genomics,genome annotation,

Human leukocyte antigen (HLA) genes play pivotal roles in numerous immunological applications. Given the immense number of polymorphisms, achieving accurate high-throughput HLA typing remains challenging. This study aimed to harness the human pan-genome reference consortium (HPRC) resources as a potential benchmark for HLA reference materials. We meticulously annotated specific four field-resolution alleles for 11 HLA genes (HLA -A , -B , -C , -DPA1 , -DPB1 , -DQA1 , -DQB1 , -DRB1 , -DRB3 , -DRB4 and -DRB5 ) from 44 high-quality HPRC personal genome assemblies...

It has been shown that kinesin family member 20A (KIF20A) is involved in the development of several cancers. However, research on clear cell renal cell carcinoma (ccRCC) and KIF20A is still exploratory. The current research was carried out to determine whether KIF20A expression has any prognosis value in ccRCC. Data were downloaded from The Cancer Genome Atlas (TCGA) database to validate the KIF20A mRNA expression and to perform clinicopathological analysis. Receiver operating characteristic (ROC) curves were used in evaluating KIF20A's diagnostic performance for ccRCC...

PURPOSE: Exercise training during the National Aeronautics and Space Administration (NASA) 70-day bed rest study effectively counteracted the decline in aerobic capacity, muscle mass, strength, and endurance. We aimed to characterize the genomic response of the participants' vastus lateralis (VL) on day 64 of bed rest with and without exercise countermeasures. METHODS: Twenty-two healthy young males were randomized into three groups: 1) bed rest only (n = 7), 2) bed rest + aerobic (6 d/wk) and resistance training (3 d/wk) on standard equipment (n = 7), and 3) bed rest + aerobic and resistance training using a flywheel device (n = 8)...

Vasospasm is a potentially preventable cause of poor prognosis in patients with aneurysmal subarachnoid hemorrhage (aSAH). Epigenetics might provide insight on its molecular mechanisms. We aimed to analyze the association between differential DNA methylation (DNAm) and development of vasospasm. We conducted an epigenome-wide association study in 282 patients with aSAH admitted to our hospital. DNAm was assessed with the EPIC Illumina chip (> 850 K CpG sites) in whole-blood samples collected at hospital admission...

Diploid wild oat Avena longiglumis has nutritional and adaptive traits which are valuable for common oat (A. sativa) breeding. The combination of Illumina, Nanopore and Hi-C data allowed us to assemble a high-quality chromosome-level genome of A. longiglumis (ALO), evidenced by contig N50 of 12.68 Mb with 99% BUSCO completeness for the assembly size of 3,960.97 Mb. A total of 40,845 protein-coding genes were annotated. The assembled genome was composed of 87.04% repetitive DNA sequences. Dotplots of the genome assembly (PI657387) with two published ALO genomes were compared to indicate the conservation of gene order and equal expansion of all syntenic blocks among three genome assemblies...

Cotoneaster glaucophyllus is a semi-evergreen plant that blossoms in late summer, producing dense, attractive, fragrant white flowers with significant ornamental and ecological value. Here, a chromosome-scale genome assembly was obtained by integrating PacBio and Illumina sequencing data with the aid of Hi-C technology. The genome assembly was 563.3 Mb in length, with contig N50 and scaffold N50 values of ~6 Mb and ~31 Mb, respectively. Most (95.59%) of the sequences were anchored onto 17 pseudochromosomes (538...

BACKGROUND: The virome obtained through virus-like particle enrichment contains a mixture of prokaryotic and eukaryotic virus-derived fragments. Accurate identification and classification of these elements are crucial to understanding their roles and functions in microbial communities. However, the rapid mutation rates of viral genomes pose challenges in developing high-performance tools for classification, potentially limiting downstream analyses. FINDINGS: We present IPEV, a novel method to distinguish prokaryotic and eukaryotic viruses in viromes, with a 2-dimensional convolutional neural network combining trinucleotide pair relative distance and frequency...

In the species-rich family Vespertilionidae, vesper yellow bats in the genus Rhogeessa include eleven species, three of them endemic to Mexico. These insectivorous bats provide important ecosystem services, including pest control. Even though some aspects of their biology are well- known, only a few genomic resources are available for these species, which limits our understanding of their biology. In this study, we assembled and annotated the mitochondrial genome of four species: R. aenea, R. genowaysi, R. mira, and R...

Mitochondrial genomes have provided significant insights into the evolution of several insects. A typical mitogenome contains 37 genes, and variations in gene order can indicate evolutionary relationships between species. In this study, we have assembled the first complete mitogenomes of Endecous chape and E. onthophagus and analyzed the phylogenetic implications for the Gryllidea infraorder. We performed DNA extractions and genome sequencing for both Endecous species. Subsequently, we searched for raw data in the Sequence Read Archive (SRA) in NCBI...

The mitochondrial (mt) genome can provide data for phylogenetic analyses and evolutionary biology. Herein, we sequenced and annotated the complete mt genome of Ergasilus anchoratus. This mt genome was 13852 bp long and comprised 13 protein-coding genes (PCGs), 22 tRNAs and 2 rRNAs. All PCGs used the standard ATN start codons and complete TAA/TAG termination codons. A majority of tRNA genes exhibited standard cloverleaf secondary structures, with the exception of one tRNA that lacked the TψC arm (trnC), and three tRNAs that lacked the DHU arm (trnR, trnS1 and trnS2)...

