Search Results (91)

Background: Complete environmental adaptation requires both survival and reproductive success. The hypoxic Qinghai-Tibet Plateau (>3000 m) challenges reproduction in indigenous species. Tibetan sheep, a key plateau-adapted breed, possess remarkable hypoxic tolerance, yet the genetic basis of their reproductive success remains poorly understood. Methods: We integrated transcriptomic and genomic data from Tibetan sheep and two lowland breeds (Small-tailed Han sheep and Hu sheep) to identify Tibetan sheep reproduction-associated genes (TSRGs). Results: We identified 165 TSRGs: four genes were differentially expressed (DEGs) versus Small-tailed Han sheep, 77 DEGs versus Hu sheep were found, and 73 genes were annotated in reproductive pathways. Functional analyses revealed enrichment for spermatogenesis, embryonic development, and transcriptional regulation. Notably, three top-ranked selection signals (VEPH1, HBB, and MEIKIN) showed differential expression. Murine Gene Informatics (MGI) confirmed that knockout orthologs exhibit significant phenotypes including male infertility, abnormal meiosis (male/female), oligozoospermia, and reduced neonatal weight. Conclusions: Tibetan sheep utilize an evolved suite of genes underpinning gametogenesis and embryogenesis under chronic hypoxia, ensuring high reproductive fitness—a vital component of their adaptation to plateaus. These genes provide valuable genetic markers for the selection, breeding, and conservation of Tibetan sheep as a critical genetic resource. Full article

Background/Objectives: Scutiger ningshanensis (Fang, 1985) is an endemic Chinese amphibian species within the genus Scutiger (Megophryidae). Despite its ecological significance, its mitochondrial genome architecture and evolutionary relationships remain poorly understood. Given the high structural variability in Megophryidae mitogenomes and unresolved phylogenetic patterns in Scutiger, this study aims to (1) characterize the complete mitogenome of S. ningshanensis, (2) analyze its molecular evolution, and (3) clarify its phylogenetic position and divergence history within Megophryidae. Methods: The complete mitochondrial genome was sequenced and annotated, followed by analyses of nucleotide composition, codon usage bias, and selection pressures (Ka/Ks ratios). Secondary structures of rRNAs and tRNAs were predicted, and phylogenetic relationships were reconstructed using maximum likelihood and Bayesian methods. Divergence times were estimated using molecular clock analysis. Results: The mitogenome of S. ningshanensis is 17,282 bp long, encoding 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and a control region, with a notable AT bias (61.05%) with nucleotide compositions of T (32.51%), C (24.64%), G (14.3%), and A (28.54%). All tRNAs exhibited cloverleaf structures except trnS1, which lacked a DHU stem. Phylogenetic analysis confirmed the monophyly of Scutiger, forming a sister clade to Oreolalax and Leptobrachium, and that S. ningshanensis and S. liubanensis are sister species with a close evolutionary relationship. Positive selection was detected in Atp8 (Ka/Ks > 1), suggesting adaptation to plateau environments, while other PCGs underwent purifying selection (Ka/Ks < 1). Divergence time estimation placed the origin of Megophryidae at~47.97 MYA (Eocene), with S. ningshanensis diverging~32.67 MYA (Oligocene). Conclusions: This study provides the first comprehensive mitogenomic characterization of S. ningshanensis, revealing its evolutionary adaptations and phylogenetic placement. The findings enhance our understanding of Megophryidae’s diversification and offer a genomic foundation for future taxonomic and conservation studies. Full article

Background: Antibiotics at sub-inhibitory concentrations can rewire bacterial regulatory networks, impacting virulence. Objective: The way that exposure to selected antibiotics (ciprofloxacin, amikacin, azithromycin, ceftazidime, and meropenem) below their minimum inhibitory concentration (sub-MIC) modulates the physiology of Pseudomonas aeruginosa is examined in this study using growth-phase-resolved analysis. Methods: Standard P. aeruginosa strain cultures were exposed to ¼ and ½ MIC to determine the growth kinetics under antibiotic stress. The study measured protease and pyocyanin production and the expression level of important quorum sensing and virulence genes (lasI/R, rhlI/R, pqsR/A, and phzA) at different growth phases. Results: Meropenem produced the most noticeable growth suppression at ½ MIC. Sub-MIC antibiotics did not completely stop growth, but caused distinct, dose-dependent changes. Azithromycin eliminated protease activity in all phases and had a biphasic effect on pyocyanin. Ciprofloxacin consistently inhibited both pyocyanin and protease in all phases. The effects of amikacin varied by phase and dose, while β-lactams markedly increased pyocyanin production during the log phase. In contrast to the plateau phase, when expression was often downregulated or unchanged, most quorum-sensing- and virulence-associated genes showed significant upregulation during the death phase under sub-MIC exposure. Conclusions: These findings indicate that sub-MIC antibiotics act as biochemical signal modulators, preserving stress-adapted sub-populations that, in late growth phases, activate quorum sensing and stress tolerance pathways. Full article

