Withdrawal from chronic alcohol exposure disrupts brain gene expression and RNA splicing programs. The multifunctional RNA-binding protein PCBP1 has been previously implicated in RNA alternative splicing in the hippocampus during withdrawal from chronic alcohol (ethanol) exposure. However, the transcriptome-wide RNA targets associated with PCBP1 during ethanol withdrawal are not known. Here, we generated a map of PCBP1 RNA binding in the hippocampus of male and female rats following a 24-h withdrawal from chronic ethanol exposure using RNA immunoprecipitation and sequencing (RIP-Seq) with an antibody to PCBP1. No individual PCBP1-associated RNA peak reached significance after correction for multiple testing; therefore, peaks meeting an unadjusted p < 0.01 threshold were considered nominally significant and are referred to here as differentially associated peaks based on this threshold. These peaks showed sex-dependent patterns, with reduced PCBP1 RNA association predominating in males and increased association predominating in females. PCBP1 differentially associated sites on RNA were primarily intronic and mapped to genes involved in synaptic organization, neuronal connectivity, cell adhesion, glutamatergic signaling, and myelination-related pathways. Motif analysis identified heterogeneous sequence features, whereas positional analysis showed enrichment of PCBP1-bound regions near exon–intron boundaries, supporting a link with RNA splicing regulation. Integration of RIP-Seq with hippocampal RNA splicing data further identified candidate PCBP1-associated transcripts that also exhibited differential splicing in males, with enrichment of transcripts in synaptic vesicle cycling, neurotransmitter release and adhesion-related pathways. These findings identify ethanol withdrawal-associated changes in hippocampal PCBP1 RNA binding and highlight PCBP1-associated RNA networks as a potential component of post-transcriptional neuroadaptation during alcohol withdrawal. More broadly, our results implicate PCBP1-associated RNA regulation in synaptic and myelination-related pathways that may contribute to the molecular adaptations occurring during alcohol withdrawal.
Species delimitation within Caryophanales remains challenging due to extensive polyphyly, particularly within the Bacillus subtilis and Bacillus cereus sensu lato groups. We compared multiple genome-based approaches – ANI (FastANI, skani), dDDH, TZMD, and single-copy gene (SCG) phylogenomics – for species assignment of six environmental strains from post-maize cultivation soils, performing comprehensive pairwise comparisons among all available RefSeq genomes at complete and chromosome assembly levels for each taxonomic neighbourhood. Results revealed highly variable species boundaries. Two strains showed unambiguous assignment to B. subtilis and B. licheniformis, with all ANI comparisons exceeding the 95
Oxidative phosphorylation (OXPHOS) is the primary source of cellular adenosine triphosphate (ATP), producing over 90
The Gayal is a rare, semi-domesticated bovine species of considerable ecological and genetic importance, yet its long-term persistence is threatened by small population size and sustained in breeding. To characterize its genomic diversity and evolutionary relationships, we performed whole-genome resequencing of 30 Gayal individuals and jointly analyzed these data with 69 publicly available genomes representing 18 domestic and wild bovine populations. High-quality variants were identified through a unified SNP-calling pipeline, and population genomic analyses were conducted to evaluate genetic diversity, population structure, inbreeding, and signatures of selection. Genetic diversity estimates, including nucleotide diversity, heterozygosity, and ROH-based inbreeding coefficients, consistently indicated markedly reduced genomic variation in Gayal compared with other cattle populations. Linkage disequilibrium decay patterns further supported the presence of historical inbreeding. Principal component analysis (PCA), phylogenetic reconstruction, and ADMIXTURE analysis revealed that Gayal forms a distinct genetic cluster, showing a closer relationship to wild bovines than to local Yunnan cattle. Genome-wide selection scans detected multiple strong selective sweeps, and candidate genes associated with immunity (TRIM77, RASGRP1, API5), meat quality (CLDN18, NAALAD2, DZIP1L, RAB3C), and reproduction (PDE4D). These findings provide new genomic evidence for the independent evolutionary origin of Gayal and highlight the urgent need for conservation strategies to prevent further genetic erosion. The candidate genes and genomic regions identified here provide a foundation for functional validation of the biological traits unique to Gayal and may inform future conservation breeding, germplasm management, and sustainable genetic improvement. Systematically evaluating the genetic diversity and population structure of Gayal provides a theoretical foundation for their conservation and utilisation. Several genes uniquely detected in Gayal, including genes related to immunity (TRIM77, RASGRP1, and API5), meat production (CLDN18, NAALAD2, DZIP1L, RAB3C, and PDE4D).
The Tibetan brown bear (Ursus arctos pruinosus) is an apex predator endemic to the Qinghai-Xizang Plateau (QXP) with crucial ecological status, while high-quality genomic resources for studying its adaptation to the plateau environment remain scarce. Here, we generated a near-T2T chromosome-level genome assembly of a female Tibetan brown bear from QXP, using PacBio HiFi and Hi-C sequencing. The final assembly spans 2.42 Gb, with scaffold N50 of 72.35 Mb, contig N50 of 66.56 Mb and GC content of 42.36
