Environmental Adaptation Research Articles

Ecogeographical Characterization of Passiflora cincinnata Mast. and Passiflora setacea DC. Native to the Central-Southern Mesoregion of Bahia

Passiflora cincinnata and Passiflora setacea are two native species from the northeastern semiarid region, with wide distribution in the central-southern mesoregion of the Bahia state. These species are recognized for the production of bioflavonoids. However, although they have economic relevance, little is known about ecogeographic, morphological and ecophysiological aspects. Therefore, the goal was to characterize the physiochemical and granulometric attributes of the soil as well as the edaphoclimatic conditions in 12 locations of naturally occurring Passiflora cincinnata and Passiflora setacea in the central-southern mesoregion of Bahia. The results showed environments belonging to the ecotones of the Cerrado, Caatinga and Mata Atlântica biomes. In these phytophysiognomies, the soils varied between cambisol, oxisol and planosol and presented a sandy texture and acidic pH. They also have varied ecogeographic characteristics with altitudes between 481 and 929 meters, precipitation between 478 and 1.644 millimeters and average temperature ranging between 15 and 31 degrees. Sites with average temperatures of up to 28 degrees, altitude between 670 and 860 meters, pH between 4.3 and 5.11, base saturation smaller than 50 and H+Al between 2-5 favor both species. Temperatures up to 31 degrees, pH between 5 and 6, base saturation bigger than 50 and H+Al smaller equal 1.5 favor P. cincinnata. Environments with temperatures of up to 27 degrees, altitudes above 900 meters, average pH of 4.5, average base saturation of 30 and average H+Al of 3, favors P. setacea. Keywords: environmental adaptation; ecogeography; genetic resources; wild passion fruit; sleep passion fruit.

Exploring the Organic Acid Secretion Pathway and Potassium Solubilization Ability of Pantoea vagans ZHS-1 for Enhanced Rice Growth.

Soil potassium deficiency is a common issue limiting agricultural productivity. Potassium-solubilizing bacteria (KSB) show significant potential in mitigating soil potassium deficiency, improving soil quality, and enhancing plant growth. However, different KSB strains exhibit diverse solubilization mechanisms, environmental adaptability, and growth-promoting abilities. In this study, we isolated a multifunctional KSB strain ZHS-1, which also has phosphate-solubilizing and IAA-producing capabilities. 16S rDNA sequencing identified it as Pantoea vagans. Scanning electron microscopy (SEM) showed that strain ZHS-1 severely corroded the smooth, compact surface of potassium feldspar into a rough and loose state. The potassium solubilization reached 20.3 mg/L under conditions where maltose was the carbon source, sodium nitrate was the nitrogen source, and the pH was 7. Organic acid metabolism profiling revealed that strain ZHS-1 primarily utilized the EMP-TCA cycle, supplemented by pathways involving pantothenic acid, glyoxylic acid, and dicarboxylic acids, to produce large amounts of organic acids and energy. This solubilization was achieved through direct solubilization mechanisms. The strain also secreted IAA through a tryptophan-dependent metabolic pathway. When strain ZHS-1 was inoculated into the rhizosphere of rice, it demonstrated significant growth-promoting effects. The rice plants exhibited improved growth and root development, with increased accumulation of potassium and phosphorus. The levels of available phosphorus and potassium in the rhizosphere soil also increased significantly. Additionally, we observed a decrease in the relative abundance of Actinobacteria and Proteobacteria in the rice rhizosphere soil, while the relative abundance of genera associated with acid production and potassium solubilization, such as Gemmatimonadota, Acidobacteria, and Chloroflexi, as well as Cyanobacteria, which are beneficial to plant growth, increased. These findings contribute to a deeper understanding of the potassium solubilization mechanisms of strain ZHS-1 and highlight its potential as a plant growth-promoting rhizobacteria.