As high-quality sheep germplasm resources in China, Hu sheep are characterized by fast growth and development, high fecundity, and tolerance to drought and cold. Tibetan sheep, adapted to high-altitude environments, have developed strong environmental adaptability. To explore the differences in the interaction among rumen microbial flora, hepatic gluconeogenesis, and mitochondrial function between Tibetan sheep and Hu sheep in the Qinghai–Tibet Plateau, this study systematically compared and analyzed the rumen flora density, key enzyme activities related to hepatic gluconeogenesis and mitochondrial function, and the expression levels of related genes in Tibetan sheep and Hu sheep under identical feeding management conditions, followed by correlation analysis. The results showed that Hu sheep had significantly higher densities of Ruminobacteramylophilus (Ram) and Fibrobacter succinogenes (Fs) associated with starch and protein degradation (p < 0.01). The expression levels of Forkhead box O1 (FOXO1), pyruvate carboxylase (PC) activity, and adenosine triphosphate (ATP) content were also significantly higher than those in Tibetan sheep (p < 0.01). In contrast, Tibetan sheep had higher densities of Butyrivibrio fibrisolvens (Bf), Ruminococcus albus (Ra), Ruminococcus flavefaciens (Rf), etc., related to cellulose degradation (p < 0.01). The gluconeogenesis-related genes, Glucose-6-phosphatase catalytic subunit 1 (G6PC1) and phosphoenolpyruvate carboxykinase1 (PCK1), and the activities of phosphoenolpyruvate carboxykinase (PEPCK) and fructose-1,6-bisphosphatase (FBPase) were significantly higher in Tibetan sheep than in Hu sheep (p < 0.01). Mitochondrial function-related genes Mitofusin-1 (Mfn1), Mitofusin-2 (Mfn2), subunit 6 of ATP synthase (ATP6), cytochrome b (Cytb), etc., also showed significantly higher expression in Tibetan sheep (p < 0.01). While no significant differences were observed in the contents of citric acid (CA), pyruvic acid (PA), glucose (Glu), etc. (p > 0.05). Correlation analysis indicated that rumen flora was associated with the key enzyme activities and gene expressions of hepatic gluconeogenesis and mitochondrial function to varying degrees. In summary, Tibetan sheep exhibit strong fiber degradation capacity, the efficient utilization of gluconeogenic intermediates, and mitochondrial oxidative phosphorylation (OXPHOS) ability, forming adaptive strategies for high-altitude environments. By contrast, Hu sheep show efficient protein and starch degradation capacity, thereby enhancing the supply of gluconeogenic precursors. It is indicated that when introducing Hu sheep to high-altitude areas, dietary intervention can be used to regulate rumen microorganisms, such as increasing fiber-decomposing bacteria or enhancing mitochondrial oxidative capacity, to counteract metabolic limitations induced by hypoxia. Full article

Hyperosmolality-gated calcium-permeable cation channel protein denoted as OSCA, which are mechanosensitive pore-forming ion channels, play a pivotal role in plants’ responses to abiotic stressors. Notopterygium franchetii, an endemic perennial plant species distributed in the Qinghai–Tibetan Plateau and its adjacent high-altitude regions, is likely to have undergone adaptive evolution in response to extreme abiotic stress conditions. The current study was conducted to characterize the genome-wide characteristics and phylogenetic evolution of the OSCA gene family in N. franchetii and identify its response patterns to drought and high-temperature stresses. We examined the gene family’s structural features, phylogenetic relationships, and response to abiotic stresses. The N. franchetii genome had 29 OSCA gene family members on 11 chromosomes. Subcellular localization showed they were mainly in the cell membrane, and a promoter cis-acting element study found that the OSCA gene family contained methyl jasmonate, abscisic acid, and various adversity and hormone response components. Under drought stress, most of the NofOSCAs genes showed a tendency to increase over time in the roots of N. franchetii, while in the aboveground parts, most of the NofOSCAs genes showed a tendency to increase and then decrease. The expression of different NofOSCAs genes in N. franchetii also showed alternating changes under high-temperature stress. Nine members of NofOSCAs were found to be linked to the PPI network, and these members were involved in membrane structure, transmembrane transport, and ion channel function. Our analysis of differential expression revealed that the expression of OSCA genes differed among the different N. franchetii tissues, with the roots exhibiting the highest average expression level, and many genes displayed tissue-specific high expression patterns. These results provided novel insights into the phylogenetic evolution and abiotic stress response mechanisms in the high-altitude medicinal herb N. franchetii. Full article

