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Background: The white-blooded Antarctic icefishes is a representative organism that survive under the stenothermal conditions of the Southern Ocean without the hemoglobin genes. To compensate for inefficient oxygen transport, distinct features such as increased heart size, greater blood volume, and reduced hematocrit density enhance the amount of dissolved oxygen and the velocity of blood flow., Results: Here, we investigated these unique characteristics by comparing high-quality genomic data between white-blooded and red-blooded fishes and identified the loss of FAAP20, which is implicated in anemia. Although the gene region containing FAAP20 is conserved in notothenioids as shown through collinear analysis, only remnants of FAAP20 persist in several icefish species. Additionally, we observed the loss of SOAT1, which plays a pivotal role in cholesterol metabolism, providing a clue for further investigations into the unique mitochondrial form of the icefish., Conclusions: The loss of FAAP20, which is known to reduce erythrocyte counts under stress conditions in mice and humans, may provide a clue to understanding the genomic characteristics related to oxygen supply, such as low hematocrit, in Antarctic icefishes., Competing Interests: Declarations Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

High-altitude and marine mammals inhabit distinct ecosystems but share a common challenge: hypoxia. To survive in low-oxygen environments, these species have evolved similar phenotypic pulmonary adaptations, characterized by a high density of elastic fibers. In this study, we explored the molecular mechanisms underlying these adaptations, focusing on pulmonary fibrosis and hypoxia tolerance through comparative genomics and convergent evolution analyses. We observed significant expansions and contractions in certain gene families across both high-altitude and marine mammals, closely associated with processes involved in pulmonary fibrosis. Notably, members of the keratin gene family, such as KRT17 and KRT14 , appear to be associated with the development of the dense elastic fiber phenotype observed in the lungs of hypoxia-tolerant mammals. Through selection pressure and amino acid substitution analyses, we identified multiple genes exhibiting convergent accelerated evolution, positive selection, and amino acid substitution in these species, associated with adaptation to hypoxic environments. Specifically, the convergent evolution of ZFP36L1 , FN1 , and NEDD9 was found to contribute to the high density of elastic fibers in the lungs of both high-altitude and marine mammals, facilitating their hypoxia tolerance. Additionally, we identified convergent amino acid substitutions and gene loss events associated with sperm development, differentiation, and spermatogenesis, such as amino acid substitutions in SLC26A3 and pseudogenization of CFAP47 , as confirmed by PCR. These genetic alterations may be linked to changes in the reproductive capabilities of these animals. Overall, this study offers novel perspectives on the genetic and molecular adaptations of high-altitude and marine mammals to hypoxic environments, with a particular emphasis on pulmonary fibrosis.

The Pacific saury (Cololabis saira) is a pelagic fish commonly found in the North Pacific Ocean. Its population diversity and migratory lifestyle have long captured global attention. Despite the inherent complexity of the C. saira genome, characterized by extremely high heterozygosity, we successfully assembled a phased chromosome-level genome. The genome analysis revealed the expansion and natural selection of numerous functional genes, likely contributing to its enduring and extensive migratory lifestyle. Notably, gpr35 and igh genes showed significant expansion in the C. saira genome, potentially associated with regulating the immune response against environmental parasites and pathogens. Moreover, genes involved in DNA repair/replication and peroxisome function, including atm, ercc6, pex14, and pex16, displayed evidence of positive selection. Based on genome-sequencing of 80 individuals from eight sampling sites, we demonstrated that the genomic divergence among C. saira populations is relatively low. However, the sampling sites could be grouped into two distinct clusters, roughly corresponding to the migratory route of C. saira. This suggests a possible genome-wide divergence for C. saira within the open ocean region. Furthermore, the trmu gene, responsible for controlling otolith development and sharpness, exhibited differentiation between the two groups, consistent with previously reported differences in otolith morphology. This study has provided a reference genome and insights into the evolution, ecology, and conservation of Pacific saury and closely-related species., Competing Interests: Competing interests The authors declare no competing of interests, (© 2024. The Author(s).)

Background: Genomic structural variations (GSVs), notably copy number variations (CNVs), significantly shape genetic diversity and facilitate adaptation in cattle populations. Despite their importance, the genome-wide characterization of CNVs in indigenous Ethiopian cattle breeds-Abigar, Fellata, and Gojjam-Highland remains largely unexplored. In this study, we applied a read-depth approach to whole genome sequencing (WGS) data to conduct the first comprehensive analysis of CNVs in these populations., Results: We identified 3,893 CNV regions (CNVRs) covering 19.15 Mb (0.71% of the cattle genome). These CNVRs ranged from 1.60 kb to 488.0 kb, with an average size of 4.92 kb. These CNVRs included deletions (1713), duplications (1929), and mixed events (251) showing notable differences in distribution among the breeds. Four out of five randomly selected CNVRs were successfully validated using real time polymerase chain reaction (qPCR). Further analyses identified candidate genes associated with high-altitude adaptation (GBE1 and SOD1), heat stress adaptation (HSPA13, DNAJC18, and DNAJC8) and resistance to tick infestations (BoLA and KRT33A). In addition, variance stabilizing transformation (V ST ) statistics highlighted population-specific CNVRs, emphasizing the unique genetic signatures of high-altitude adaptation in the Gojjam-Highland cattle breed. Among the detected CNVRs, 4.93% (192 out of 3,893) overlapped with 520 quantitative traits loci (QTLs) associated with six economically important trait categories suggesting that these CNVRs may significantly contribute to the genetic variation underlying these traits., Conclusions: Our comprehensive analysis reveals significant CNVRs associated with key adaptive traits in Ethiopian cattle breeds highlighting their genetic diversity and resilience. These findings offer valuable insights into the genetic basis of adaptability and can inform sustainable breeding practices and conservation efforts. Future research should prioritize the functional validation of these CNVRs and their integration into breeding programs to enhance traits such as disease resistance and environmental adaptability., Competing Interests: Declarations Ethics approval and consent to participate Blood samples were collected in the study area after obtaining informed consent from each cattle owner. All animals were handled strictly with good animal handling practices, as outlined by the animal ethics procedures of the People’s Republic of China. The study protocol was reviewed and approved by the Animal Administration and Ethics Committee of the Lanzhou Institute of Husbandry and Pharmaceutical Science, CAAS Institutional Review Board (Permit No. SYXK-2014-0002). Consent for publication Not Applicable. Competing interests The authors declare no competing interests., (© 2024. Crown.)

During the past 3000 years, cattle on the Qinghai-Xizang Plateau have developed adaptive phenotypes under the selective pressure of hypoxia, ultraviolet (UV) radiation, and extreme cold. The genetic mechanism underlying this rapid adaptation is not yet well understood. Here, we present whole-genome resequencing data for 258 cattle from 32 cattle breeds/populations, including 89 Tibetan cattle representing eight populations distributed at altitudes ranging from 3400 m to 4300 m. Our genomic analysis revealed that Tibetan cattle exhibited a continuous phylogeographic cline from the East Asian taurine to the South Asian indicine ancestries. We found that recently selected genes in Tibetan cattle were related to body size (HMGA2 and NCAPG) and energy expenditure (DUOXA2). We identified signals of sympatric introgression from yak into Tibetan cattle at different altitudes, covering 0.64%-3.26% of their genomes, which included introgressed genes responsible for hypoxia response (EGLN1), cold adaptation (LRP11), DNA damage repair (LATS1), and UV radiation resistance (GNPAT). We observed that introgressed yak alleles were associated with noncoding variants, including those in present EGLN1. In Tibetan cattle, three yak introgressed SNPs in the EGLN1 promoter region reduced the expression of EGLN1, suggesting that these genomic variants enhance hypoxia tolerance. Taken together, our results indicated complex adaptation processes in Tibetan cattle, where recently selected genes and introgressed yak alleles jointly facilitated rapid adaptation to high-altitude environments., (Copyright © 2024 Science China Press. Published by Elsevier B.V. All rights reserved.)

