data from the nonredundant protein sequence database (NR), eukaryotic orthology groups (KOG), the Gene Ontology (GO) project, and the KEGG Orthology (KO) database. Additionally, 19,324 alternative polyadenylation sites, 101,625 alternative splicing events, 12,392 long noncoding RNAs, and 5916 transcription factors were identified. Smad4, Wif1, and 17-β-hsd were identified as female-biased genes, while Nkd2 and Prp18 held a higher expression level in males than females. In summary, we found differences between male and female P. sinensis individuals in AS, lncRNA, genes, and transcripts, which relate to the Wnt pathway, oocyte meiosis, and the TGF-β pathway. Female-biased genes such as Smad4, Wif1, and 17-β-hsd and male-biased genes such as Nkd2 and Prp18 played important roles in the sex determination of P. sinensis. FL transcripts are a precious resource for characterizing the transcriptome of P. sinensis, laying the foundation for further research on the sex-determination mechanisms of P. sinensis. Full article