The genomic mechanisms underlying large-scale chromosomal rearrangements and their evolutionary consequences remain poorly understood. Here, we generated chromosome-level genomes for two sister species pairs of blind mole rats that differ in chromosome numbers. We identified five chromosome fusions during the divergence from a common ancestor (2n = 60). Three shared fusions gave rise to the Spalax galili (2n = 52)-S. golani (2n = 54) clade and accompanied its divergence from the S. carmeli (2n = 58)-S. judaei (2n = 60) clade. Both S. galili and S. carmeli further underwent an independent fusion. These fusions, facilitated by repetitive elements, were associated with changes in three-dimensional genome architecture. Notably, we found reduced gene flow near fusion points. Chromosomal fusions correlated with signatures of selection and may have become fixed through centromeric repeat expansion. Together, these findings provide a genome-wide framework for investigating how chromosomal fusions relate to genome organization and lineage divergence.

Murine double minute 2 (MDM2) and murine double minute 4 (MDMX) are critical for the regulation of tumor protein 53 (p53) function and apoptosis. This study compares the Mdm2/x gene sequences and functional variations of subterranean zokors from the High Plateau and the Loess Plateau. The findings reveal the molecular mechanisms by which Mdm2/x variations drive adaptation to extremely high-altitude conditions—including low oxygen, cold temperatures, and perpetual darkness in underground environments. We cloned and analyzed Mdm2/x sequences from two distinct ecological groups of subterranean rodents, Myospalax baileyi (plateau zokor) and Myospalax cansus (Gansu zokor), and reconstructed phylogenetic trees for a series of subterranean rodents and mammals, as well as the aboveground laboratory rat and humans. We found that MDM2/X in M. baileyi and M. cansus are involved in the p53-dependent low apoptosis rate, and the variations of phosphorylation sites at the C-terminus of MDM2 contribute to upregulation of p53 transcription and protein expression. We propose that gene evolutionary mechanisms enable survival under these severe combined pressures, and believe that our findings provide critical insight into how genetic modifications drive physiological resilience in Earth’s most challenging ecosystems.

Ecological speciation refers to the process in which divergent natural selection drives lineage diversification within a species. The Upper Galilee blind mole rat (Nannospalax galili) provides a compelling model for studying ecological speciation because it inhabits a landscape lacking physical barriers yet characterized by a stark ecological contrast between rendzina and basaltic soils in northern Israel. These soils differ in multiple biologically relevant properties that strongly influence mole rat biology. Here, we examined differences in energetics and bite force in mole rats from basaltic and rendzina soils to assess whether such differences might contribute to local adaptation and facilitate ecological speciation. We found no population-level differences in resting metabolic rate, digging metabolic rate, body heat dissipation patterns, or bite force. In contrast, basalt-dwelling mole rats maintained approximately 1.6°C lower body temperatures than rendzina-dwelling counterparts, exhibited a larger post-digging increase in body temperature after burrowing in either soil type, and showed higher digging efficiency. These physiological differences are consistent with the dual challenges of basaltic soil, namely its higher mechanical resistance to digging and the seasonally more hypoxic, CO2-rich atmosphere within its burrows. Collectively, our results support a scenario in which thermal and hypoxia-related physiological traits underpin local adaptations and may contribute to ecological speciation of blind mole rats across contrasting soil habitats.

Chromosomal fusion and fission are widespread across species, yet the underlying genomic mechanisms and their evolutionary implications remain poorly understood. Here, we present high-quality chromosome-level genome assemblies for two closely related subterranean rodent species, Eospalax rufescens and E. rothschildi. Through comparative genomic and synteny analyses, we identified two species-specific chromosomal fusions in E. rothschildi, likely mediated by ectopic recombination through repetitive elements and by mutations affecting genome stability. Despite minimal changes in base-level genomic features, the fused chromosomes are associated with altered three-dimensional (3D) chromatin architecture, including increased chromatin entropy, topologically associating domain (TAD) rearrangement, and compartment switching. Reduced gene flow on the fused chromosomes suggests a role in reproductive isolation. Additionally, molecular signals of relaxed selection and adaptive evolution in pathways related to DNA repair, chromatin dynamics, and environmental sensing highlight the interplay between structural and ecological factors in shaping divergence. Together, our findings provide a mechanistic and evolutionary framework linking chromosomal fusions with genome architecture remodeling, epigenetic changes, and barriers to gene flow in mammals, offering a valuable resource for future evolutionary genomics studies.