High altitude adapted livestock species (cattle, yak, goat, sheep, and horse) has critical role in the human socioeconomic sphere and acts as good source of animal source products including milk, meat, and leather, among other things. These species sustain production and reproduction even in harsh environments on account of adaptation resulting from continued evolution of beneficial traits. Selection pressure leads to various adaptive strategies in livestock whose footprints are evident at the different genomic sites as the "Selection Signature". Scrutiny of these signatures provides us crucial insight into the evolutionary process and domestication of livestock adapted to diverse climatic conditions. These signatures have the potential to change the sphere of animal breeding and further usher the selection programmes in right direction. Technological revolution and recent strides made in genomic studies has opened the routes for the identification of selection signatures. Numerous statistical approaches and bioinformatics tools have been developed to detect the selection signature. Consequently, studies across years have identified candidate genes under selection region found associated with numerous traits which have a say in adaptation to high-altitude environment. This makes it pertinent to have a better understanding about the selection signature, the ways to identify and how to utilize them for betterment of livestock populations as well as farmers. This review takes a closer look into the general concept, various methodologies, and bioinformatics tools commonly employed in selection signature studies and summarize the results of recent selection signature studies related to high-altitude adaptation in various livestock species. This review will serve as an informative and useful insight for researchers and students in the field of animal breeding and evolutionary biology., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Background: Indigenous buffaloes, as the important livestock species contributing to economy of the country, are the lifeline of livelihood in Nepal. They are distributed across diverse geographical regions of the country and have adapted to various feeding, breeding, and management conditions. The larger group of these native buffalo breeds are present in narrow and stiff hilly terrains. Their dispersal indicates a possible environmental adaptation mechanism, which is crucial for the conservation of these breeds., Results: We utilized whole-genome sequencing (WGS) to investigate the genetic diversity, population structure, and selection signatures of Nepalese indigenous buffaloes. We compared 66 whole-genome sequences with 118 publicly available sequences from six river and five swamp buffalo breeds. Genomic diversity parameters indicated genetic variability level in the Nepalese buffaloes comparable to those of Indian breeds, and population genetic structure revealed distinct geography-mediated genetic differentiation among these breeds. We used locus-specific branch length analysis (LSBL) for genome-wide scan, which revealed a list of potentially selected genes in Lime and Parkote breeds that inhabit the hilly region. A gene ontology (GO) analysis discovered that many GO terms were associated with cardiac function regulation. Furthermore, complementary analyses of local selection signatures, tissue expression profiles, and haplotype differences identified candidate genes, including KCNE1, CSF1R, and PDGFRB, related to the regulation of cardiac and pulmonary functions., Conclusions: This study is a comprehensive WGS-based genetic analysis of the native Nepalese buffalo breeds. Our study suggested that the Nepalese "hilly" buffaloes, especially the Lime and Parkote breeds, have undergone some characteristic genetic changes and evolved increased cardiac and pulmonary function for their adaptation to the steep hilly terrains of the country., Competing Interests: Declarations Ethics approval and consent to participate The animal study protocol was approved by the Animal Welfare Committee of China Agricultural University (protocol code AW42303202-2-1, March 24, 2023). We obtained informed consent from each owner to use the animals in the study. Consent for publication Not applicable. Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

Waterlogging stands as a common environmental challenge, significantly affecting plant growth, yield, and, in severe cases, survival. In response to waterlogging stress, plants exhibit a series of intricate physiologic, metabolic, and morphologic adaptations. Notably, the gaseous phytohormone ethylene is rapidly accumulated in the plant submerged tissues, assuming an important regulatory factor in plant-waterlogging tolerance. In this review, we summarize recent advances in research on the mechanisms of ethylene in the regulation of plant responses to waterlogging stress. Recent advances found that both ethylene biosynthesis and signal transduction make indispensable contributions to modulating plant adaptation mechanisms to waterlogged condition. Ethylene was also discovered to play an important role in plant physiologic metabolic responses to waterlogging stress, including the energy mechanism, morphologic adaptation, ROS regulation and interactions with other phytohormones. The comprehensive exploration of ethylene and its associated genes provides valuable insights into the precise strategies to leverage ethylene metabolism for enhancing plant resistance to waterlogging stress., Competing Interests: Declarations Competing interests The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Deep-sea hydrothermal vents are characterized by high hydrostatic pressure, hypoxia, darkness and toxic substances. However, how organisms adapt to such extreme marine ecosystems remain poorly understood. We hypothesize that adaptive evolution plays an essential role in generating novelty for evolutionary adaptation to the deep-sea environment because adaptive evolution has been found to be critical for species origin and evolution. In this project, the chromosome-level genome of the deep-sea hydrothermal vent gastropod T. jamsteci was constructed for the first time to examine molecular mechanisms of its adaptation to the deep-sea environment. The genome size was large (2.54 Gb), ranking at the top of all species in the Vetigastropoda subclass, driven primarily by the bursts of transposable elements (TEs). The transposition of TEs may also trigger chromosomal changes including both inter-chromosomal fusions and intra-chromosomal activities involving chromosome inversions, rearrangements and fusions, as revealed by comparing the genomes of T. jamsteci and its closely related shallow-sea species Gibbula magus. Innovative changes including the expansion of the ABC transporter gene family that may facilitate detoxification, duplication of genes related to endocytosis, immunity, apoptosis, and anti-apoptotic domains that may help T. jamsteci fight against microbial pathogens, were identified. Furthermore, comparative analysis identified positive selection signals in a large number of genes including the hypoxia up-regulated protein 1, which is a chaperone that may promote adaptation of the T. jamsteci to hypoxic deepsea environments, hox2, Rx2, Pax6 and cilia-related genes BBS1, BBS2, BBS9 and RFX4. Notably, because of the critical importance of cilia and IFT in development, positive selection in cilia-related genes may play a critical role in facilitating T. jamsteci to adapt to the high-pressure deep-sea ecosystem. Results from this study thus revealed important molecular clues that may facilitate further research on the adaptation of molluscs to deep-sea hydrothermal vents., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Background: The genomes within organelles are crucial for physiological functions such as respiration and photosynthesis and may also contribute to environmental adaptation. However, the limited availability of genetic resources, particularly mitochondrial genomes, poses significant challenges for in-depth investigations., Results: Here, we explored various assembly methodologies and successfully reconstructed the complex organelle genomes of two Rhododendron species: Rhododendron nivale subsp. boreale and Rhododendron vialii. The mitogenomes of these species exhibit various conformations, as evidenced by long-reads mapping. Notably, only the mitogenome of R. vialii can be depicted as a singular circular molecule. The plastomes of both species conform to the typical quadripartite structure but exhibit elongated inverted repeat (IR) regions. Compared to the high similarity between plastomes, the mitogenomes display more obvious differences in structure, repeat sequences, and codon usage. Based on the analysis of 58 organelle genomes from angiosperms inhabiting various altitudes, we inferred the genetic adaptations associated with high-altitude environments. Phylogenetic analysis revealed partial inconsistencies between plastome- and mitogenome-derived phylogenies. Additionally, evolutionary lineage was determined to exert a greater influence on codon usage than altitude. Importantly, genes such as atp4, atp9, mttB, and clpP exhibited signs of positive selection in several high-altitude species, suggesting a potential link to alpine adaptation., Conclusions: We tested the effectiveness of different organelle assembly methods for dealing with complex genomes, while also providing and validating high-quality organelle genomes of two Rhododendron species. Additionally, we hypothesized potential strategies for high-altitude adaptation of organelles. These findings offer a reference for the assembly of complex organelle genomes, while also providing new insights and valuable resources for understanding their adaptive evolution patterns., (© 2024. The Author(s).)

It is well established that several Homo sapiens populations experienced admixture with extinct human species during their evolutionary history. Sometimes, such a gene flow could have played a role in modulating their capability to cope with a variety of selective pressures, thus resulting in archaic adaptive introgression events. A paradigmatic example of this evolutionary mechanism is offered by the EPAS1 gene, whose most frequent haplotype in Himalayan highlanders was proved to reduce their susceptibility to chronic mountain sickness and to be introduced in the gene pool of their ancestors by admixture with Denisovans. In this study, we aimed at further expanding the investigation of the impact of archaic introgression on more complex adaptive responses to hypobaric hypoxia evolved by populations of Tibetan/Sherpa ancestry, which have been plausibly mediated by soft selective sweeps and/or polygenic adaptations rather than by hard selective sweeps. For this purpose, we used a combination of composite-likelihood and gene network-based methods to detect adaptive loci in introgressed chromosomal segments from Tibetan WGS data and to shortlist those presenting Denisovan-like derived alleles that participate to the same functional pathways and are absent in populations of African ancestry, which are supposed to do not have experienced Denisovan admixture. According to this approach, we identified multiple genes putatively involved in archaic introgression events and that, especially as regards TBC1D1 , RASGRF2 , PRKAG2 , and KRAS , have plausibly contributed to shape the adaptive modulation of angiogenesis and of certain cardiovascular traits in high-altitude Himalayan peoples. These findings provided unprecedented evidence about the complexity of the adaptive phenotype evolved by these human groups to cope with challenges imposed by hypobaric hypoxia, offering new insights into the tangled interplay of genetic determinants that mediates the physiological adjustments crucial for human adaptation to the high-altitude environment., Competing Interests: GF, PA, MA, AD, PS, PC, MT, MD, GG, LN, AC, GM, DP, SS, MS No competing interests declared, (© 2023, Ferraretti, Abondio et al.)