Climatic fluctuations, geographic features, and evolutionary forces: Shaping high genomic diversity and local adaptation in Muntiacus reevesi

AbstractAimGenetic diversity is crucial for species adaptability. Understanding the mechanisms behind its formation and maintenance is essential for effective conservation. Recent studies have demonstrated that despite experiencing severe population bottlenecks, Muntiacus reevesi retains high genetic diversity and continues its northward migration, indicative of ongoing adaptive evolution. However, our comprehension of this phenomenon remains incomplete. The objective of this study is to explore the mechanisms underlying the formation of high genetic diversity and the genomic characteristics associated with local adaptation, using M. reevesi as a case study.LocationSouthern China.MethodsWe analysed resequencing data from 62 genomes and identified 29,124,081 high‐quality single‐nucleotide polymorphisms (SNPs). We used population genetics, demographic history, population differentiation, gene flow analysis software, and genotype‐environment association (GEA) models to assess the factors that have contributed to high genetic diversity and environmental adaptability in the historical climate and geographical context.ResultsThe study identified that during Pleistocene climatic fluctuations, M. reevesi diverged into eastern (DB and WJW populations) and western lineages (WL, BA, and QL populations), all displayed high genetic diversity. Historically, M. reevesi maintained large effective populations, but contemporary human‐induced threats have led to a significant decline. Population differentiation models suggest distinct expansion pathways for eastern and western lineages, resulting in population admixture, with mountain corridors facilitating gene flow and maintaining high genetic diversity. Additionally, environmental‐genotype analysis revealed local adaptation in the QL‐BA population, highlighting candidate adaptive genes (ME3 and PRKG1) potentially linked to cold adaptation and foraging behaviour.ConclusionThis study enhances our understanding of the mechanisms behind the high genetic diversity and environmental adaptability of M. reevesi, offering insights into how bottleneck populations maintain diversity, crucial for biogeographic research and conservation strategies for similar species.

Novel design and motion analysis of an omni-tread snake-like robot for narrow space inspection

Snake-like robots have a slender body and strong environmental adaptability. This paper aims to propose an omni-tread snake-like robot that can adapt to the needs of specific narrow space exploration missions and provide a basis for design work through necessary motion analysis. The robot adopts the form of three modules in series, and the modules are connected through differential driving joints, which increases the joint torque of the robot. The nested omni-tread structure improves the robot's motion efficiency and environmental adaptability. This paper conducts configuration and motion analysis of the robot. The simulation is performed using the optimization solution method to obtain the joint torque and walking torque of the robot, which guides the design of the robot. The experiment is also conducted with the developed prototype to verify the robot's performance. From the simulation results, the joint torque and walking torque are obtained, and the motors are selected. The motion performance and field applicability of the robot are verified through experiment tests. The experiment results further verify the robot design and analysis work. The structural design of robots and optimization solution method in this paper has certain reference values for other researchers.

Exploring the regulatory landscape of non-coding RNAs in aquaculture bacterial pathogens: Piscirickettsia salmonis and Francisella noatunensis

In aquaculture, bacterial pathogens like Francisella noatunensis subsp. noatunensis and Piscirickettsia salmonis significantly impact economic sustainability, causing chronic infections in diverse aquatic environments. Non-coding RNAs (ncRNAs) play crucial roles in bacterial gene regulation, influencing metabolic pathways and stress responses, essential for environmental adaptability. Our comprehensive analysis uncovers a broad spectrum of ncRNAs, both shared across and unique to each pathogen, implicated in essential biological functions such as thiamine biosynthesis, temperature adaptation, and manganese homeostasis. Specifically, the examination of RNA-seq data from the P. salmonis LF-89 strain, representing the LF-89 genogroup, led to the identification of 43 novel trans-small RNAs. This discovery significantly enhances our understanding of the ncRNA-mediated regulatory framework within this genogroup. These novel ncRNAs are suggested to play roles in regulating critical cellular processes, including mobile genetic element management and chromosome partitioning, highlighting their potential influence on bacterial virulence and host-pathogen dynamics. Our findings advance the genomic insight into Francisella noatunensis subsp. noatunensis and Piscirickettsia salmonis, offering a foundation for developing targeted interventions. By elucidating ncRNA roles in pathogenicity, this research contributes to creating innovative strategies to mitigate bacterial diseases in aquaculture, enhancing industry sustainability and economic flexibility.