Oxygen-sensing and the hypoxia stress response play vital roles in physiological homeostasis. Subterranean species that are naturally adapted to hypoxia provide powerful tools for understanding the mechanisms of hypoxia tolerance. The plateau zokor Eospalax baileyi and the Gansu zokor Eospalax cansus, which inhabit the Qinghai-Tibet Plateau of China, and the blind mole rat Spalax galili, which lives in Israel, are all subterranean rodents adapted to hypoxic environments. Here, we showed that the T480S variant of the hypoxia-inducible factor-2ɑ (encoded by the endothelial PAS domain protein 1 gene, Epas1) in Chinese zokors stabilized EPAS1 by reducing phosphorylation, thereby regulating fibrosis and contributing to hypoxia adaptation on the Qinghai-Tibet Plateau. In Israeli blind mole rats, variants at positions -2023/-1810 in the Epas1 regulatory region distinguish two abutting populations undergoing incipient sympatric speciation by altering the binding of cMYB and hepatocyte nuclear factor 4 gamma, linking transcriptional activity to the interferon mRNA transcription. This finding reveals an adaptive regulation of metabolism and O2 homeostasis by the Epas1 gene in adaptation to diverse habitats, providing evidence for both divergent and convergent functional molecular evolution.

Corticotropin-releasing factor (CRF) and its receptor (CRFR1) are critical components of the hypothalamic-pituitary-adrenocortical (HPA) axis. Ochotona curzoniae (O. curzoniae), Myospalax baileyi (M. baileyi), and Microtus oeconomus (M. oeconomus) have diversely evolved adaptive strategies to the extreme environment at high altitude. Here, we found blunted HPA axis responsiveness in native Tibetan mammals. CRF was 100

Resistance to wheat powdery mildew is commonly mediated by individual resistance proteins, most of which encode nucleotide-binding leucine-rich repeat (NLR) receptors. Here we report that the powdery mildew resistance gene MLIW170/PM26 in wild emmer and bread wheat derivatives is determined by a genetically linked atypical NLR pair TdCNL1/TdCNL5. Map-based cloning and PacBio HiFi long-read sequencing revealed that TdCNL1 encodes an atypical coiled-coil-domain-containing NLR protein (CNL) fused with a new potassium-dependent sodium-calcium exchanger integrated domain, whereas TdCNL5 encodes a canonical CNL protein. Mutagenesis and virus-induced gene silencing experiments indicated that both TdCNL1 and TdCNL5 are essential for powdery mildew resistance. Transgenic plants with TdCNL1 alone or TdCNL1/TdCNL5 together show resistance, whereas Fielder with TdCNL5 alone was susceptible. Geographically, MLIW170/PM26 occurs in a few Southern populations of wild emmer wheat. Our study highlights an atypical NLR pair coordinately regulating powdery mildew resistance and provides a diversified resistance gene resource for wheat improvement.

Ecological speciation is an evolutionary process driven by divergent natural selection in heterogeneous environments characterised by diverse resources and habitats. Increasing evidence supports the occurrence of this phenomenon in nature. One frequently cited example among mammals is the Upper Galilee Mountains blind mole rat, Nannospalax galili. Over a decade ago, it was proposed that this species is undergoing incipient ecological speciation due to the sharply contrasting ecological conditions resulting from the presence of pale rendzina and dark basaltic soils. In this study, we examined the population genetic structure and gene flow between mole rats inhabiting these two distinct soil types at two localities in Northern Israel, Rihaniya and Gush Halav, each containing sites on both rendzina and basaltic soil types. We used eight microsatellite markers to assess genetic differentiation. The results indicate that in Rihaniya, where blind mole rats from both soils were sampled in close proximity, the genetic divergence between animals from the different soil types was the lowest. In Gush Halav, the genetic differentiation increased with geographic distance between sampled sites, indicating an isolation-by-distance effect. The presence of migrants and first-generation hybrids in both soils at both localities suggests that blind mole rats migrate and mate relatively frequently between the two soil types. These findings imply that ecological speciation in N. galili may be in its very early stages, with no clear evidence of assortative mating yet. Further research is needed to understand this phenomenon in this study system.

Climate change is increasing the frequency and severity of drought worldwide, threatening the environmental resilience of cultivated grasses. However, the genetic diversity in many wild grasses could contribute to the development of climate-adapted varieties. Here, we elucidated the impact of polyploidy on drought responses using allotetraploid Brachypodium hybridum (B. hybridum) and its progenitor diploid species Brachypodium stacei (B. stacei). Our findings suggest that progenitor species' genomic legacies resulting from hybridization and whole-genome duplications conferred greater ecological adaptive advantages to B. hybridum compared with B. stacei. Genes related to stomatal regulation and the immune response from S-subgenomes were under positive selection during speciation, underscoring their evolutionary importance in adapting to environmental stresses. Biased expression in polyploid subgenomes (B. stacei-type and B. distachyon-type) significantly influenced differential gene expression, with the dominant subgenome exhibiting more differential expression. B. hybridum adapted a drought escape strategy characterized by higher photosynthetic capacity and lower intrinsic water-use efficiency than B. stacei, driven by a highly correlated coexpression network involving genes in the circadian rhythm pathway. In summary, our study shows the influence of polyploidy on ecological and environmental adaptation and resilience in model Brachypodium grasses. These insights hold promise for informing the breeding of climate-resilient cereal crops and pasture grasses.