Mechanisms of abdominal obesity GWAS variants have remained largely unknown. To elucidate these mechanisms, we leveraged subcutaneous adipose tissue (SAT) single nucleus RNA-sequencing and genomics data. After discovering that heritability of abdominal obesity is enriched in adipocytes, we focused on a SAT unique adipocyte marker gene, the transcription factor TBX15, and its abdominal obesity-associated deleterious missense variant, rs10494217. The allele frequency of rs10494217 revealed a north-to-south decreasing gradient, with consistent significant F ST values observed for 25 different populations when compared to Finns, a population with a history of genetic isolation. Given the role of Tbx15 in mouse thermogenesis, the frequency may have increased as an adaptation to cold in Finns. Our selection analysis provided significant evidence of selection for the abdominal obesity risk allele T of rs10494217 in Finns, with a north-to-south decreasing trend in other populations, and demonstrated that latitude significantly predicts the allele frequency. We also discovered that the risk allele status significantly affects SAT adipocyte expression of multiple adipocyte marker genes in trans in two cohorts. Two of these trans genes have been connected to thermogenesis, supporting the thermogenic effect of the TBX15 missense variant as a possible cause of its selection. Adipose expression of one trans gene, a lncRNA, AC002066.1, was strongly associated with adipocyte size, implicating it in metabolically unhealthy adipocyte hypertrophy. In summary, the abdominal obesity variant rs10494217 was selected in Finns, and individuals with the risk allele have trans effects on adipocyte expression of genes relating to thermogenesis and adipocyte hypertrophy., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Background: Evolutionary adaptation drives organismal adjustments to environmental pressures, exemplified in the diverse morphological and ecological adaptations seen in Decapoda crustaceans, particularly brachyuran crabs. Crabs thrive in diverse ecosystems, from coral reefs to hydrothermal vents and terrestrial habitats. Despite their ecological importance, the genetic mechanisms underpinning their developmental processes, reproductive strategies, and nutrient acquisition remain poorly understood., Results: Here, we report a comprehensive genomic analysis of the green mud crab Scylla paramamosain using ultralong sequencing technologies, achieving a high-quality chromosome-level assembly. The refined 1.21 Gb genome, with an impressive contig N50 of 11.45 Mb, offers a valuable genomic resource. The genome exhibits 33,662 protein-coding genes, enriched in various pathways related to development and environmental adaptation. Gene family analysis shows expansion in development-related pathways and contraction in metabolic pathways, indicating niche adaptations. Notably, investigation into Hox gene regulation sheds light on their role in pleopod development, with the Abd-A gene identified as a linchpin. Post-transcriptional regulation involving novel-miR1317 negatively regulates Abd-A levels. Furthermore, the potential role of fru gene in ovarian development and the identification of novel-miR35 as a regulator of Spfru2 add complexity to gene regulatory networks. Comparative functional analysis across Decapoda species reveals neo-functionalization of the elovl6 gene in the synthesis of long-chain polyunsaturated fatty acids (LC-PUFA), suggesting its importance in environmental adaptation., Conclusions: Our findings shed light on various aspects of crab biology, including genome sequencing, assembly, and annotation, as well as gene family expansion, contraction, and regulatory mechanisms governing crucial developmental processes such as metamorphosis, reproductive strategies, and fatty acid metabolism., (© 2024. The Author(s).)

Background: Echolocation was a key development in toothed whale evolution, enabling their adaptation and diversification across various environments. Previous bioacoustic and morphological studies suggest that environmental pressures have influenced the evolution of echolocation in toothed whales. This hypothesis demands further investigation, especially regarding the molecular mechanisms involved in the adaptive radiation of toothed whales across multiple habitats. Here we show that the coding sequences of four hearing genes involved in echolocation (CDH23, prestin, TMC1, and CLDN14) have different signatures of molecular evolution among riverine, coastal, and oceanic dolphins, suggesting that the evolutionary constraints of these habitats shaped the underlying genetic diversity of the toothed whale sonar., Results: Our comparative analysis across 37 odontocete species revealed patterns of accelerated evolution within coastal and riverine lineages, supporting the hypothesis that shallow habitats pose specific selective pressures to sonar propagation, which are not found in the deep ocean. All toothed whales with genes evolving under positive selection are shallow coastal species, including three species that have recently diverged from freshwater lineages (Cephalorhynchus commersonii, Sotalia guianensis, and Orcaella heinsohni - CDH23), and three species that operate specialized Narrow Band High Frequency (NBHF) Sonars (Phocoena sinus - prestin, Neophocaena phocaenoides - TMC1 and Cephalorhynchus commersonii - CDH23). For river dolphins and deep-diving toothed whales, we found signatures of positive selection and molecular convergence affecting specific sites on CDH23, TMC1, and prestin. Positively selected sites (PSS) were different in number, identity, and substitution rates (dN/dS) across riverine, coastal, and oceanic toothed whales., Conclusion: Here we shed light on potential molecular mechanisms underlying the diversification of toothed whale echolocation. Our results suggest that toothed whale hearing genes changed under different selective pressures in coastal, riverine, and oceanic environments., (© 2024. The Author(s).)

High altitude is characterized by low oxygen, low pressure, and high radiation. When migrates from low to high altitudes, the body's tissues and organs experience hypoxic stress and will present acoustic adaptation as the protective response. However, the mechanisms of acoustic adaptation at high altitudes remain unclear. In this study, cochlear tissues from Wistar rats were collected at 15, 30, 60, 120, and 180 days after high-altitude migration. Transcriptome sequencing was conducted and DESeq algorithm revealed expression patterns of Differentially Expressed Genes(DEGs) after high altitude migration. Day 60 is a critical stage for cochlear tissue "damage" and "repair" in high-altitude conditions. Transmission Electron Microscopy (TEM) observations of structures also support the findings. A time-series gene co-expression network algorithm was used to investigate gene regulatory patterns and key genes after migration. Immunofluorescence, immunohistochemistry, and qPCR were per-formed for key gene validation and localization. At Day 60, the peak DEG count occurs in rats migrating to high altitude, aligning with the critical phase for cochlear tissue damage and repair at high altitudes. Repair hinges on synaptic plasticity and myelination-linked processes, influencing modules M4 to M6. Module M4's activation gradually diminishes from its peak. However, the 'damage' effect is orchestrated by inflammation-related processes in modules M3 to M5, with module M3's activation also waning. Key gene module M4, pivotal for repair during this pivotal phase, encompasses Sptbn5, Cldn1, Gfra2, and Lims2 as its core genes. Immunohistochemistry reveals Sptbn5's presence in cochlear neurons, hair cells, Schwann cells and stria vascularis tissue. Cldn1 and Gfra2 predominantly localize within the cochlear neuron region. These results may suggest new directions for future research on acoustic acclimatization to high altitude., (© 2024. The Author(s).)

The amount of standing variation present within populations is a fundamental quantity of interest in population genetics, commonly represented by calculating the average number of differences between pairs of nucleotide sequences (nucleotide diversity, π). It is well understood that both background and positive selection can cause reductions in nucleotide diversity, but less clear how local adaptation affects it. Depending on the assumptions and parameters, some theoretical studies have emphasized how local adaptation can reduce nucleotide diversity, while others have shown that it can increase it. Here, we explore how local adaptation shapes genome-wide patterns in within-population nucleotide diversity, extending previous work to study the effects of polygenic adaptation, genotypic redundancy, and population structure. We show that local adaptation produces two very different patterns depending on the relative strengths of migration and selection, either markedly decreasing or increasing within-population diversity at linked sites at equilibrium. At low migration, regions of depleted diversity can extend large distances from the causal locus, with substantially more diversity eroded than expected with background selection. With higher migration, peaks occur over much smaller genomic distances but with much larger magnitude changes in diversity. Across spatially extended environmental gradients, both patterns can be found within a single species, with increases in diversity at the center of the range and decreases towards the periphery. Our results demonstrate that there is no universal diagnostic signature of local adaptation based on within-population nucleotide diversity, so it will not be broadly useful for explaining increased FST. However, given that neither background nor positive selection inflate diversity, when peaks are found they suggest local adaptation may be acting on a causal allele in the region., Competing Interests: Conflicts of interest The authors declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