The plateau environments are always harsh, with low pressure, low oxygen, and low temperature, which are detrimental to the survival of organisms. The Qinghai toad-headed lizard Phrynocephalus vlangalii has a wide range of altitude adaptation from 2000 to 4600 m. But it is still unclear how organisms maintain tissue function by balancing energy supply and demand changes in high-altitude environments of P. vlangalii. We investigated the plateau metabolic adaptation through transcriptome and metabolome analyses of P. vlangalii from three populations at different altitudes of the Qinghai-Tibet Plateau. The genes related to carbohydrate metabolism were significantly down-regulated at the high altitude. The metabolites alpha-D-glucose 1-phosphate, beta-D-fructose 6-phosphate, D-glycerate 1,3-diphosphate, 3-phosphoglycerate, and phosphoenolpyruvate in glycolysis/gluconeogenesis were down-regulated, too. The lipid metabolic and fatty acid synthase-related genes were up-regulated at a high altitude. In conclusion, the glycogen utilization-related genes and metabolites experienced broad down-regulation, while lipid-related genes and metabolites had a clear trend of up-regulation. Thus, we suggest that P. vlangalii tends to increase lipid utilization and reduce the dependence on glycogen consumption to acclimatize to the high-altitude environment. Full article

‘Dianheyou615’ (DHY615) is an elite Dian (D1)-type hybrid japonica rice variety, renowned for its high yield, exceptional grain quality, and unique adaptability to both irrigated and rainfed conditions in the Yungui Plateau of southwestern China. However, the genetic mechanisms underlying the agronomic performance of the D1-type hybrid japonica rice remain unclear. In this study, a comprehensive analysis of ‘DHY615’’s agronomic performance, genetic genealogy, and molecular genetic foundation was conducted to dissect its desirable traits for upland rainfed cultivation across diverse ecological environments. The main findings indicate that ‘DHY615’ possesses 6432 heterozygous SNPs, with 57.48% and 14.43% located in the promoter and coding regions, respectively, potentially affecting key phenotypic traits. High-impact SNPs variants and numerous well-known functional genes were identified, such as OsAAP6, GS3, Sd1, Rf1, BADH2, BPh14, Rymv1, OsFRO1, NRT1.1B, SKC1, OsNCED2, and qUVR-10, which are likely linked to traits including plant architecture, grain yield, grain quality, and resistance to various biotic and abiotic stresses (e.g., disease, cold, drought, salt, high iron, and high UV radiation). Notably, ‘Nan615’ harbors a greater number of functional allele variants compared to ‘H479A’, which potentially explaining its superior grain yield and remarkable adaptability. This study offers novel and valuable insights into the molecular genetic foundation of the plateau D1-type hybrid japonica rice, underscoring its potential for sustainable rice production across diverse ecological zones, especially with its unparalleled high-altitude adaptability to rainfed upland planting. Full article

(1) Background: Hippophae gyantsensis, a drought-tolerant plant native to the Tibetan Plateau, plays a crucial ecological and economic role. While its drought tolerance mechanisms have been extensively studied, the role of alternative splicing (AS) in drought resistance remains insufficiently explored. This study aims to elucidate how AS events regulate gene expression to enhance drought tolerance in H. gyantsensis under water-deficit conditions. (2) Methods: H. gyantsensis plants were subjected to progressive drought stress followed by rehydration. Physiological responses, transcriptomic data, and hormonal profiles were analyzed to investigate the plant’s adaptive mechanisms to drought stress, with a particular focus on abscisic acid (ABA) signaling-related genes. (3) Results: The results showed that H. gyantsensis maintained high leaf water content even under severe drought stress, emphasizing its strong drought resistance. A transcriptomic analysis revealed 11,962 differentially expressed genes, primarily enriched in hormone signaling and metabolic pathways. Notably, the accumulation of ABA was closely associated with AS events in ABA-related genes, such as ZEPs, ABCG, and PP2C. These genes produced multiple splice variants, indicating their role in modulating the ABA signaling pathway and enhancing drought tolerance. (4) Conclusions: This study highlights the pivotal role of AS in ABA signaling and drought tolerance in H. gyantsensis. It provides new insights into how AS contributes to plant adaptation to drought stress, bridging the knowledge gap in drought resistance mechanisms and emphasizing the importance of AS in plant stress responses. Full article

