The vulnerable goonch catfish Bagarius bagarius is an ecologically important riverine species whose evolutionary history and mitochondrial regulation remain poorly understood. In this study, we generated and analyzed the complete mitogenome of B. bagarius using Oxford Nanopore long-read sequencing with adaptive sampling, followed by de novo assembly, annotation, and comprehensive comparative analyses. The circular mitogenome (16,524 bp) contains the typical vertebrate complement of 13 protein-coding genes, 22 tRNAs, two rRNAs, and a control region, and exhibits pronounced AT richness and strand-specific compositional asymmetry. Phylogenetic reconstruction based on complete mitogenomes robustly resolves B. bagarius as sister to Bagarius yarrelli, confirming the monophyly of the genus and supporting its placement as an early-diverging lineage within Sisorinae. Homoplasy analyses reveal limited recurrent mutation at shallow phylogenetic scales but substantial homoplasy across deeper sisorid divergences, highlighting both the strengths and limits of mitochondrial inference. Nanopore-based modified-base calling identified candidate adenine- and cytosine-associated signals across the mitogenome, with variation in their strand-wise and regional distributions. Because these signals were derived from a single individual and were not independently validated, they are interpreted as preliminary candidate modification patterns rather than definitive evidence of mitochondrial DNA methylation or functional regulation. Overall, this study provides a complete mitogenomic resource for B. bagarius together with an exploratory dataset of nanopore-derived candidate modified-base signals, supporting future phylogenetic, conservation-genetic, and independently validated investigations of mitochondrial DNA modification in fishes.
The rumen microbiome plays a central role in degrading dietary fiber and producing volatile fatty acids, thereby contributing to carcass traits in cattle. Although breed-associated differences in rumen microbial composition have been reported, the microbial characteristics of Japanese Black × Holstein crossbred (F1) cattle, an economically important beef breed in Japan, remain poorly understood. Here, the rumen microbiome of F1 cattle (n = 51) was characterized at both the taxonomic and functional levels using metagenomics and compared it with a previously published Japanese Black (JB) cattle metagenomic dataset to identify microbial features associated with cattle breed and carcass traits. Rumen microbial community structure and functional profiles based on KEGG orthologs and CAZyme families differed significantly between JB and F1 cattle. Comparison of metagenome-assembled genomes (MAGs) abundances between JB and F1 cattle identified a total of 116 MAGs showing significant differences in abundance between the two breeds. F1 cattle were enriched in MAGs affiliated with Ruminococcoides and Prevotella, along with glycoside hydrolase families related to starch metabolism, suggesting a fermentation profile oriented toward readily fermentable carbohydrates. In contrast, JB cattle exhibited enrichment of Ruminococcus- and Verrucomicrobiota-affiliated MAGs harboring glycoside hydrolase families associated with lignocellulose degradation. Functional pathway analysis identified 38 KEGG pathways that differed significantly between JB and F1 cattle, with several amino acid metabolism pathways enriched in F1 cattle. Several MAGs, which harbor diverse glycoside hydrolase families, were significantly correlated with carcass weight and ribeye area in F1 cattle and were positively associated with ruminal acetate proportion, indicating that an acetate-oriented fermentation pattern may contribute to enhanced carcass deposition. These findings reveal distinct taxonomic and functional characteristics of the rumen microbiome in JB and F1 cattle and provide insights into how variation in microbial carbohydrate-processing capacity may be associated with carcass traits such as carcass weight and ribeye area. Together, these results highlight the potential importance of rumen microbial metabolic functions in shaping productivity-related traits in beef cattle.
Parent-of-origin effects (POEs) violate the assumption of additive genetic models by allowing allelic effects to depend on parental origin, yet their mechanistic basis remains incompletely understood. Here, we combine genome-wide POE mapping in an F2 Eurasian pig population with haplotype-resolved transcriptomes and epigenomes from reciprocal crosses. We uncover widespread POEs affecting growth traits, many outside canonical imprinted regions, indicating that canonical imprinting explains only a subset of parent-of-origin-dependent variation. We recapitulate known imprinting effects at loci such as IGF2 and KCNQ1, and link distal POE loci for rib length to IGF2 by long-range chromatin interactions. Strikingly, some POEs emerge from parent-specific 3D chromatin architecture, independent of allele-specific expression or histone marks. Cross-species comparisons nominate additional candidate imprinted genes. Together, our results reveal POEs as pervasive and mechanistically diverse, and show chromatin topology as a plausible candidate mechanism of parental-origin regulation, reshaping our understanding of complex trait inheritance.