Peanut (Arachis hypogaea L.) is a globally important oil and food crop frequently grown in arid, semi-arid, or dryland environments. Improving drought tolerance is a key goal for peanut crop improvement efforts. Here, we present the genome assembly and gene model annotation for "Line8," a peanut genotype bred from drought-tolerant cultivars. Our assembly and annotation are the most contiguous and complete peanut genome resources currently available. The high contiguity of the Line8 assembly allowed us to explore structural variation both between peanut genotypes and subgenomes. We detect several large inversions between Line8 and other peanut genome assemblies, and there is a trend for the inversions between more genetically diverged genotypes to have higher gene content. We also relate patterns of subgenome exchange to structural variation between Line8 homeologous chromosomes. Unexpectedly, we discover that Line8 harbors an introgression from A.cardenasii, a diploid peanut relative and important donor of disease resistance alleles to peanut breeding populations. The fully resolved sequences of both haplotypes in this introgression provide the first in situ characterization of A.cardenasii candidate alleles that can be leveraged for future targeted improvement efforts. The completeness of our genome will support peanut biotechnology and broader research into the evolution of hybridization and polyploidy., Competing Interests: Conflicts of interest The author(s) declare no conflicts of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

We consider how the genetic architecture underlying locally adaptive traits determines the strength of a barrier to gene flow in a mainland-island model. Assuming a general life cycle, we derive an expression for the effective migration rate when local adaptation is due to genetic variation at many loci under directional selection on the island, allowing for arbitrary fitness and dominance effects across loci. We show how the effective migration rate can be combined with classical single-locus diffusion theory to accurately predict multilocus differentiation between the mainland and island at migration-selection-drift equilibrium and determine the migration rate beyond which local adaptation collapses, while accounting for genetic drift and weak linkage. Using our efficient numerical tools, we then present a detailed study of the effects of dominance on barriers to gene flow, showing that when total selection is sufficiently strong, more recessive local adaptation generates stronger barriers to gene flow. We then study how heterogeneous genetic architectures of local adaptation affect barriers to gene flow, characterizing adaptive differentiation at migration-selection balance for different distributions of fitness effects. We find that a more heterogeneous genetic architecture generally yields a stronger genome-wide barrier to gene flow and that the detailed genetic architecture underlying locally adaptive traits can have an important effect on observable differentiation when divergence is not too large. Lastly, we study the limits of our approach as loci become more tightly linked, showing that our predictions remain accurate over a large biologically relevant domain., Competing Interests: Conflicts of interest The author(s) declare no conflicts of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

Background: Forage sorghum is a highly valued crop in livestock feed production due to its versatility, adaptability, high productivity, and resilience under adverse environmental conditions, making it a crucial option for sustainable forage production. This study aimed to investigate ninety-five forage sorghum genotypes and identify the marker - trait associations (MTAs) in adaptive traits, including yield and flowering through genome-wide association studies (GWAS)., Results: Using 41,854 polymorphic SNPs, a GWAS involving the GLM, MLM, and FarmCPU models was performed to analyse fourteen adaptive traits. The population structure revealed the presence of two subpopulation groups. Linkage disequilibrium (LD) plots showed varying degrees of LD decay across the chromosomes, with an average LD decay of 19.49 kbp. Twelve common significant QTNs, encoding 17 putative candidate genes, were simultaneously co-detected and studied by at least two or more GWAS methods. Three QTNs were associated to days to 50% flowering; two each to leaf-to-stem ratio and number of nodes per plant; and one each to plant height, leaf width, number of leaves per plant, stem girth, and internodal length. Six candidate genes were associated with days to 50% flowering, two each with leaf width, stem girth, leaf-to-stem ratio, and number of nodes per plant, and one each with plant height, number of leaves per plant, and internodal length., Conclusion: FarmCPU was identified as the most suitable and effective among all the models for controlling both false positives and false negatives. Further in-depth analysis of the newly discovered QTNs may lead to the identification of new candidate genes for the trait of interest. These studies elucidate gene functions and could transform forage sorghum breeding through marker-assisted selection and transgenic approaches, accelerating the development of superior forage sorghum varieties and enhancing global food security., (© 2024. The Author(s).)

The precise control of flowering time is of utmost importance for crop adaptation to varying environmental conditions and consequently determines grain yield and plant fitness. Soybean E2 , the homolog of Arabidopsis GIGANTEA , is a major locus contributing to high-latitude adaptation and is involved in photoperiod sensitivity. However, due to major effects of E2 , additional genetic loci controlling soybean flowering and adaptation have historically been masked and difficult to identify. Here, by eliminating the effect of E2 , we identified a Tof9 locus controlling flowering in which ZEITLUPE 2 ( ZTL2 ) is the causal gene. ZTL2 encodes an F-box E3 ubiquitin ligase with homology to Arabidopsis ZEITLUPE and is shown to play a key role in the soybean photoperiodic flowering pathway. ZTL2 physically interacts with E2 to mediate its degradation. Intriguingly, ZTL2 and FKF1, both belong to the F-box-type E3 ubiquitin-ligase family, exhibit opposite roles in regulating soybean flowering. ZTL2 degrades E2, leading to early flowering, while FKF1 stabilizes E2, resulting in delayed flowering. The balance between ZTL2-mediated degradation and FKF1-mediated stabilization enables soybeans to finetune flowering time and maximize grain yield. Field-grown ztl2 mutants are taller, flower late, and have increased yield parameters. ZTL2 and FKF1b bear contrasting artificial-selection patterns to adapt to different latitudes. This antagonistic regulation is crucial for soybean adaptation to diverse ecological settings and allows plants to fine-tune their flowering time in response to photoperiod and latitudinal changes., Competing Interests: Competing interests statement:The authors declare no competing interest.

Live-bearing fish have repeatedly adapted to life in sulfidic hot springs. A new study finds consistent changes in morphology, physiology and gene expression but no repeated genomic adaptation. This raises further questions about genetic redundancy, polygenic adaptation and the broader significance of repeated adaptation in natural systems., Competing Interests: Declaration of interests The author declares no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)

The yeast Candida albicans is usually a harmless member of the normal microbiota in healthy persons but is also a major fungal pathogen that can colonize and infect almost every human tissue. A successful adaptation to environmental changes encountered in different host niches requires an appropriate regulation of gene expression. The zinc cluster transcription factors are the largest family of transcriptional regulators in C. albicans and are involved in the control of virtually all aspects of its biology. Under certain circumstances, mutations in these transcription factors that alter their activity and the expression of their target genes confer a selective advantage, which results in the emergence of phenotypically altered variants that are better adapted to new environmental challenges. This review describes how gain-of-function mutations in different zinc cluster transcription factors enable C. albicans to overcome antifungal therapy and to successfully establish itself in specific host niches., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Joachim Morschhäuser. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The evolution of independent lineages along replicated environmental transitions frequently results in convergent adaptation, yet the degree to which convergence is present across multiple levels of biological organization is often unclear. Additionally, inherent biases associated with shared ancestry and variation in selective regimes across geographic replicates often pose challenges for confidently identifying patterns of convergence. We investigated a system in which three species of poeciliid fishes sympatrically occur in a toxic spring rich in hydrogen sulfide (H 2 S) and an adjacent nonsulfidic stream to examine patterns of adaptive evolution across levels of biological organization. We found convergence in morphological and physiological traits and genome-wide patterns of gene expression among all three species. In addition, there were shared signatures of selection on genes encoding H 2 S toxicity targets in the mitochondrial genomes of each species. However, analyses of nuclear genomes revealed neither evidence for substantial genomic islands of divergence around genes involved in H 2 S toxicity and detoxification nor substantial congruence of strongly differentiated regions across population pairs. These non-convergent, heterogeneous patterns of genomic divergence may indicate that sulfide tolerance is highly polygenic, with shared allele frequency shifts present at many loci with small effects along the genome. Alternatively, H 2 S tolerance may involve substantial genetic redundancy, with non-convergent, lineage-specific variation at multiple loci along the genome underpinning similar changes in phenotypes and gene expression. Overall, we demonstrate variability in the extent of convergence across organizational levels and highlight the challenges of linking patterns of convergence across scales., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Global climate change is exacerbating biological invasions; however, the roles of genomic and epigenomic variations and their interactions in future climate adaptation remain underexplored. Using the model invasive ascidian Botryllus schlosseri across the Northern Hemisphere, we investigated genomic and epigenomic responses to future climates and developed a framework to assess future invasion risks. We employed generalized dissimilarity modeling and gradient forest analyses to assess genomic and epigenomic offsets under climate change. Our results showed that populations with genomic maladaptation did not geographically overlap with those experiencing epigenomic maladaptation, suggesting that genomic and epigenomic variations play complementary roles in adaptation to future climate conditions. By integrating genomic and epigenomic offsets into the genome-epigenomic index, we predicted that populations with lower index values were less maladapted, indicating a higher risk of future invasions. Native populations exhibited lower offsets than invasive populations, suggesting greater adaptive potentials and higher invasion risks under future climate change scenarios. These results highlight the importance of incorporating multi-omics data into predictive models to study future climate (mal)adaptation and assess invasion risks under global climate change., (© 2024 John Wiley & Sons Ltd.)