The Bazhou yak, a major native meat yak breed in Xinjiang, China, is renowned for its fast growth rate, strong adaptability, and particularly high intramuscular fat (IMF) content. However, limited knowledge regarding its phylogenetic history and genomic composition has hindered its long-term conservation and utilization. This study evaluated the genetic diversity, population phylogenetics, and genome-wide selective sweep analysis (GWSA) of 100 newly obtained Bazhou yaks through genome resequencing, as well as 340 public yak genomes from nine other populations on the Qinghai–Tibet Plateau. The results revealed moderate diversity, lower genomic inbreeding levels, and rapid linkage disequilibrium (LD) decay in Bazhou yaks. Principal component analysis (PCA) and phylogenetic analysis showed a clear separation of Bazhou yaks from other yak populations, indicating the Bazhou yak as an independent genetic population. Furthermore, less genetic differentiation was found between the Bazhou yak and the Huanhu yak, while ADMIXTURE analysis revealed a common ancestral lineage between Bazhou yaks and Huanhu yaks, indicating an important genetic contribution of the Qinghai yak population to Bazhou yaks. The GWSA identified a total of 833 selected genes in Bazhou yaks using the top 5% interaction windows of both parameters (F_ST, Pi ratio, and XP-EHH). A significant number of these genes are related to fat synthesis and deposition, such as MTOR, APOA1, and GPAT4. In summary, this study sheds light on the phylogenetic status and distinctive genomic features of Bazhou yaks, which facilitates our understanding of the genetic basis of the IMF phenotype in Bazhou yaks. Full article

The plateau pika (pl-pika), a resilient mammal of the Qinghai-Tibet Plateau, exhibits remarkable adaptations to extreme conditions. This study delves into mutations within the Endothelial PAS Domain Protein 1 (EPAS1) gene, crucial for high-altitude survival. Surprisingly, a novel 6-bp insertion/deletion (indel) mutation in EPAS1’s Intron 13, along with an additional repeat unit downstream, was discovered during PCR amplification. Genetic analysis across altitude gradients revealed a correlation between this indel’s frequency and altitude, hinting at its role in altitude adaptation. Fluorescence enzyme assays unveiled enhancer activity within Intron 13, where the deletion of repeat units led to increased activity, indicating potential transcription factor binding. Notably, GCM1 emerged as a candidate transcription factor binding to the indel site, suggesting its involvement in EPAS1 regulation. These findings enrich our comprehension of high-altitude adaptation in plateau pikas, shedding light on the intricate interplay between genetic mutations, transcriptional regulation, and environmental pressures in evolutionary biology. Full article

Background: The Niemann–Pick C2 (NPC2) gene family plays an important role in olfactory communication, immune response, and the recognition of host plants associated with environmental adaptation for insects. Methods: In this study, we conducted a genomic analysis of the structural characteristics and physicochemical properties of the NPC2 genes of eleven butterfly species available, focusing on the alpine Parnassius species, especially Parnassius glacialis, to investigate their duplication and expression patterns. Results: Our results indicate that a significant expansion of NPC2 genes was detected in P. glacialis compared to other butterflies; in addition, the expansion of these unevenly distributed P. glacialis NPC2 chromosome genes was shaped by tandem duplication mediated by transposons. Furthermore, the PgNPC2 genes had relatively higher expression in P. glacialis antennae and other head tissues. These facts were verified by quantitative real-time PCR (qRT-PCR). Conclusions: These findings suggest that the expansion of NPC2 genes may have contributed to the local adaptation of P. glacialis during its dispersal ‘out of the Qinghai–Tibet Plateau’, although further functional tests are needed to confirm their specific role in this adaptive process. Full article

Plant growth-promoting rhizobacteria (PGPR) are beneficial bacteria residing in the rhizosphere and are capable of enhancing plant growth through various mechanisms. Streptomyces sp. GD-4 is a plant growth-promoting bacterium isolated from the rhizosphere soil of Leymus secalinus. To further elucidate the molecular mechanisms underlying the beneficial effects of the strain on plant growth, we evaluated the growth-promoting effects of Streptomyces sp. GD-4 on forage grasses and conducted comprehensive genome mining and comparative genomic analysis of the strain. Strain GD-4 effectively colonized the rhizosphere of three forages and significantly promoted the growth of both plant roots and leaves. Genome sequence functional annotation of GD-4 revealed lots of genes associated with nitrogen, phosphorus, and sulfur metabolism. Additionally, genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, and phosphate solubilization were annotated. Whole-genome analysis revealed that GD-4 may possess molecular mechanisms involved in soil nutrient cycling in rhizosphere soil and plant growth promotion. The bacteria also possess genes associated with adaptability to abiotic stress conditions, further supporting the ability of Streptomyces sp. GD-4 to colonize nutrient-poor soils. These findings provide a foundation for further research into soil remediation technologies in plateau regions. Full article

