Amphioxus, a basal chordate with highly heterozygous genomes (3.2 ~ 4.2% in sequenced species), represents a key model for understanding vertebrate origins. However, the extreme heterozygosity poses challenges for many genomic analyses, including studying meiotic recombination. Here, we present a novel bioinformatic pipeline that enables direct detection of crossover (CO) and non-crossover (NCO) recombination events using short-read whole-genome sequencing of a two-generation pedigree (two parents and 104 F1 offspring) of the amphioxus Branchiostoma floridae. Using parental assemblies generated by Platanus-allee as a custom reference for read alignment, we tracked inheritance patterns in offspring and phased contig-level haplotypes in parents, allowing us to detect recombination events. We identified 2,329 paternal and 2,288 maternal COs, yielding recombination rates of 4.66 cM/Mb and 4.57 cM/Mb, respectively. We found CO coldspots spanning > 140 Mb in each parent and these are likely associated with large-scale heterozygous inversions. CO rates were positively correlated with transposable element and gene density in both sexes, but showed weak or no correlation with GC content. We further identified ~ 10,000 paternal and ~ 5,800 maternal NCO events, predominantly shorter than 200 bp in tract length, and found evidence of GC-biased gene conversion. This work provides the first direct and genome-wide measurement of recombination in amphioxus and demonstrates how high heterozygosity, often considered a barrier, can be leveraged for fine-scale recombination mapping. Our findings illuminate conserved and divergent features of recombination in chordates and establish a framework for studying recombination in other highly heterozygous organisms.

Microplastics (MPs) and bisphenol A (BPA) frequently co-occur in freshwater ecosystems, yet their combined impacts on host–pathogen interactions remain poorly understood. Here, we exposed juvenile largemouth bass (Micropterus salmoides) to environmentally relevant concentrations of MPs, BPA, and their mixture. Co-exposure markedly inhibited NRF2-mediated antioxidant signaling, leading to downregulation of antioxidant enzymes (SOD1, CAT, GPx), elevated hepatic reactive oxygen species and malondialdehyde, and depletion of ATP. These redox disturbances were accompanied by mitochondrial damage, increased expression of pro-apoptotic genes (Bax, Caspase-3), and accumulation of TUNEL-positive nuclei, indicative of apoptosis. Strikingly, only co-exposed fish exhibited enhanced replication of nervous necrosis virus (NNV), a response absent under single exposures. Our findings demonstrate that MPs and BPA act synergistically to disrupt redox homeostasis and compromise antiviral defense, thereby heightening viral susceptibility in a freshwater aquaculture species. This study highlights the overlooked infection risks posed by pollutant mixtures and emphasizes the need to incorporate mixture toxicity into freshwater ecotoxicological risk assessments.

The use of functional microorganisms is a widely adopted, green, and efficient industrial technique for enhancing tobacco leaf quality. These microorganisms accelerate the degradation of macromolecular organic substances. However, their impact on the chemical composition of tobacco leaves across different aging durations and the mechanisms of polysaccharide degradation remain unclear. This study analyzed the degradation patterns of starch, pectin, cellulose, and hemicellulose at different time points (3 h, 2 months, 6 months, 36 months) during the tobacco aging process after the addition of Microbacterium testaceum, and compared the differences in microbial community structure, diversity, and molecular ecological networks. The results showed that compared with sterile water treatment of the tobacco leaf aging process, the exogenous addition of Microbacterium testaceum accelerated the degradation of polysaccharide macromolecules, and the highest degradation rate of starch was 17.4% at the aging stage of 2–6 months, and the highest degradation rate of pectin was 45.46% at the aging stage of 6–36 months. At the same time, the exogenous addition of Microbacterium testaceum altered the microbial community structure during the tobacco aging process by increasing the number of core functional microorganisms, such as Delftia and Proteus, which promoted microorganisms that play a role in material degradation in the ecological environment of tobacco aging. This study provided a theoretical basis for the regulation of interspecific microbial interactions by exogenous functional strains over a broad timescale (from 3 h to 36 months) during tobacco aging, thereby promoting the degradation of polysaccharide macromolecules.

Among eukaryotes, alternative splicing (AS) plays a role in mechanisms involved in processes such as regulation, development, and stress response. In animals, AS mainly functions in tissue development, whereas in plant species, AS plays a major role in stress response, a function additionally mirrored in microalgae. The latter species are highly valued for their ability to produce a variety of useful compounds. Furthermore, their productivity is directly intertwined with stress response, placing the mechanisms behind it in the spotlight. As stress can spur an increased production of pigments, lipids, fatty acids, and carbohydrates utilized in the synthesis of products such as nutraceuticals, pharmaceuticals, and biofuels. Delving into microalgae, we assess AS processes and the regulation of various developmental stages and stress conditions. Additionally, cyanobacteria also have high economic value. As prokaryotes with the ability to undergo self-splicing, research focus has promoted the phylum’s use in biotechnology to catalyze protein splicing. Although self-splicing and AS are two different types of splicing processes, there are some connections between them. For instance, the small nuclear RNA required for AS originates from group II introns. Therefore, this review focuses on elaborating on two distinct but related topics: the AS of microalgae and the three main forms of self-splicing intervening sequences (group I introns, group II introns, and inteins) in cyanobacteria.