Bacteria employ two-component systems (TCSs) to rapidly sense and respond to their surroundings often and during plant infection. Poplar canker caused by Lonsdalea populi is an emerging woody bacterial disease that leads to high mortality and poplar plantation losses in China. Nonetheless, the information about the underlying mechanism of pathogenesis remains scarce. Therefore, in this study, we reported the role of a TCS pair CpxA/CpxR in regulating virulence and stress responses in L. populi. The CpxA/R system is essential during infection, flagellum formation, and oxidative stress response. Specifically, the Cpx system affected flagellum formation by controlling the expression of flagellum-related genes. CpxR, which was activated by phosphorylation in the presence of CpxA, participated in the transcriptional regulation of a chaperone sctU and the type III secretion system (T3SS)-related genes, thereby influencing T3SS functions during L. populi infection. Phosphorylated CpxR directly manipulated the transcription of a membrane protein-coding gene yccA and the deletion of yccA resulted in reduced virulence and increased sensitivity to H 2 O 2 . Furthermore, we mutated the conserved phosphorylation site of CpxR and found that CpxR D51A could no longer bind to the yccA promoter but could still bind to the sctU promoter. Together, our findings elucidate the roles of the Cpx system in regulating virulence and reactive oxygen species resistance and provide further evidence that the TCS is crucial during infection and stress response., (© 2024 The Author(s). Molecular Plant Pathology published by British Society for Plant Pathology and John Wiley & Sons Ltd.)

Understanding the genetic basis of local adaptation in thermal performance is useful for predicting species distribution shifts under anthropogenic climate change. Many species are distributed across multiple biogeographic regions, and the uniquely adapted populations in each region may respond to future ocean warming with distinct distribution changes. In the present study, we investigated phylogeographic patterns, thermal sensitivity, and genetic differentiation in the intertidal snail Littorina brevicula along China's coast. Whole-genome sequencing results based on a newly assembled chromosome-level genome revealed two genetic lineages, with a north-south divergence that is linked to the thermal environment. Within each lineage, individuals could be further subdivided into genetic subgroups that differ at key genomic loci underpinning differences in upper heat tolerance. Heat stress drives adaptive divergence across multiple levels of organization, from the individual to the biogeographic level. Taking into account genetic diversity associated with variation in heat tolerance, a physiological species distribution model (pSDM) was applied to predict the distributions of the different genetic subgroups in response to climate change. Both northern and southern lineages were predicted to experience declines in habitat suitability under a 4°C future warming scenario, and that a genotypic subset of snails from the southern lineage may even be driven to extinction. These findings illustrate that even when a species' range is maintained, it can nonetheless experience a significant decrease in adaptive diversity as a result of climate change. The integrated approach presented here, which considered both physiological and adaptive genetic variation at the level of individuals within a biogeographical context, provided new insights into how marine species can respond to global warming., (© 2024 John Wiley & Sons Ltd.)

A joint analysis of dendrochronological and genomic data was performed to identify genetic mechanisms of adaptation and assess the adaptive genetic potential of Siberian stone pine ( Pinus sibirica Du Tour) populations. The data obtained are necessary for predicting the effect of climate change and mitigating its negative consequences. Presented are the results of an association analysis of the variation of 84,853 genetic markers (single nucleotide polymorphisms-SNPs) obtained by double digest restriction-site associated DNA sequencing (ddRADseq) and 110 individual phenotypic traits, including dendrophenotypes based on the dynamics of tree-ring widths (TRWs) of 234 individual trees in six natural populations of Siberian stone pine, which have a history of extreme climatic stresses (e.g., droughts) and outbreaks of defoliators (e.g., pine sawfly [ Neodiprion sertifer Geoff.]). The genetic structure of studied populations was relatively weak; samples are poorly differentiated and belong to genetically similar populations. Genotype-dendrophenotype associations were analyzed using three different approaches and corresponding models: General Linear Model (GLM), Bayesian Sparse Linear Mixed Model (BSLMM), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), respectively. Thirty SNPs were detected by at least two different approaches, and two SNPs by all three. In addition, three SNPs associated with mean values of recovery dendrophenotype (Rc) averaged across multiple years of climatic stresses were also found by all three methods. The sequences containing these SNPs were annotated using genome annotation of a very closely related species, whitebark pine ( P. albicaulis Engelm.). We found that most of the SNPs with supposedly adaptive variation were located in intergenic regions. Three dendrophenotype-associated SNPs were located within the 10 Kbp regions and one in the intron of the genes encoding proteins that play a crucial role in ensuring the integrity of the plant's genetic information, particularly under environmental stress conditions that can induce DNA damage. In addition, we found a correlation of individual heterozygosity with some dendrophenotypes. Heterosis was observed in most of these statistically significant cases; signs of homeostasis were also detected. Although most of the identified SNPs were not assigned to a particular gene, their high polymorphism and association with adaptive traits likely indicate high adaptive potential that can facilitate adaptation of Siberian stone pine populations to the climatic stresses and climate change.

With the advent of advanced sequencing technologies, new insights into the genomes of pathogens, including those in the genus Curtobacterium, have emerged. This research investigates a newly isolated C. flaccumfaciens strain 208 (Cf208) from Arthrocereus glaziovii, and endemic plant from Iron Quadrangle. Previous results show that Cf208 exhibits the potential to remediate soils, facilitating the growth of tomato plants. Furthermore, Cf208 showed no virulence towards bean plants, thus, confounding its phytopathogenic origins. Using a comprehensive comparative genomics approach, we analyzed the Cf208 genome against 34 other Curtobacterium strains, aiming to discern the genomic landmarks associated with its adaptation as an endophyte and its avirulence in bean crops. This revealed a predominant core genome comprising about 2426 genes (68%). Notably, Cf208 possesses a unique plasmid, pCF208-73, which contains 84 unique genes (2.5%). However, unlike the plasmids previously described for pathogenic strains, pCF208-73 does not feature genes associated with virulence induction. In contrast, while several genes traditionally linked to virulence, like pectate lyases and proteases were identified, but the T4P apparatus emerged as new crucial factor for understanding virulence in the Curtobacterium genus. The presence or absence of this apparatus, especially in strains from different clades, may determine their virulence towards leguminous plants. In conclusion, this work highlights the significance of comparative genomics in unraveling the complexities of pathogenicity within the Curtobacterium genus. Our findings suggest that, although the limited genetic variations, specific genes, particularly those linked to the T4P apparatus, play a fundamental role in their interactions with host plants., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Background: The Changthangi sheep thrive at high altitudes in the cold desert regions of Ladakh, India while Muzaffarnagri sheep are well-suited to the low altitude plains of northern India. This study investigates the molecular mechanisms of pulmonary adaptation to diverse environments by analyzing gene expression profiles of lung tissues through RNA sequencing., Methods and Results: Four biological replicates of lung tissue from each breed were utilized to generate the transcriptomic data. Differences in gene expression analysis revealed discrete expression profiles in lungs of each breed. In Changthangi sheep, genes related to immune responses, particularly cytokine signaling, were significantly enriched. Pathway analysis highlighted the activation of NF-kB signaling, a key mediator of inflammation and immune response. Additionally, the gene network analysis indicated a strong association between cytokine signaling, hypoxia-inducible factor (HIF) and NF-kB activation, suggesting a coordinated response to hypoxic stress in lungs of Changthangi sheep. In Muzaffarnagri sheep, the gene expression profiles were enriched for pathways related to energy metabolism, homeostasis and lung physiology. Key pathways identified include collagen formation and carbohydrate metabolism, both of which are crucial for maintaining lung function and structural integrity. Gene network analysis further reinforced this by revealing a strong connection between genes associated with lung structure and function., Conclusions: Our findings shed light on the valuable insights into gene expression mechanisms that enable these sheep breeds to adapt to their respective environments and contribute to a better understanding of high altitude adaptation in livestock., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Around 252 million years ago (Late Permian), Earth experienced one of its most significant drought periods, coinciding with a global climate crisis, resulting in a devastating loss of forest trees with no hope of recovery. In the current epoch (Anthropocene), the worsening of drought stress is expected to significantly affect forest communities. Despite extensive efforts, there is significantly less research at the molecular level on forest trees than on annual crop species. Would it not be wise to allocate equal efforts to woody species, regardless of their importance in providing essential furniture and sustaining most terrestrial ecosystems? For instance, the poplar genome is roughly quadruple the size of the Arabidopsis genome and has 1.6 times the number of genes. Thus, a massive effort in genomic studies focusing on forest trees has become inevitable to understand their adaptation to harsh conditions. Nevertheless, with the emerging role and development of high-throughput DNA sequencing systems, there is a growing body of literature about the responses of trees under drought at the molecular and eco-physiological levels. Therefore, synthesizing these findings through contextualizing drought history and concepts is essential to understanding how woody species adapt to water-limited conditions. Comprehensive genomic research on trees is critical for preserving biodiversity and ecosystem function. Integrating molecular insights with eco-physiological analysis will enhance forest management under climate change., (© 2024 Scandinavian Plant Physiology Society.)