Genetic diversity accelerates canine distemper virus adaptation to ferrets.

RNA viruses adapt rapidly to new host environments by generating highly diverse genome sets, so-called "quasispecies." Minor genetic variants promote their rapid adaptation, allowing for the emergence of drug-resistance or immune-escape mutants. Understanding these adaptation processes is highly relevant to assessing the risk of cross-species transmission and the safety and efficacy of vaccines and antivirals. We hypothesized that genetic memory within a viral genome population facilitates rapid adaptation. To test this, we investigated the adaptation of the Morbillivirus canine distemper virus to ferrets and compared an attenuated, Vero cell-adapted virus isolate with its recombinant derivative over consecutive ferret passages. Although both viruses adapted to the new host, the reduced initial genetic diversity of the recombinant virus resulted in delayed disease onset. The non-recombinant virus gradually increased the frequencies of beneficial mutations already present at very low frequencies in the input virus. In contrast, the recombinant virus first evolved de novo mutations to compensate for the initial fitness impairments. Importantly, while both viruses evolved different sets of mutations, most mutations found in the adapted non-recombinant virus were identical to those found in a previous ferret adaptation experiment with the same isolate, indicating that mutations present at low frequency in the original virus stock serve as genetic memory. An arginine residue at position 519 in the carboxy terminus of the nucleoprotein shared by all adapted viruses was found to contribute to pathogenesis in ferrets. Our work illustrates the importance of genetic diversity for adaptation to new environments and identifies regions with functional relevance.IMPORTANCEWhen viruses encounter a new host, they can rapidly adapt to this host and cause disease. How these adaptation processes occur remains understudied. Morbilliviruses have high clinical and veterinary relevance and are attractive model systems to study these adaptation processes. The canine distemper virus is of particular interest, as it exhibits a broader host range than other morbilliviruses and frequently crosses species barriers. Here, we compared the adaptation of an attenuated virus and its recombinant derivative to that of ferrets. Pre-existing mutations present at low frequency allowed faster adaptation of the non-recombinant virus compared to the recombinant virus. We identified a common point mutation in the nucleoprotein that affected the pathogenesis of both viruses. Our study shows that genetic memory facilitates environmental adaptation and that erasing this genetic memory by genetic engineering results in delayed and different adaptation to new environments, providing an important safety aspect for the generation of live-attenuated vaccines.

Comparative evaluation of 16S rRNA primer pairs in identifying nitrifying guilds in soils under long-term organic fertilization and water management.