Butyric acid is a volatile saturated monocarboxylic acid, which is widely used in the chemical, food, pharmaceutical, energy, and animal feed industries. This study focuses on producing butyric acid from pre-treated rape straw using simultaneous enzymatic hydrolysis semi-solid fermentation (SEHSF). Clostridium beijerinckii BRM001 screened from pit mud of Chinese nongxiangxing baijiu was used. The genome of C. beijerinckii BRM001 was sequenced and annotated. Using rape straw as the sole carbon source, fermentation optimization was carried out based on the genomic analysis of BRM001...

L1 elements are retrotransposons currently active in mammals. Although L1s are typically silenced in most normal tissues, elevated L1 expression is associated with a variety of conditions, including cancer, aging, infertility and neurological disease. These associations have raised interest in the mapping of human endogenous de novo L1 insertions, and a variety of methods have been developed for this purpose. Adapting these methods to mouse genomes would allow us to monitor endogenous in vivo L1 activity in controlled, experimental conditions using mouse disease models...

Endogenous retroviruses (ERVs) derived from the long terminal repeat (LTR) family of transposons constitute a significant portion of the mammalian genome, with origins tracing back to ancient viral infections. Despite comprising approximately 8% of the human genome, the specific role of ERVs in the pathogenesis of COVID-19 remains unclear. In this study, we conducted a genome-wide identification of ERVs in human peripheral blood mononuclear cells (hPBMCs) and primary lung epithelial cells from monkeys and mice, both infected and uninfected with SARS-CoV-2...

Functional annotation based on Gene Ontology has provided a structured and comprehensive system to access the current knowledge about the function of genes. For model plants such as Arabidopsis thaliana , there is a constant updating and restructuring of the functional annotation that increases the reliability of the analyses that use it. For tomato ( Solanum lycopersicum ), a crop widely used as a model plant for the study of fleshy fruits, there is no functional annotation, at least not freely accessible, even though its genome has long been sequenced and annotated...

SUMMARY: Chromatin accessibility serves as a critical measurement of physical contact between nuclear macromolecules and DNA sequence, providing valuable insights into the comprehensive landscape of regulatory mechanisms, thus we previously developed the OpenAnnotate web server. However, as an increasing number of epigenomic analysis software tools emerged, web-based annotation often faced limitations and inconveniences when integrated into these software pipelines. To address these issues, we here develop two software packages named OpenAnnotatePy and OpenAnnotateR...

Background: Allele-specific expression (ASE) analysis provides a nuanced view of cis-regulatory mechanisms affecting gene expression. Results: An equine ASE analysis was performed, using integrated Iso-seq and short-read RNA sequencing data from four healthy Thoroughbreds (2 mares and 2 stallions) across 9 tissues from the Functional Annotation of Animal Genomes (FAANG) project. Allele expression was quantified by haplotypes from long-read data, with 42,900 allele expression events compared. Within these events, 635 (1...

Humans evolved an extraordinarily expanded and complex cerebral cortex, associated with developmental and gene regulatory modifications 1-3 . Human accelerated regions (HARs) are highly conserved genomic sequences with human-specific nucleotide substitutions. Although there are thousands of annotated HARs, their functional contribution to human-specific cortical development is largely unknown 4,5 . HARE5 is a HAR transcriptional enhancer of the WNT signaling receptor Frizzled8 (FZD8) active during brain development 6 ...

BACKGROUND & AIMS: Irritable bowel syndrome (IBS) shows genetic predisposition, and large-scale genome-wide association studies (GWAS) are emerging, based on heterogeneous disease definitions. We aimed at investigating the genetic architecture of IBS defined according to gold-standard Rome Criteria. METHODS: We conducted GWAS meta-analyses of Rome III IBS and its subtypes in 24,735 IBS cases and 77,149 asymptomatic controls from two independent European cohorts (UK Biobank and Lifelines)...

In this study, we present the complete annotated genome of a novel Salmonella phage, vB_SenS_ST1UNAM. This phage exhibits lytic activity against several Salmonella enterica serotypes, such as S. Typhi, S. Enteritidis, and S. Typhimurium strains, which are major causes of foodborne illness worldwide. Its genome consists of a linear, double-stranded DNA of 47,877 bp with an average G+C content of 46.6%. A total of 85 coding regions (CDS) were predicted, of which only 43 CDS were functionally assigned. Neither genes involved in the regulation of lysogeny, nor antibiotic resistance genes were identified...

Skeletonema tropicum is a marine diatom of the genus Skeletonema that also includes many well-known species including S. marinoi. S. tropicum is a high temperature preferring species thriving in tropical ocean regions or temperate ocean regions during summer-autumn. However, mechanisms of ecological adaptation of S. tropicum remain poorly understood due partially to the lack of a high-quality whole genome assembly. Here, we report the first high-quality chromosome-scale genome assembly for S. tropicum, using cutting-edge technologies including PacBio single molecular sequencing and high-throughput chromatin conformation capture...