Originating 30 million years ago, shrews (Soricidae) have diversified into around 400 species worldwide. Shrews display a wide array of adaptations, with some species having developed distinctive traits such as echolocation, underwater diving, and venomous saliva. Accordingly, these tiny insectivores are ideal to study the genomic mechanisms of evolution and adaptation. We conducted a comparative genomic analysis of four shrew species and 16 other mammals to identify genomic variations unique to shrews. Using two existing shrew genomes and two de novo assemblies for the maritime (Sorex maritimensis) and smoky (Sorex fumeus) shrews, we identified mutations in conserved regions of the genomes, also known as accelerated regions, gene families that underwent significant expansion, and positively selected genes. Our analyses unveiled shrew-specific genomic variants in genes associated with the nervous, metabolic, and auditory systems, which can be linked to unique traits in shrews. Notably, genes suggested to be under convergent evolution in echolocating mammals exhibited accelerated regions in shrews, and pathways linked to putative body size plasticity were detected. These findings provide insight into the evolutionary mechanisms shaping shrew species, shedding light on their adaptation and divergence over time., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Environmental transitions, such as the salinity divide separating marine and fresh waters, shape biodiversity over both shallow and deep timescales, opening up new niches and creating opportunities for accelerated speciation and adaptive radiation. Understanding the genetics of environmental adaptation is central to understanding how organisms colonise and subsequently diversify in new habitats. We used time-resolved transcriptomics to contrast the hyposalinity stress responses of two diatoms. Skeletonema marinoi has deep marine ancestry but has recently invaded brackish waters. Cyclotella cryptica has deep freshwater ancestry and can withstand a much broader salinity range. Skeletonema marinoi is less adept at mitigating even mild salinity stress compared to Cyclotella cryptica, which has distinct mechanisms for rapid mitigation of hyposaline stress and long-term growth in low salinity. We show that the cellular mechanisms underlying low salinity tolerance, which has allowed diversification across freshwater habitats worldwide, includes elements that are both conserved and variable across the diatom lineage. The balance between ancestral and lineage-specific environmental responses in phytoplankton have shaped marine-freshwater transitions on evolutionary timescales and, on contemporary timescales, will affect which lineages survive and adapt to changing ocean conditions., (© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

Natural populations of Arabidopsis thaliana provide powerful systems to study the adaptation of wild plant species. Previous research has predominantly focused on global populations or accessions collected from regions with diverse climates. However, little is known about the genetics underlying adaptation in regions with mild environmental clines. We have examined a diversity panel consisting of 192 A. thaliana accessions collected from the Netherlands, a region with limited climatic variation. Despite the relatively uniform climate, we identified evidence of local adaptation within this population. Notably, semidwarf accessions, due to mutation of the GIBBERELLIC ACID REQUIRING 5 (GA5) gene, occur at a relatively high frequency near the coast and these displayed enhanced tolerance to high wind velocities. Additionally, we evaluated the performance of the population under iron deficiency conditions and found that allelic variation in the FE SUPEROXIDE DISMUTASE 3 (FSD3) gene affects tolerance to low iron levels. Moreover, we explored patterns of local adaptation to environmental clines in temperature and precipitation, observing that allelic variation at LA RELATED PROTEIN 1C (LARP1c) likely affects drought tolerance. Not only is the genetic variation observed in a diversity panel of A. thaliana collected in a region with mild environmental clines comparable to that in collections sampled over larger geographic ranges but it is also sufficiently rich to elucidate the genetic and environmental factors underlying natural plant adaptation., (© 2024 The Author(s). The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Mammalian prions are neurotropic pathogens formed from PrP Sc assemblies, a misfolded variant of the host-encoded prion protein PrP C . Multiple PrP Sc conformations or strains self-propagate in host populations or mouse models of prion diseases, exhibiting distinct biological and biochemical phenotypes. Constrained interactions between PrP Sc and PrP C conformations confer species specificity and regulate cross-species transmission. The pathogenicity of fibrillar assemblies derived from bacterially expressed recombinant PrP (rPrP) has been instrumental in demonstrating the protein-only nature of prions. Yet, their ability to encode different strains and transmit between species remains poorly studied, hampering their use in exploring structure-to-strain relationships. Fibrillar assemblies from rPrP with hamster, mouse, human, and bovine primary structures were generated and tested for transmission and adaptation in tg7 transgenic mice expressing hamster PrP C . All assemblies, except the bovine ones, were fully pathogenic on the primary passage, causing clinical disease, PrP Sc brain deposition, and spongiform degeneration. They exhibited divergent adaptation processes and strain properties upon subsequent passage. Assemblies of hamster origin propagated without apparent need for adaptation, those of mouse origin adapted abruptly, and those of human origin required serial passages for optimal fitness. Molecular analyses revealed the presence of endogenously truncated PrP Sc species in the resulting synthetic strains that lack the 90-140 amino acid region considered crucial for infectivity. In conclusion, rPrP assemblies provide a facile means of generating novel prion strains with adaptative/evolutive properties mimicking genuine prions. The PrP amino acid backbone is sufficient to encode different strains with specific adaptative properties, offering insights into prion transmission and strain diversity., (© 2024 The Author(s). The FEBS Journal published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.)

The yellow dung fly Scathophaga stercoraria is a widely distributed species in high-altitude regions of the Northern Hemisphere. It plays important roles as a decomposer, predator, and pollinator in the ecosystem. As a staple model organism, S. stercoraria serves as a standard test species for assessing the toxicity of drug residues in livestock dung and has been the focus of numerous studies. The genetic mechanisms underlying the ecological adaptability of S. stercoraria remain poorly understood. To fill the gap, we first assembled a high-quality chromosome-level genome of S. stercoraria, resulting in a final assembly size of 549.64 Mb, with a contig N50 of 4.06 Mb, and 92.53 % of the sequence anchored to six chromosomes. Gene family analysis revealed an expansion of Toll (Toll1), GNBP3, Cyp303a1, Cyp4d14, Cyp6g1, OR67d, and yolk protein genes in the S. stercoraria genome. Transcriptome analysis indicated that most genes in the trypsin and carboxypeptidase gene families are predominantly expressed during the larval stage, whereas the α-Amylase gene family is mainly expressed during the adult stage. Additionally, PGRP-SC is highly expressed during the larval stage, OBPs are primarily expressed during the adult stage, and yolk protein genes exhibit female-biased expression. Our study not only provides a new resource for the dung flies genomic pool, but also identifies the expression patterns of key ecologically adaptative genes and gene families at the developmental stages, which provides new insights into the ecological adaptive evolution of dung flies., Competing Interests: Declaration of competing interest The authors have no competing interests., (Copyright © 2024 Elsevier B.V. All rights reserved.)

