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<i>Oleidesulfovibrio alaskensis</i> G20 is a gram-negative, mesophilic, sulfate-reducing bacterium known for its biofilm-forming and bio-corroding characteristics. A total of 173 new gene annotations have been identified, encoding electron transportation proteins, among others. These genes are …
Read PDFShort-read sequencing has enabled the de novo assembly of several individual human genomes, but with inherent limitations in characterizing repeat elements. Here we sequence a Chinese individual HX1 by single-molecule real-time (SMRT) long-read sequencing, construct …
Read PDFPiperacillin-tazobactam (TZP) resistance in <i>Klebsiella pneumoniae</i> involves diverse mechanisms with unclear prevalence and phenotypic impact. To elucidate these mechanisms, we analyzed <i>K. pneumoniae</i> clinical isolates resistant to TZP but susceptible to cefotaxime and cefepime. Among …
Read PDFThe 2q31 region is commonly associated with pathogenic alleles of the HOXD cluster leading to various clinical phenotypes related to skeletal development. We present a proband with tetralogy of Fallot and multiple congenital anomalies. Genomic …
Read PDFHere, we present the complete genome sequence of a porcine endogenous retrovirus determined by Pacific Biosciences sequencing. A comparison of the genome of this isolate with those of other strains revealed the operation of a …
Read PDFA genetic diagnosis of autosomal-dominant polycystic kidney disease (ADPKD) is challenging due to allelic heterogeneity, high GC content, and homology of the PKD1 gene with six pseudogenes. Short-read next-generation sequencing approaches, such as whole-genome sequencing …
Read PDFDespite the key role of the human ribosome in protein biosynthesis, little is known about the extent of sequence variation in ribosomal DNA (rDNA) or its pre-rRNA and rRNA products. We recovered ribosomal DNA segments …
Read PDFSplicing, including alternative splicing, is a fundamental post-transcriptional mechanism in eukaryotes that generates functional proteins and transcript diversity. Canonical splicing follows well-defined rules, such as sufficient intron and exon lengths, specific splice junction orientations, consensus …
Read PDFAAV integration has become an important safety consideration in gene therapy. However, accurately determining integration sites remains challenging due to biases introduced by library preparation methods, sequencing technologies, and bioinformatic pipelines. In this study, we …
Read PDFNumerous proteins display pleiotropic functions in different clinical contexts. However, the molecular mechanism underlying such effects is rarely understood. Speckle-type POZ protein (<i>SPOP</i>) is a typical example, exhibiting tumor-suppressing or tumor-promoting effects in different tumor …
Read PDF<h4>Background</h4>Many neurodegenerative diseases are caused by nucleotide repeat expansions, but most expansions, like the C9orf72 'GGGGCC' (G<sub>4</sub>C<sub>2</sub>) repeat that causes approximately 5-7% of all amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) cases, are too …
Read PDFAmplification of DNA is required as a mandatory step during library preparation in most targeted sequencing protocols. This can be a critical limitation when targeting regions that are highly repetitive or with extreme guanine-cytosine (GC) …
Read PDFPolyploidization contributes to the complexity of gene expression, resulting in numerous related but different transcripts. This study explored the transcriptome diversity and complexity of the tetraploid Arabica coffee (Coffea arabica) bean. Long-read sequencing (LRS) by …
Read PDFLong-read sequencing technologies are transforming our ability to assemble highly complex genomes. Realizing their full potential is critically reliant on extracting high-quality, high-molecular-weight (HMW) DNA from the organisms of interest. This is especially the case …
Read PDFAccurate and comprehensive characterization of genetic variation is essential for deciphering the genetic basis of diseases and other phenotypes. A vast amount of genetic variation stems from large-scale sequence changes arising from the duplication, deletion, …
Read PDFIGH@ proto-oncogene translocation is a common oncogenic event in lymphoid lineage cancers such as B-ALL, lymphoma and multiple myeloma. Here, to investigate the interplay between IGH@ proto-oncogene translocation and IGH allelic exclusion, we perform long-read …
Read PDF<h4>Background</h4>Ctenocephalides felis is a common ectoparasite of dogs and cats and can transmit a variety of pathogens including Bartonella and Rickettsia species. These bacteria, along with the known endosymbiont Wolbachia, are well-documented members of the …
Read PDFIt is widely acknowledged that transcriptional diversity largely contributes to biological regulation in eukaryotes. Since the advent of second-generation sequencing technologies, a large number of RNA sequencing studies have considerably improved our understanding of transcriptome …
Read PDFRNA sequencing (RNA-seq) technologies enable comprehensive transcriptomic profiling, yet systematic comparisons using identical biological samples remain limited. Here, we performed a multi-faceted comparison of long-read (PacBio) and short-read (Illumina) RNA-seq using the same RNA from …
Read PDF<h4>Background</h4>Identifying the genetic basis of hypotonia and muscle weakness is critical for patient management and family counseling. However, diagnosis is often hindered by diverse genomic alterations, including repeat expansions, structural variants (SVs), and methylation defects. …
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