Apocynum venetum is an ecologically and medicinally important subshrub with notable stress tolerance, yet its mitochondrial genome (mitogenome) remains uncharacterized. A reference mitogenome is needed to support evolutionary and comparative genomic studies in the Apocynaceae family, where mitogenomic data are currently scarce. Using PacBio HiFi sequencing, we generated the first complete mitochondrial genome assembly of A. venetum, which was subsequently annotated to reveal a 477,173 bp circular molecule with distinctive structural features. Our analysis identified 61 genes, including 38 protein-coding genes (PCGs) exhibiting distinct codon usage bias (particularly GCU for Alanine, RSCU = 1.65) and 439 predicted RNA editing sites, with nad4 showing the highest editing frequency (37 sites). Notably, we discovered: (1) two large repeat sequences (5,554 bp and 2,076 bp) potentially mediating recombination; (2) 19 chloroplast-derived fragments (12,540 bp) containing 11 functional genes, which provide evidence of intracellular gene transfer (IGT); and (3) a total of 333 dispersed repeats, including 187 palindromic, 145 forward repeats and one reverse repeats, highlighting the structural complexity of this mitogenome. Phylogenetic analysis using 34 angiosperm species revealed A. venetum’s closest relationship with Trachelospermum jasminoides, supported by conserved synteny blocks. This study provides the first complete mitogenome reference for A. venetum, revealing abundant repeat content and evidence of chloroplast-to-mitochondrion gene transfer. These resources establish a foundation for future comparative genomic investigations within the Apocynaceae and contribute to the growing repertoire of plant mitochondrial genomes in stress-adapted lineages.
Pigeon meat is increasingly favored by the public for its unique flavor and nutritional value. Previous studies have identified meat quality differences between Mimas pigeon and pigeon Tianxiang 1 strain. To investigate the biological basis of these differences, this study conducted an integrated analysis of intestinal morphology, gut microbiome, and breast muscle metabolomics and transcriptomics. The pigeon Tianxiang 1 strain exhibited enhanced intestinal development and immune characteristics, as evidenced by significantly higher villus height, villus height-to-crypt depth (V/C) ratio, and goblet cell density, along with reduced intestinal wall thickness. Marked differences in ileal microbiota composition were observed between the two breeds. Functional enrichment indicated that the microbiota of pigeon Tianxiang 1 strain was mainly associated with intestinal growth and immune regulation, whereas that of Mimas pigeon was predominantly involved in carbohydrate metabolism and lipid biosynthesis. GO and KEGG enrichment analyses of the breast muscle transcriptome further revealed significant enrichment of lipid metabolism-related pathways in Mimas pigeon, raising the possibility of coordinated variation between intestinal microbial function and muscle metabolism. Exploratory multi-omics correlation analysis showed that Turicibacter and Lactobacillus in pigeon Tianxiang 1 strain were associated with intestinal morphological parameters, whereas Acinetobacter and Pseudomonas in Mimas pigeon were positively associated with the expression levels of KIF2C, BIRC5, PRC1, and RACGAP1 genes, and negatively associated with glycolytic intermediates. The pigeon Tianxiang 1 strain exhibited intestinal morphological features under H E-stained sections that may be associated with improved digestive and absorptive capacity and immune function. Together with its characteristic genera, such as Turicibacter and Lactobacillus, these features may synergistically support intestinal development and immune function, potentially contributing to a greater digestive capacity than that of the Mimas pigeon. In contrast, Mimas pigeon showed an exploratory gut-muscle association pattern in which Acinetobacter and Pseudomonas were associated with higher expression of KIF2C and BIRC5 in breast muscle and with changes in glycolytic metabolism and intramuscular fat deposition. These findings provide candidate links between gut microbiota and meat quality that require further validation in larger and mechanistic studies.