When environmental change is rapid or unpredictable, phenotypic plasticity can facilitate adaptation to new or stressful environments to promote population persistence long enough for adaptive evolution to occur. However, the underlying genetic mechanisms that contribute to plasticity and its role in adaptive evolution are generally unknown. Two main opposing hypotheses dominate-genetic compensation and genetic assimilation. Here, we predominantly find evidence for genetic compensation over assimilation in adapting the freshwater algae Chlamydomonas reinhardtii to 36 g/L salt environments over 500 generations. More canalized genes in the high-salt (HS) lines displayed a pattern of genetic compensation (63%) fixing near or at the ancestral native expression level, rather than genetic assimilation of the salt-induced level, suggesting that compensation was more common during adaptation to salt. Network analysis revealed an enrichment of genes involved in energy production and salt-resistance processes in HS lines, while an increase in DNA repair mechanisms was seen in ancestral strains. In addition, whole-transcriptome similarity among ancestral and HS lines displayed the evolution of a similar plastic response to salt conditions in independently reared HS lines. We also found more cis-acting regions in the HS lines; however, the expression patterns of most genes did not mimic that of their inherited sequence. Thus, the expression changes induced via plasticity offer temporary relief, but downstream changes are required for a sustainable solution during the evolutionary process., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Understanding the molecular mechanisms of thermal adaptation is crucial to predict the impacts of global warming. However, there is still a lack of research on the effects of rising temperatures over time and of studies involving different populations from the same species. The present study focuses on these two aspects, which are of great importance in understanding how organisms cope and adapt to ongoing changes in their environment. This study investigates the impact of global warming on the gene expression patterns of Drosophila subobscura populations from two different latitudinal locations after 23 generations of evolution. Our results indicate that evolutionary changes depend on the genetic background of the populations, with different starting points for thermal evolution, and that high-latitude populations show more pronounced evolutionary changes, with some evidence of convergence towards low-latitude populations. We found an interplay between plasticity and selection, with the high-latitude population showing fewer initial plastic genes and lower levels of adaptive plasticity, but a greater magnitude of change in both plastic and selective responses during evolution under warming conditions compared with its low-latitude counterpart. A substantial proportion of the transcriptome was observed to be evolving, despite the lack of observable response at higher-order phenotypic traits. The interplay between plasticity and selection may prove to be an essential component in shaping species' evolutionary responses to climate change. Furthermore, the value of conducting studies on multiple populations of the same species is emphasised, given the identification of differences between populations with different backgrounds in several contexts., (© 2024 John Wiley & Sons Ltd.)

Haemoglobin (HB) protein comprises four subunits: two identical α-subunits (HBA) and two identical β-subunits (HBB), encoded by the HBA and HBB genes. In this investigation, 5'/3' RACE PCR (Rapid Amplification of cDNA Ends) was used to obtain complete coding sequences (CDSs) of both the genes from farmed Labeo catla. The resulting CDSs were 432 base pairs and 447 base pairs for HBA and HBB, respectively, corresponding to 143 and 148 amino acids. Phylogenetic analysis revealed close relationships with other cyprinids, with Labeo rohita being the closest relative. Functional analysis and protein structure prediction were conducted using bioinformatics tools. Expression profiling of both genes was checked in various tissues under control (C) and hypoxic (H) conditions. Notably, under hypoxia, HBA and HBB genes were significantly upregulated (P < 0.05) initially, followed by a return to normal expression levels. Similar trends were observed for Hif1α (Hypoxia-inducible factor one alpha) and EPO (Erythropoietin) genes. Additionally, haematological indices also significantly increased corresponding to the gene expressions. However, with the decrease in the expression of these genes an onset of mortality was observed in the hypoxia (H) treated groups. The results of the current study explored the role of haemoglobin genes in adaptation to the hypoxic condition., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Drought stress is a key limitation for plant growth and colonization of arid habitats. We study the evolution of gene expression response to drought stress in a wild tomato, Solanum chilense, naturally occurring in dry habitats in South America. We conduct a transcriptome analysis under standard and drought experimental conditions to identify drought-responsive gene networks and estimate the age of the involved genes. We identify two main regulatory networks corresponding to two typical drought-responsive strategies: cell cycle and fundamental metabolic processes. The metabolic network exhibits a more recent evolutionary origin and a more variable transcriptome response than the cell cycle network (with ancestral origin and higher conservation of the transcriptional response). We also integrate population genomics analyses to reveal positive selection signals acting at the genes of both networks, revealing that genes exhibiting selective sweeps of older age also exhibit greater connectivity in the networks. These findings suggest that adaptive changes first occur at core genes of drought response networks, driving significant network re-wiring, which likely underpins species divergence and further spread into drier habitats. Combining transcriptomics and population genomics approaches, we decipher the timing of gene network evolution for drought stress response in arid habitats., (© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

The mobilization of transposable elements is a potent source of mutations. In plants, several stransposable elements respond to external cues, fuelling the hypothesis that natural transposition can create environmentally sensitive alleles for adaptation. Here we report on the detailed characterization of a retrotransposon insertion within the first intron of the Arabidopsis floral-repressor gene FLOWERING LOCUS C (FLC) and the discovery of its role for adaptation. The insertion mutation augments the environmental sensitivity of FLC by affecting the balance between coding and non-coding transcripts in response to stress, thus expediting flowering. This balance is modulated by DNA methylation and orchestrated by IBM2, a factor involved in the processing of intronic heterochromatic sequences. The stress-sensitive allele of FLC has spread across populations subjected to recurrent chemical weeding, and we show that retrotransposon-driven acceleration of the life cycle represents a rapid response to herbicide application. Our work provides a compelling example of a transposable element-driven environmentally sensitive allele that confers an adaptive response in nature., Competing Interests: Competing interests The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

This study investigated the acid adaptation and antimicrobial resistance of seven pathogenic Escherichia coli strains and one commensal strain under nutrient-rich acidic conditions. After acid adaptation, three pathogenic E. coli survived during 100 h incubation in tryptic soy broth at pH 3.25. Acid-adapted (AA) strains showed increased resistance to antimicrobials including ampicillin, ciprofloxacin and especially polymyxins (colistin and polymyxin B), the last resort antimicrobial for multidrug-resistant Gram-negative bacteria. Enterotoxigenic E. coli strain (NCCP 13717) showed significantly increased resistance to acids and polymyxins. Transcriptome analysis of the AA NCCP 13717 revealed upregulation of genes related to the acid fitness island and the arn operon, which reduces lipopolysaccharide binding affinity at the polymyxin site of action. Genes such as eptA, tolC, and ompCF were also upregulated to alter the structure of the cell membrane, reducing the outer membrane permeability compared to the control, which is likely to be another mechanism for polymyxin resistance. This study highlights the emergence of antimicrobial resistance in AA pathogenic E. coli strains, particularly polymyxin resistance, and the mechanisms behind the increased antimicrobial resistance, providing important insights for the development of risk management strategies to effectively control the antimicrobial resistant foodborne pathogens., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Pseudomonas aeruginosa demonstrates a remarkable capacity for adaptation and survival in diverse environments. Furthermore, its clinical importance is underscored by its intrinsic and acquired resistance to a wide range of antimicrobial agents, posing a substantial challenge in healthcare settings. Amidst this complex landscape of resistance, the Type VI Secretion System (T6SS) in P. aeruginosa adds yet another layer of intricacy and allows bacteria to engage in interbacterial competition, potentially influencing their resilience and pathogenicity. Whole genome sequencing (WGS) was conducted on the five isolates under investigation, enabling the identification of antibiotic resistance genes (ARGs) and mutations associated with resistance. All isolates exhibit class C and D β-lactamases, displaying variant differences. The Resistance-nodulation-division (RND) antibiotic efflux pumps, crucial for multidrug resistance, have been encoded chromosomally. When exploring the role of the T6SS in urinary tract infections involving other bacteria, it was noted that P. aeruginosa isolates exhibited reduced counts when co-cultivated with other bacteria. The downregulation of the tssJ gene, associated with the T6SS under bacterial stress, and the exclusion of several cluster genes in this study suggest the hypothesis of a basal state rather than an attack/defence mechanism in the initial contact., Competing Interests: Declaration of competing interest The authors declare no competing interests., (Copyright © 2024. Published by Elsevier Ltd.)

Aneuploidy, while detrimental to untransformed cells, is notably prevalent in cancer. Aneuploidy is found as an early event during tumorigenesis which indicates that cancer cells have the ability to surmount the initial stress responses associated with aneuploidy, enabling rapid proliferation despite aberrant karyotypes. To generate more insight into key cellular processes and requirements underlying adaptation to aneuploidy, we generated a panel of aneuploid clones in p53-deficient RPE-1 cells and studied their behavior over time. As expected, de novo-generated aneuploid clones initially display reduced fitness, enhanced levels of chromosomal instability (CIN), and an upregulated inflammatory response. Intriguingly, after prolonged culturing, aneuploid clones exhibit increased proliferation rates while maintaining aberrant karyotypes, indicative of an adaptive response to the aneuploid state. Interestingly, all adapted clones display reduced CIN and reduced inflammatory signaling, suggesting that these are common aspects of adaptation to aneuploidy. Collectively, our data suggests that CIN and concomitant inflammation are key processes that require correction to allow for fast proliferation in vitro. Finally, we provide evidence that amplification of oncogenic KRAS can promote adaptation., (© 2024. The Author(s).)