Compared with 454 sequencing technology, short-read sequencing (e.g., Illumina) technology generates sequences of high accuracy, but limited length (<500 bp). Such a limitation can prove that studying a target gene using a large amplicon (>500 bp) is challenging. The ammonia monooxygenase subunit A (amoA) gene of ammonia-oxidizing archaea (AOA), which plays a crucial part in the nitrification process, is such a gene. By providing a full overview of the community of a functional microbial guild, 16S ribosomal ribonucleic acid (rRNA) gene sequencing could overcome this problem. However, it remains unclear how 16S rRNA primer selection influences the quantification of relative abundance and the identification of community composition of nitrifiers, especially AOA. In the present study, a comparison was made between the performance of primer pairs 338F-806R, 515F-806R, and 515F-907R to a shotgun metagenome approach. The structure of nitrifier communities subjected to different long-term organic matter amendment and water management protocols was assessed. Overall, we observed higher Chao1 richness diversity of soil total bacteria by using 515F-806R compared to 338F-806R and 515F-907R, while higher Pielou's evenness diversity was observed by using 515F-806R and 515F-907R compared to 338F-806R. The studied primer pairs revealed different performances on the relative abundance of Thaumarchaeota, AOB, and NOB. The Thaumarchaeota 16S rRNA sequence was rarely detected using 338F-806R, while the relative abundances of Thaumarchaeota detected using 515F-806R were higher than those detected by using 515F-907R. AOB showed higher proportions in the 338F-806R and 515F-907R data, than in 515F-806R data. Different primers pairs showed significant change in relative proportion of NOB. Nonetheless, we found consistent patterns of the phylotype distribution of nitrifiers in different treatments. Nitrosopumilales (NP) and Nitrososphaerales (NS) clades were the dominant members of the AOA community in soils subject to controlled irrigation, whereas Ca. Nitrosotaleales (NT) and NS clades dominated the AOA community in soils subject to flooding irrigation. Nitrospira lineage II was the dominant NOB phylotype in all samples. Overall, ideal 16S rRNA primer pairs were identified for the analysis of nitrifier communities. Moreover, NP and NT clades of AOA might have distinct environmental adaptation strategies under different irrigation treatments.

Assessing black soldier fly pupation and survival in lunar regolith simulant: Implications for sustainable controlled habitats on the Moon

Bioregenerative life-support systems (BLSSs) will be crucial for extended space missions and extraterrestrial habitats. The black soldier fly, Hermetia illucens, is recognized for its efficient organic waste consumption, making it well-suited for closed environments like spacecraft. Our study assessed H. illucens adaptability to different substrates, including a lunar regolith simulant, pertinent to future lunar colonization. Remarkably resilient, H. illucens prepupal larvae successfully pupated in all tested substrates, but pupation timing varied, with no-substrate larvae pupating later. Pupal stage duration also differed, particularly with lunar regolith simulant and sand treatments resulting in longer durations. Substrate treatments significantly influenced the number of emerged adults, with lunar regolith simulant yielding more adults than the no-substrate treatment. Additionally, sand and wood shavings treatments produced more adults, highlighting H. illucens adaptability to various substrates, including lunar regolith. These findings are crucial for future BLSSs design. Additionally, H. illucens adaptability to lunar regolith provides insights into life's adaptability in space environments, guiding future experiments on celestial bodies. This study provides critical data on how different substrates, including lunar regolith simulants, influence H. illucens development and survival, advancing BLSSs and ecological science in both space and terrestrial contexts.

Online Flow Measurement of Liquid Metal Solutions Based on Impact Force Sequences: Modeling Analysis, Simulation, and Validation of Experimental Results.

Aiming at the existing high-temperature liquid metal flow online accurate measurement by the metal melt characteristics, installation space, and high-temperature environment adaptability limitations, this paper innovatively puts forward a soft measurement method based on the impact force generated in the fluid flow process as an observational variable series. Fluid mechanics theory and simulation software are used to analyze and verify the feasibility of the impact force as an observable variable to measure the flow rate, followed by the construction of the CNN-LSTM-CNN-Double (CLCD) flow measurement model of impact force and flow rate based on the parameters of the learning rate and the number of training times, and finally the construction of a test platform for the flow measurement, and the validity of the method is verified through actual operation.

Evaluation of the Synergistic Oil Displacement Effect of a CO2 Low Interfacial Tension Viscosity-Increasing System in Ultra-Low Permeability Reservoirs