The extreme environmental conditions of the Qinhai–Tibetan Plateau (QTP) challenge livestock survival and productivity, yet little is known about how high-altitude environments impact the gut microbiota of dairy cows. To fill this gap, we systematically investigated the differences in the hindgut microbiome between 87 plateau Holstein cows and 72 plain Holstein cows using 16S rRNA gene sequencing. Our analysis revealed that the hindgut microbiota of the plateau group exhibited lower species richness but higher evenness than that in the plain group. Additionally, significant separation in hindgut microbiota composition between the two groups was observed based on altitude, while parity, days in milk, and age did not show a comparable impact. Moreover, altitude had a lasting impact on bacterial communities and their co-occurrence networks, resulting in reduced microbial interactions and lower modularity in the plateau group. Furthermore, we identified four key microbial taxa, the Bacteroidaceae and Rikenellaceae families, as well as the Prevotella and Treponema genera, which were associated with the regulation of carbohydrate digestion and energy metabolism and might help the Holstein cows adapt to the plateau environment. Our findings provide insights into strategies for enhancing the adaptability of dairy cows to high-altitude environments through microbiota modulation, which could ultimately contribute to improving livestock management and sustainability in these extreme environments. Full article

Yaks are a rare and unique animal species inhabiting the Qinghai–Tibet Plateau; they are renowned for their remarkable ability to thrive in harsh environments. Milk-derived exosomes, tiny vesicles containing various biological molecules, play crucial roles in numerous pathological and physiological processes, including cell growth, development, and immune regulation. This study delved into the microRNA expression profiles of yak milk-derived exosomes collected from both high- and low-altitude populations using small RNA sequencing. These miRNAs were found to be implicated in pathways associated with mammary gland inflammation, virus infection regulation, and heat stress response. Functional enrichment analyses, utilizing GO and KEGG databases, revealed that the target genes of these differentially expressed miRNAs are enriched in signaling pathways crucial for Th17 cell differentiation and the Ras-MAPK signaling pathway. In conclusion, this research illuminates the adaptive mechanisms of yaks through the differential expression of miRNAs in their milk-derived exosomes across varying environmental conditions. These findings provide a valuable foundation for future investigations into yak resilience and the potential of milk-derived exosomes as tools for disease management and immune modulation. Full article

Schizothoracine fishes in saltwater lakes of the Tibetan Plateau are important models for studying the evolution and uplift of the Tibetan Plateau. Examining their adaptation to the high-salt environment is interesting. In this study, we first assembled the RNA-Seq data of each tissue of G. przewalskii, G. selincuoensis, and G. namensis from Qinghai Lake, Selincuo Lake, and Namtso Lake, respectively, obtained by the group previously. After obtaining reliable results, the adaptation of the gills, kidneys, and livers of the three species to the high-salinity environment was assessed by weighted gene co-expression network analysis (WGCNA). Using module eigengenes (ME), 21, 22, and 22 gene modules were identified for G. przewalskii, G. selincuoensis, and G. nemesis, respectively. Functional clustering analysis of genes in the significant association module identified several genes associated with osmolarity-regulated potential KEGG pathways in the gills of three species of Schizothoracine fish. Th17 cell differentiation pathway was up-regulated in the gills of all three species; histocompatibility class 2 II antigen and E alpha (h2-ea) were up-regulated genes in this pathway. Functional clustering analysis of genes in apparently related modules in the kidney unveiled several differential KEGG pathways. The pentose phosphate pathway was up-regulated in the three Schizothoracine fishes, and glucose-6-phosphate dehydrogenase (g6pd) was an up-regulated gene in this pathway. In the livers of the three Schizothorax species, the propanoate metabolism pathway was up-regulated, and succinate-CoA ligase GDP-forming subunit beta (suclg2) was an up-regulated gene in this pathway. The above analyses provide reference data for the adaptation of Schizothorax to high-salt environments and lay the foundation for future studies on the adaptive mechanism of Schizothorax in the plateau. These results partly fill the void in the knowledge gap in the survival adaptations of Schizothoracine fishes to highland saline lakes. Full article