Sheep (Ovis aries), among the first domesticated species, are now globally widespread and exhibit remarkable adaptability to diverse environments. In this study, we perform whole-genome sequencing of 266 animals from 18 distinct Chinese sheep populations, each displaying unique phenotypes indicative of adaptation to varying environmental conditions. Integrating 131 environmental factors with single nucleotide polymorphism variations, we conduct a comprehensive genetic-environmental association analysis. This analysis identifies 35 key genes likely integral to the environmental adaptation of sheep. The functions of these genes include fat tail formation (HOXA10, HOXA11, JAZF1), wool characteristics (FER, FGF5, MITF, PDE4B), horn phenotypes (RXFP2), reproduction (HIBADH, TRIM71, C6H4orf22), and growth traits (ADGRL3, TRHDE). Notably, we observe a significant correlation between the frequency of missense mutations in the PAPSS2 and RXFP2 genes and variations in altitude. Our study reveals candidate genes for adaptive variation in sheep and demonstrates the diversity in how sheep adapt to their environment., Competing Interests: Conflict of interest The authors declare that they have no competing interests., (Copyright © 2024 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.)

Trehalose-6-phosphate synthase (TPS) genes play an active role in the trehalose metabolism pathway that regulates the responses of plants to diverse stresses. However, the functional identification, comparison, and conservatism of TPS genes in the responses of woody plants, especially poplars, to drought stress remain unclear. Here, the trehalose content of 84K (Populus alba × P. glandulosa) poplars was down-regulated and PagTPS and PagTPP genes had diverse response patterns under drought stress. Physicochemical properties, expression patterns, and functions of PagTPS1 and PagTPS10, two class I members of TPS gene family, were identified and compared. Transgenic 84K poplars overexpressing PagTPS1 and PagTPS10 had significantly higher trehalose content with approximately 138% and 123%, respectively, and stronger drought tolerance compared to WT. PagTPS1 and PagTPS10 promoted the expression of TPPA genes and drought-responsive genes. Accordingly, poplars inhibiting PagTPS1 and PagTPS10 expression via RNA interference had lower trehalose content and drought tolerance. Simultaneously, overexpressing PagTPS1 and PagTPS10 improved the trehalose content and drought tolerance of Arabidopsis. Overall, we proposed a model of the effects of PagTPS1 and PagTPS10 as conservative regulators on the responses of plants to drought, which would provide new insights into the functional explorations of TPS genes in plants., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Waterlogging stress is a severe abiotic challenge that impedes plant growth and development. Ramie (Boehmeria nivea L.) is a Chinese traditional characteristic economic crop, valued for its fibers and by-products. To investigate the waterlogging tolerance of ramie and provide the scientific basis for selecting waterlogging-tolerant ramie varieties, this study examined the morphological, physiological, biochemical, and molecular responses of 15 ramie germplasms (varieties) under waterlogging stress. The results revealed varied impacts of waterlogging stress across the 15 ramie varieties, characterized by a decrease in SPAD values, net photosynthesis rates, and relative water content of ramie leaves, along with a significant increase in relative conductivity and the activities of antioxidant enzymes such as SOD, POD, CAT, and APX. Additionally, the levels of soluble sugars, soluble proteins, and free proline exhibited varying degrees of increase. Through Principal Component Analysis (PCA), ZZ&#95;2 and ZSZ&#95;1 were identified as relatively tolerant and susceptible varieties. Transcriptome analysis showed that the differential expressed genes between ZZ&#95;2 and ZSZ&#95;1 were significantly enriched in metabolic pathways, ascorbate and aldarate metabolism, and inositol phosphate metabolism, under waterlogging stress. In addition, the expression of hypoxia-responsive genes was higher in ZZ&#95;2 than in ZSZ&#95;1 under waterlogging stress. These differences might account for the varied waterlogging responses between the two varieties. Therefore, this study explored the morpho-physiological responses of ramie under waterlogging stress and identified the molecular mechanisms involved, providing valuable insights for improving ramie varieties and breeding new ones., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Masson SAS. All rights reserved.)

Soil nitrogen (N) significantly influences the interaction between plants and pathogens, yet its impact on host defenses and pathogen strategies via alterations in plant metabolism remains unclear. Through metabolic and genetic studies, this research demonstrates that high-N-input exacerbates tomato bacterial wilt by altering γ-aminobutyric acid (GABA) metabolism of host plants. Under high-N conditions, the nitrate sensor NIN-like protein 7 (SlNLP7) promotes the glutamate decarboxylase 2/4 (SlGAD2/4) transcription and GABA synthesis by directly binding to the promoters of SlGAD2/4. The tomato plants with enhanced GABA levels showed stronger immune responses but remained susceptible to Ralstonia solanacearum. This led to the discovery that GABA produced by the host actually heightens the pathogen's virulence. We identified the R. solanacearum LysR-type transcriptional regulator OxyR protein, which senses host-derived GABA and, upon interaction, triggers a response involving protein dimerization that enhances the pathogen's oxidative stress tolerance by activating the expression of catalase (katE/katGa). These findings reveal GABA's dual role in activating host immunity and enhancing pathogen tolerance to oxidative stress, highlighting the complex relationship between tomato plants and R. solanacearum, influenced by soil N status., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)

Plant responses to cold stress include either induction of flavonoid biosynthesis as part of defense responses or initially elevated levels of these substances to mitigate sudden temperature fluctuations. The role of chromatin modifying factors and, in general, epigenetic variability in these processes is not entirely clear. In this work, we review the literature to establish the relationship between flavonoids, cold and chromatin modifications. We demonstrate the relationship between cold acclimation and flavonoid accumulation, and then describe the cold adaptation signaling pathways and their relationship with chromatin modifying factors. Particular attention was paid to the cold signaling module OST1-HOS1-ICE1 and the novel function of the E3 ubiquitin protein ligase HOS1 (a protein involved in chromatin modification during cold stress) in flavonoid regulation., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Masson SAS. All rights reserved.)

Superfamily of cytochromes P450 (CYPs) is composed of heme-thiolate-containing monooxygenase enzymes, which play crucial roles in the biosynthesis, bioactivation, and detoxification of a variety of organic compounds, both endogenic and exogenic. Majority of CYP monooxygenase systems are multi-component and contain various redox partners, cofactors and auxiliary proteins, which contribute to their diversity in both prokaryotes and eukaryotes. Recent progress in bioinformatics and computational biology approaches make it possible to undertake whole-genome and phylogenetic analyses of CYPomes of a variety of organisms. Considerable variations in sequences within and between CYP families and high similarity in secondary and tertiary structures between all CYPs along with dramatic conformational changes in secondary structure elements of a substrate binding site during catalysis have been reported. This provides structural plasticity and substrate promiscuity, which underlie functional diversity of CYPs. Gene duplication and mutation events underlie CYP evolutionary diversity and emergence of novel selectable functions, which provide the involvement of CYPs in high adaptability to changing environmental conditions and dietary restrictions. In our review, we discuss the recent advancements and challenges in the elucidating the evolutionary origin and mechanisms underlying the CYP monooxygenase system diversity and plasticity. Our review is in the view of hypothesis that diversity of CYP monooxygenase systems is translated into the broad metabolic profiles, and this has been acquired during the long evolutionary time to provide structural plasticity leading to high adaptative capabilities to environmental stress conditions., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

The fourfinger threadfin fish (Eleutheronema tetradactylum) is an economically significant species renowned for its ability to adapt to varying salinity environments, with gills serving as their primary organs for osmoregulation and immune defense. Previous studies focused on tissue and morphological levels, whereas ignored the cellular heterogeneity and the crucial gene information related to core cell subsets within E. tetradactylum gills. In this study, we utilized high-throughput single-cell RNA sequencing (scRNA-seq) to analyze the gills of E. tetradactylum, characterizing 16 distinct cell types and identifying unique gene markers and enriched functions associated within each cell type. Additionally, we subdivided ionocyte cells into four distinct subpopulations for the first time in E. tetradactylum gills. By employing weighted gene co-expression network analysis (WGCNA), we further investigated the cellular heterogeneity and specific response mechanisms to salinity fluctuant. Our findings revealed the intricate osmoregulation and immune functions of gill cells, highlighting their crucial roles in maintaining homeostasis and adapting to fluctuating salinity levels. This comprehensive cell-type atlas provides valuable insights into the species adaptive strategies, contributing to the conservation and management of this commercially significant fish as well as other euryhaline species., (Copyright © 2024 Elsevier Ltd. All rights reserved.)