The effects of runs-of-homozygosity on pig domestication and breeding.

Background: Since their domestication, recent inbreeding together with intensive artificial selection and population bottlenecks have allowed the prevalence of deleterious mutations and the increase of runs-of-homozygosity (ROH) in domestic pigs. This makes pigs a good model to understand the genetic underpinnings of inbreeding depression.

Results: Here we integrated a comprehensive dataset comprising 7239 domesticated pigs and wild boars genotyped by single nucleotide polymorphism (SNP) chips, along with phenotypic data encompassing growth, reproduction and disease-associated traits.

Genome sequencing and assembly of feral chickens in the wild of Sulawesi, Indonesia.

The feralization of domestic chicken makes the conservation and management of red jungle fowl (Gallus gallus) more complicated and challenging. We collected two Sulawesi feral chickens, located east of the Wallace Line, for whole-genome sequencing and de novo genome assembly. Phylogenetic and f4-statistics analyses indicated that the Sulawesi feralized domestic chickens (G.

iDog: a multi-omics resource for canids study.

iDog (https://ngdc.cncb.ac.

Repressor elements provide insights into tissue development and phenotypes in pigs.

Repressor elements significantly influence economically relevant phenotypes in pigs; however, their precise roles and characteristics are inadequately understood. In the present study, we employed H3K27me3 profiling, assay for transposase-accessible chromatin with highthroughput sequencing (ATAC-seq), and RNA sequencing (RNA-seq) data across six tissues derived from three embryonic layers to identify and map 2 034 super repressor elements (SREs) and 22 223 typical repressor elements (TREs) in the pig genome. Notably, many repressor elements were conserved across mesodermal and ectodermal tissues.

VDGE: a data repository of variation database for gene-edited animals across multiple species.

Gene-edited animals are crucial for addressing fundamental questions in biology and medicine and hold promise for practical applications. In light of the rapid advancement of gene editing technologies over the past decade, a dramatically increased number of gene-edited animals have been generated. Genome editing at off-target sites can, however, introduce genomic variations, potentially leading to unintended functional consequences in these animals.

An integrated platform for investigating drug-microbial interactions to support pharmacomicrobiomics studies.

Investigation of drug-microbial interactions has gained prominence due to the increasing need to study pharmacomicrobiomics. Previous research has revealed the microbiome's role in drug metabolism, influencing efficacy, bioavailability, and toxicity. Several potential interactions have reported between drugs and microbes, including bioaccumulation, biotransformation, and the influence of drugs on microbial growth.

Comprehensive evaluation and guidance of structural variation detection tools in chicken whole genome sequence data.

Background: Structural variations (SVs) are widespread across genome and have a great impact on evolution, disease, and phenotypic diversity. Despite the development of numerous bioinformatic tools, commonly referred to as SV callers, tailored for detecting SVs using whole genome sequence (WGS) data and employing diverse algorithms, their performance necessitates rigorous evaluation with real data and validated SVs. Moreover, a considerable proportion of these tools have been primarily designed and optimized using human genome data.

Molecular phylogeny and species diversity of the genus Dichaetophora Duda and related taxa (Diptera: Drosophilidae).

Our intensive surveys of wild drosophilids in East and Southeast Asia discovered a great species diversity (more than 100 putatively new species) of the genus Dichaetophora, which is currently comprised of 67 formally described species assigned into five species groups, i.e., agbo, tenuicauda, acutissima, sinensis and trilobita.

Presence of Flazin in Miso and Identification of Four Tryptophan-Derived ß-Carbolines Formed during Fermentation.

In miso, due to the substantial presence of genistein, flazin is often overlapped and masked by genistein in HPLC analysis. Flazin in the miso extracts could be resolved with genistein through medium-pressure liquid chromatography run under a nonacidified methanol-water system and subsequently fractionated by semipreparative HPLC and identified by NMR spectroscopic analysis. As referenced, flazin was detected in all 11 locally marketed miso products, with contents ranging from 3.

Puzzle Hi-C: An accurate scaffolding software.

High-quality, chromosome-scale genomes are essential for genomic analyses. Analyses, including 3D genomics, epigenetics, and comparative genomics rely on a high-quality genome assembly, which is often accomplished with the assistance of Hi-C data. Curation of genomes reveal that current Hi-C-assisted scaffolding algorithms either generate ordering and orientation errors or fail to assemble high-quality chromosome-level scaffolds.

Hidden hotspots of amphibian biodiversity in China.

Identifying and protecting hotspots of endemism and species richness is crucial for mitigating the global biodiversity crisis. However, our understanding of spatial diversity patterns is far from complete, which severely limits our ability to conserve biodiversity hotspots. Here, we report a comprehensive analysis of amphibian species diversity in China, one of the most species-rich countries on Earth.

Erythrodermic mycosis fungoides: A case report.

Background: Mycosis fungoides is the most common primary cutaneous T-cell lymphoma, whereas generalized erythroderma is rare. In this report, we describe a case of mycosis fungoides with generalized erythroderma using complete clinical data and [18F]fluoroDglucose positron emission tomography/computed tomography (18F-FDG PET/CT) images.

Case Summary: Systemic skin redness with desquamation for three years confirmed mycosis fungoides within one month.

Germline gene fusions across species reveal the chromosomal instability regions and cancer susceptibility.

The canine transmissible venereal tumor (CTVT) is a clonal cell-mediated cancer with a long evolutionary history and extensive karyotype rearrangements in its genome. However, little is known about its genetic similarity to human tumors. Here, using multi-omics data we identified 11 germline gene fusions (GGFs) in CTVT, which showed higher genetic susceptibility than others.

A human-specific insertion promotes cell proliferation and migration by enhancing TBC1D8B expression.

Human-specific insertions play important roles in human phenotypes and diseases. Here we reported a 446-bp insertion (Insert-446) in intron 11 of the TBC1D8B gene, located on chromosome X, and traced its origin to a portion of intron 6 of the EBF1 gene on chromosome 5. Interestingly, Insert-446 was present in the human Neanderthal and Denisovans genomes, and was fixed in humans after human-chimpanzee divergence.

Modeling SHANK3-associated autism spectrum disorder in Beagle dogs via CRISPR/Cas9 gene editing.

Despite intensive studies in modeling neuropsychiatric disorders especially autism spectrum disorder (ASD) in animals, many challenges remain. Genetic mutant mice have contributed substantially to the current understanding of the molecular and neural circuit mechanisms underlying ASD. However, the translational value of ASD mouse models in preclinical studies is limited to certain aspects of the disease due to the apparent differences in brain and behavior between rodents and humans.

Remote regulation of rs80245547 and rs72673891 mediated by transcription factors C-Jun and CREB1 affect expression.

Chronic obstructive pulmonary disease (COPD), the third leading cause of death worldwide, is influenced by genetic factors. The genetic signal rs10516526 in the glutathione S-transferase C-terminal domain containing () gene is a highly significant and reproducible signal associated with lung function and COPD on chromosome 4q24. In this study, comprehensive bioinformatics analyses and experimental verifications were detailly implemented to explore the regulation mechanism of rs10516526 and in COPD.

Target capture sequencing for the first Nigerian genotype I ASFV genome.

African swine fever (ASF) is a contagious viral disease that affects domestic pigs and wild boars, causing significant economic losses globally. After the first Nigerian outbreak in 1997, there have been frequent reports of ASF in pig-producing regions in the country. To facilitate control, it is important to understand the genotype and phylogenetic relationship of ASF viruses (ASFVs).