The gut microbiome plays pivotal roles in the host’s metabolic response to dietary interventions. Dietary macroalgae supplementation represents a promising strategy for enhancing animal growth and health via microbiome modulation. However, the underlying mechanism of how macroalgae supplementation regulates microbiome-host interactions in aquatic species remains unclear. This study investigated the effects of three dietary macroalgae—Sargassum hemiphyllum (S), Asparagopsis taxiformis (A), and Gracilaria lemaneiformis (G)—each supplemented at 5% in feed, on the gut microbiome and metabolism of grass carp (Ctenopharyngodon idella), using integrated approaches of 16S rRNA sequencing, metagenomics, and metabolomics. While all three macroalgae influenced host growth, supplementation of S provided the most comprehensive benefits, with significant enhancement of body weight and hepatic superoxide dismutase activity. Integrated multi-omics analysis revealed that dietary macroalgae supplementation increased the relative abundance of the key gut bacterial genus Shewanella, with the most notable effect observed in the supplementation of S. Subsequent analysis of a metagenome-assembled genome (MAG) of Shewanella (MAG C3_bin52) demonstrated its considerable potential for amino acid biosynthesis and metabolism. This genomic potential was further supported by metabolomic profiling, which indicated significant upregulation of amino acid-related metabolites, particularly in the supplementation S. Pathway analysis confirmed enrichment in processes associated with protein digestion and absorption, amino acid biosynthesis, and related metabolic pathways. These findings highlight the modulation of a macroalgae-microbiome-metabolite axis in grass carp, primarily mediated by the enrichment of Shewanella in gut ecosystem for enhancing host amino acid metabolism. This study advances understanding of dietary modulation of the gut microbiome and provides insights for the sustainable development of aquaculture.

Feeding strategies critically influence intestinal homeostasis in farmed fish, however, their underlying regulatory mechanisms remain poorly understood. Nibea coibor, a fish species with local characteristics in Zhanjiang (Guangdong Province, China), was chosen as the experimental model for studying feeding strategies. This study employed integrated multi-omics analyses to systematically dissect the multidimensional regulatory networks of four different feeding strategies on intestinal morphology, transcriptome, and microbiota in Nibea coibor. Feeding strategies reshaped gut microbiota composition and significantly altered gene expression. Compared with daytime feeding (DF), continuous fasting (CF) induced villus atrophy and goblet cell loss, disrupted microbial homeostasis (Vibrio, Actinomyces, Photobacterium, and Akkermansia upregulation), and triggered transcriptional reprogramming (pfkfb4, pla2g12b, rptor, and pecam1 downregulation; col1a upregulation). In contrast, intermittent fasting (IF, two-day fasting/one-day feeding) achieved optimal intestinal health with the highest goblet cell density, villus height, and microbial diversity, suggesting microbiota-mediated gut plasticity and adaptation. Nighttime feeding (NF) elicited minor downregulation of energy metabolism genes without causing significant morphological or microbial alterations, indicating limited short-term circadian effects. Finally, the PLS-PM model delineated the cascade regulatory relationships linking gut microbiota, transcriptome, and intestinal morphology. These findings highlight intermittent fasting as a promising strategy to sustain intestinal homeostasis through microbiota-host synergy, while underscoring the risks of prolonged fasting-induced metabolic and barrier dysfunction. This work provides valuable insights for refining feeding protocols in marine fish aquaculture, especially N. coibor.

Trypanosoma brucei, the causative agent of African trypanosomiasis, develops from the long slender (LS) to the short stumpy (SS) form in the mammalian host. The SS trypanosomes are critical for transmission to the insect vector but face significant challenges within the vertebrate host. The role of the immune response in controlling the parasitaemia is well studied, however, the mechanism underpinning the rapid degeneration of SS trypanosomes during the first parasitaemic peak in mice remains somewhat elusive. We demonstrate that fever is a critical yet underexplored factor in facilitating the clearance of SS trypanosomes, suggesting that temperature may play a critical role in regulating the natural turnover of SS trypanosomes. The elevated body temperature correlates with the parasitaemic dynamics, accelerating SS trypanosome elimination in the mammalian host. The SS trypanosomes exhibited high thermo-sensitivity to elevated temperatures, accompanied with apoptosis-like events, mitochondrial damage and oxidative stress. Metabolomic profiling also revealed disruptions in glycolysis and the TCA cycle, shedding light on the processes in compromising the SS trypanosomes. Interestingly, antibodies during the acute phase did not directly cause SS trypanosomes death, but the combination of elevated temperature and antibodies enhanced the clearance of SS trypanosomes, highlighting the critical role of fever in eliminating the first parasitaemic peak. Our findings detail the mechanism of vulnerability of SS trypanosome to elevated temperatures and suggest that host fever serves as a neglected, but critical mechanism, for T. brucei SS trypanosome clearance.

Skeletal muscle serves as a valuable source of nutrition, with distinct muscle fiber types exhibiting different physicochemical properties that influence both meat quality and muscle function. Bama miniature pigs (BM) are recognized for their superior meat quality and their relevance as models for human medical research. Therefore, investigating the differences between slow and fast muscles at various developmental stages (from 57 days post-fertilization to 120 days postnatally) in BM is crucial for both the pork industry and biomedical studies. In this study, we employed a non-targeted data-independent acquisition (nDIA) -based proteomic approach for the first time to porcine embryonic skeletal muscle fibers. A total of 616 differentially expressed genes (DEGs) and 272 differentially abundant proteins (DAPs) were identified in the fast-twitch longissimus dorsi (LD) and slow-twitch semitendinosus (SD) muscles of BM. Domain enrichment analysis and in vitro experiments demonstrated that the NEK3 gene, containing the S_TKc domain, inhibits fast-twitch muscle fiber differentiation postnatally. Additionally, cross-species analysis showed upregulation of skeletal muscle development organ genes in pigs at postnatal day 28. In summary, our results provide both fundamental data and novel insights to further uncover the mechanisms underlying pig skeletal muscle development and muscle fiber transition.