In addressing the issue of poor control over gas permeability during the CO2 flooding process in ultra-low permeability reservoirs, this study proposes the use of a low interfacial tension viscosity-increasing system as a substitute for water in CO2–water alternating flooding to enhance CO2 mobility control and increase oil recovery. The performance of the system was evaluated through tests of viscosity, interfacial tension, wettability, and emulsification properties, and the injection behavior and gas channeling prevention effect of the viscosity-increasing system with CO2 alternate flooding were investigated. The results indicate that the low interfacial tension viscosity-increasing fluid exhibits good thickening properties, interfacial activity, hydrophilic wettability, and oil–water emulsification performance, also demonstrating strong environmental adaptability. The CO2–low interfacial tension viscosity-increasing fluid alternate flooding shows good injectivity in ultra-low permeability cores (1.085 mD). Following water flooding in heterogeneous ultra-low permeability cores, the implementation of CO2 low interfacial tension viscosity-increasing fluid alternate flooding can lead to a 15.91% increase in overall recovery compared to water flooding, outperforming CO2 flooding and CO2–water alternating flooding. The mechanisms by which the CO2 low interfacial tension viscosity-increasing fluid enhances oil recovery include reducing interfacial tension, improving mobility ratio, altering rock surface wettability, and emulsification effects. The low interfacial tension viscosity-increasing systems demonstrate effective mobility control and oil displacement capabilities and synergistically enhance the efficiency of CO2, presenting potential application prospects in the development of CO2 flooding in ultra-low permeability reservoirs.

Scans for Signatures of Selection in Genomes of Wagyu and Buryat Cattle Breeds Reveal Candidate Genes and Genetic Variants for Adaptive Phenotypes and Production Traits.

Past and ongoing selection shapes the genomes of livestock breeds. Identifying such signatures of selection allows for uncovering the genetic bases of affected phenotypes, including economically important traits and environmental adaptations, for the further improvement of breed genetics to respond to climate and economic challenges. Turano-Mongolian cattle are a group of taurine breeds known for their adaptation to extreme environmental conditions and outstanding production performance. Buryat Turano-Mongolian cattle are among the few breeds adapted to cold climates and poor forage. Wagyu, on the other hand, is famous for high productivity and unique top-quality marbled meat. We used hapFLK, the de-correlated composite of multiple signals (DCMS), PBS, and FST methods to search for signatures of selection in their genomes. The scans revealed signals in genes related to cold adaptation (e.g., STAT3, DOCK5, GSTM3, and CXCL8) and food digestibility (SI) in the Buryat breed, and growth and development traits (e.g., RBFOX2 and SHOX2) and marbling (e.g., DGAT1, IQGAP2, RSRC1, and DIP2B) in Wagyu. Several putatively selected genes associated with reproduction, immunity, and resistance to pathogens were found in both breed genomes. The results of our work could be used for creating new productive adapted breeds or improving the extant breeds.

Toward Practical Applications of Engineered Living Materials with Advanced Fabrication Techniques.

Engineered Living Materials (ELMs) are materials composed of or incorporating living cells as essential functional units. These materials can be created using bottom-up approaches, where engineered cells spontaneously form well-defined aggregates. Alternatively, top-down methods employ advanced materials science techniques to integrate cells with various kinds of materials, creating hybrids where cells and materials are intricately combined. ELMs blend synthetic biology with materials science, allowing for dynamic responses to environmental stimuli such as stress, pH, humidity, temperature, and light. These materials exhibit unique "living" properties, including self-healing, self-replication, and environmental adaptability, making them highly suitable for a wide range of applications in medicine, environmental conservation, and manufacturing. Their inherent biocompatibility and ability to undergo genetic modifications allow for customized functionalities and prolonged sustainability. This review highlights the transformative impact of ELMs over recent decades, particularly in healthcare and environmental protection. We discuss current preparation methods, including the use of endogenous and exogenous scaffolds, living assembly, 3D bioprinting, and electrospinning. Emphasis is placed on ongoing research and technological advancements necessary to enhance the safety, functionality, and practical applicability of ELMs in real-world contexts.

A novel deep-benthic sea cucumber species of Benthodytes (Holothuroidea, Elasipodida, Psychropotidae) and its comprehensive mitochondrial genome sequencing and evolutionary analysis

BackgroundThe holothurians, commonly known as sea cucumbers, are marine organisms that possess significant dietary, nutritional, and medicinal value. However, the National Center for Biotechnology Information (NCBI) currently possesses only approximately 70 complete mitochondrial genome datasets of Holothurioidea, which poses limitations on conducting comprehensive research on their genetic resources and evolutionary patterns. In this study, a novel species of sea cucumber belonging to the genus Benthodytes, was discovered in the western Pacific Ocean. The genomic DNA of the novel sea cucumber was extracted, sequenced, assembled and subjected to thorough analysis.ResultsThe mtDNA of Benthodytes sp. Gxx-2023 (GenBank No. OR992091) exhibits a circular structure spanning 17,386 bp, comprising of 13 protein-coding genes (PCGs), 24 non-coding RNAs (2 rRNA genes and 22 tRNA genes), along with two putative control regions measuring 882 bp and 1153 bp, respectively. It exhibits a high AT% content and negative AT-skew, which distinguishing it from the majority of sea cucumbers in terms of environmental adaptability evolution. The mitochondrial gene homology between Gxx-2023 and other sea cucumbers is significantly low, with less than 91% similarity to Benthodytes marianensis, which exhibits the highest level of homology. Additionally, its homology with other sea cucumbers is below 80%. The mitogenome of this species exhibits a unique pattern in terms of start and stop codons, featuring only two types of start codons (ATG and ATT) and three types of stop codons including the incomplete T. Notably, the abundance of AT in the Second position of the codons surpasses that of the First and Third position. The gene arrangement of PCGs exhibits a relatively conserved pattern, while there exists substantial variability in tRNA. Evolutionary analysis revealed that it formed a distinct cluster with B. marianensis and exhibited relatively distant phylogenetic relationships with other sea cucumbers.ConclusionsThese findings contribute to the taxonomic diversity of sea cucumbers in the Elasipodida order, thereby holding significant implications for the conservation of biological genetic resources, evolutionary advancements, and the exploration of novel sea cucumber resources.

Unveiling the translational dynamics of lychee (Litchi chinesis Sonn.) in response to cold stress

Cold stress poses a significant threat to the quality and productivity of lychee (Litchi chinensis Sonn.). While previous research has extensively explored the genomic and transcriptomic responses to cold stress in lychee, the translatome has not been thoroughly investigated. This study delves into the translatomic landscape of the 'Xiangjinfeng' cultivar under both control and low-temperature conditions using RNA sequencing and ribosome profiling. We uncovered a significant divergence between the transcriptomic and translatomic responses to cold exposure. Additionally, bioinformatics analyses underscored the crucial role of codon occupancy in lychee's cold tolerance mechanisms. Our findings reveal that the modulation of translation via codon occupancy is a vital strategy to abiotic stress. Specifically, the study identifies ribosome stalling, particularly at the E site AAU codon, as a key element of the translation machinery in lychee's response to cold stress. This work enhances our understanding of the molecular dynamics of lychee's reaction to cold stress and emphasizes the essential role of translational regulation in the plant's environmental adaptability.

How to investigate differences in indoor environmental comfort and adaptation? Mixed methods research with patients

ABSTRACT Ensuring hospitalized patients’ comfort requires understanding differences in comfort and adaptation to discomfort, as well as the role of the built environment therein. Shortcomings in this understanding result from limitations of existing research methods. Therefore the potential of a mixed methods research design to investigate when and why experiences of and adaption to (dis)comfort differ among hospitalized patients was explored. A convergent mixed methods case study was conducted in two hospital wards of a Belgian hospital. Qualitative data included interviews with 19 patients about their experiences and information about the patients at the two wards during the fieldwork; quantitative data included sensor measurements of indoor environmental quality parameters (i.e. illuminance and indoor temperature), a questionnaire among 238 patients about their assessment of the indoor conditions, and simulations of these conditions. Joint displays allowed comparing situations in which characteristics related to the patients or their setting differed in an integrated way. The displays provide an intermediate step between purely qualitative descriptions of comfort and adaptation and purely quantitative models that predict both. Scenarios that the joint displays allow identifying inform about characteristics that could improve these models, and about roles of the built environment in experiences.

XK-III: A Spherical Robot with Redundant Degrees of Freedom

The spherical robot XK-III, designed with redundant degrees of freedom, addresses the limitations of existing pendulum spherical robot structures by enhancing mobility and environmental adaptability. A nonlinear dynamic model is developed for XK-III’s new drive structure, along with a nonlinear disturbance observer (NDOB) to mitigate perturbations. Additionally, a Fuzzy PID controller (FPID) is implemented to further enhance XK-III’s environmental adaptability. Experimental results confirm the effectiveness of the new design, showing that XK-III equipped with FPID and NDOB outperforms traditional control systems in terms of anti-disturbance capabilities. This research provides valuable insights for the use of spherical robots in complex environments.

RNA N6-adenine methylation dynamics impact Hyaloperonospora arabidopsidis resistance in Arabidopsis.

In plants, epitranscriptomic mark N6-adenine methylation (m6A) is dynamically regulated in response to environmental cues. However, little is known about m6A dynamics under biotic stresses and their role in environmental adaptation. Additionally, current methodologies limit the investigation of m6A dynamics at single-nucleotide resolution on specific RNA molecules. Using Oxford Nanopore Technology direct RNA sequencing and a neural network model, we show transcript-specific dynamics of m6A modification at single-nucleotide resolution during Hyaloperonospora arabidopsidis (Hpa) infection in Arabidopsis (Arabidopsis thaliana). In wild-type seedlings, pathogen infection causes a significant reduction in global m6A ratios, which corresponds with the activation of m6A-modified transcripts. Defect of m6A deposition in the m6A mutant hakai-1 mimics m6A reduction from Hpa infection at ∼70% of sites, resulting in constitutive overexpression of basal defense genes and enhanced resistance against the pathogen. Our results demonstrate that m6A dynamics impact defense response against Hpa, providing a promising target for future crop improvement strategies.

Whole-genome analysis reveals distinct adaptation signatures to diverse environments in Chinese domestic pigs

BackgroundLong-term natural and artificial selection has resulted in many genetic footprints within the genomes of pig breeds across distinct agroecological zones. Nevertheless, the mechanisms by which these signatures contribute to phenotypic diversity and facilitate environmental adaptation remain unclear.ResultsHere, we leveraged whole-genome sequencing data from 82 individuals from 6 domestic pig breeds originating in tropical, high-altitude, and frigid regions. Population genetic analysis suggested that habitat isolation significantly shaped the genetic diversity and contributed to population stratification in local Chinese pig breeds. Analysis of selection signals revealed regions under selection for adaptation in tropical (55.5 Mb), high-altitude (43.6 Mb), and frigid (17.72 Mb) regions. The potential functions of the selective sweep regions were linked to certain complex traits that might play critical roles in different geographic environments, including fat coverage in frigid environments and blood indicators in tropical and high-altitude environments. Candidate genes under selection were significantly enriched in biological pathways involved in environmental adaptation. These pathways included blood circulation, protein degradation, and inflammation for adaptation to tropical environments; heart and lung development, hypoxia response, and DNA damage repair for high-altitude adaptation; and thermogenesis, cold-induced vasodilation (CIVD), and the cell cycle for adaptation to frigid environments. By examining the chromatin state of the selection signatures, we identified the lung and ileum as two candidate functional tissues for environmental adaptation. Finally, we identified a mutation (chr1: G246,175,129A) in the cis-regulatory region of ABCA1 as a plausible promising variant for adaptation to tropical environments.ConclusionsIn this study, we conducted a genome-wide exploration of the genetic mechanisms underlying the adaptability of local Chinese pig breeds to tropical, high-altitude, and frigid environments. Our findings shed light on the prominent role of cis-regulatory elements in environmental adaptation in pigs and may serve as a valuable biological model of human plateau-related disorders and cardiovascular diseases.

Evolution and Genetic Differentiation of Pleurotus tuoliensis in Xinjiang, China, Based on Population Genomics.

Pleurotus tuoliensis is a unique species discovered in Xinjiang, China, which is recognized for its significant edible, medicinal, and economic value. It has been successfully incorporated into industrial production. Controversy has emerged concerning the evolution and environmental adaptability of this species due to inadequate interspecific ecology and molecular data. This study examines the germplasm resources of P. tuoliensis in the Xinjiang region. A total of 225 wild and cultivated strains of P. tuoliensis were gathered from seven representative regions. Phylogenetic analysis revealed that seven populations were notably segregated into three distinct groups, primarily attributed to environmental factors as the underlying cause for this differentiation. Population historical size data indicate that P. tuoliensis underwent two expansion events, one between 2 and 0.9 Mya (Miocene) and the other between 15 and 4 Mya (Early Pleistocene). The ancient climate fluctuations in the Xinjiang region might have contributed to the comparatively modest population size during the Pliocene epoch. Moreover, through the integration of biogeography and ancestral state reconstruction, it was determined that group C of P. tuoliensis emerged initially and subsequently dispersed to groups D and B, in that order. Subsequently, group D underwent independent evolution, whereas group B continued to diversify into groups A and EFG. The primary factor influencing this mode of transmission route is related to the geographical conditions and prevailing wind direction of each group. Subsequent research endeavors focused on assessing the domestication adaptability of P. tuoliensis to different substrates. It was found that the metabolic processes adapted during the domestication process were mainly related to energy metabolism, DNA repair, and environmental adaptability. Processes adapted to the host adaptability include responses to the host (meiosis, cell cycle, etc.) and stress in the growth environment (cysteine and methionine metabolism, sulfur metabolism, etc.). This study analyzed the systematic evolution and genetic differentiation of P. tuoliensis in Xinjiang. The identified loci and genes provide a theoretical basis for the subsequent improvement of germplasm resources and conducting molecular breeding.

Population structure and selection signal analysis of indigenous sheep from the southern edge of the Taklamakan Desert

Analyzing the genetic diversity and selection characteristics of sheep (Ovis aries) holds significant value in understanding their environmental adaptability, enhancing breeding efficiency, and achieving effective conservation and rational utilization of genetic resources. In this study, we utilized Illumina Ovine SNP 50 K BeadChip data from four indigenous sheep breeds from the southern margin of the Taklamakan Desert (Duolang sheep: n = 36, Hetian sheep: n = 74, Kunlun sheep: n = 27, Qira black sheep: n = 178) and three foreign meat sheep breeds (Poll Dorset sheep: n = 105, Suffolk sheep: n = 153, Texel sheep: n = 150) to investigate the population structure, genetic diversity, and genomic signals of positive selection within the indigenous sheep. According to the Principal component analysis (PCA), the Neighbor-Joining tree (NJ tree), and Admixture, we revealed distinct clustering patterns of these seven sheep breeds based on their geographical distribution. Then used Cross Population Extended Haplotype Homozygosity (XP-EHH), Fixation Index (FST), and Integrated Haplotype Score (iHS), we identified a collective set of 32 overlapping genes under positive selection across four indigenous sheep breeds. These genes are associated with wool follicle development and wool traits, desert environmental adaptability, disease resistance, reproduction, and high-altitude adaptability. This study reveals the population structure and genomic selection characteristics in the extreme desert environments of native sheep breeds from the southern edge of the Taklimakan Desert, providing new insights into the conservation and sustainable use of indigenous sheep genetic resources in extreme environments. Additionally, these findings offer valuable genetic resources for sheep and other mammals to adapt to global climate change.