Hortiboletus (the former Xerocomus rubellus species complex) is one of the most taxonomically critical and difficult genera for species identification in the family Boletaceae. Here, we provide a detailed morphological and molecular re-assessment of European and Levantine species of Hortiboletus. A new species, H. hershenzoniae, is described from Israel. It is sister to H. engelii and associated with the evergreen oak Quercus calliprinos and potentially also with Q. ithaburensis. Based on the sequence retrieved from INSDC, this species is also found in Lebanon. Accurate morphological descriptions, comprehensive sampling, type studies, biogeography, macro- and microphotographs and a historical overview on the nomenclatural issues surrounding H. rubellus, H. bubalinus, H. engelii, and H. hershenzoniae are given. An epitype collection is designated for H. rubellus. A key is provided for identification of the European and Levantine taxa. In addition, we propose a novel taxonomic combination Hortiboletus flavorubellus, which is conspecific with Boletus rubellus var. flammeus, based on the DNA barcoding and phylogenetic analysis of type material. Boletus harrisonii is also shown to be conspecific with H. campestris. A multilocus phylogenetic analysis of four markers (ITS, LSU, tef1-α, and rpb2) reveals that Hortiboletus is a sister genus to Xerocomellus. Using the Genealogical Concordance Phylogenetic Species Recognition method, at least 19 phylogenetic species and eight putative phylogenetic species of the genus Hortiboletus can be delimited. Based on multilocus analysis, it contains from 24 to 25 species-level clades worldwide, 17 out of which represent known species, one newly described and potentially six to seven undescribed species. Tandem repeat insertions within the ITS region (both in ITS1 and ITS2) are reported for the first time, not only in the genus Hortiboletus, but in the entire subfamily Boletoideae. Their identification and characterisation were based on Tandem Repeat Finder analysis and visual assessment of the ITS alignment.

Chromosomal fissions and fusions are common, yet the molecular mechanisms and implications in speciation remain poorly understood. Here, we confirm a fission event in one zokor species through multiple-omics and functional analyses. We traced this event to a mutation in a splicing enhancer of the DNA repair gene Aplf in the fission-bearing species, which caused exon skipping and produced a truncated protein that disrupted DNA repair. An intronic deletion in Dna2, known to facilitate neo-telomere formation when knocked out, reduced gene activity. These variants collectively drove chromosomal fission in this zokor species. The newly formed chromosome became fixed due to carrying essential genes and strong selective pressure. While geographic isolation likely initiated the divergence of this species and the sister one, the fission event and associated decline at the chromosome level in gene flow probably exacerbated the speciation process. Our work elucidates the genetic basis of chromosomal fission and underscores its role in speciation dynamics.

Mammals exhibit diverse adaptations to varied habitats, yet the genomic mechanisms underlying these transitions remain incompletely understood. Here, we present a comparative genomic, epigenomic, and three-dimensional chromatin analysis of two closely related zokor species, Myospalax aspalax and Myospalax psilurus, which inhabit arid and humid subterranean environments, respectively. We identified subterranean lineage-specific positively selected and rapidly evolving genes enriched for DNA repair, hypoxia response, blood vessel development, and fructose metabolism. M. psilurus showed a notable loss of olfactory receptor genes, expansion of pheromone-related gene families, and widespread activation of a specific ERVK transposable element family, accompanied by elevated DNA methylation, suggesting enhanced epigenetic defenses and ecological specialization. In contrast, M. aspalax showed selection in kidney and lipid metabolism genes. Large chromosomal inversions (> 1 Mb) overlapped islands of high genetic divergence (high-FST or high Dxy) and were enriched for sensory, reproductive, and DNA repair genes. Although chromatin compartments remained largely stable, large inversions disrupted topologically associating domains and preferentially occurred in regions characterized by longer chromatin loops. Inversion breakpoints were flanked by inverted repeats and segmental duplications—features characteristic of the formation mechanism of non-allelic homologous recombination, suggesting that both the spatial proximity and sequence architecture of these regions may predispose them to large inversions. Overall, our results illuminate the structural, regulatory, and evolutionary mechanisms underlying ecological divergence and highlight how genome architecture contributes to adaptive evolution in subterranean mammals.

Understanding how microbiomes influence the life cycle and fitness of crops, and how global change drivers disrupt this network, is pivotal for an understanding of the crop as a holobiont, and of how to provide solutions for Nordic agricultural crop resilience under climate change. Despite decades of use of plant growth-promoting rhizobacteria (PGPR), there is an intrinsic problem with their applications, as it has become evident that their functionality and performance rely on interactions with the environment and with other microorganisms. The synthetic crop promoting rhizobacterial community strains are being outcompeted by native communities, or their colonisation and active principles are being reduced to ineffective levels. This is the result of the communities being selected on taxonomic criteria rather than qualitative analysis of the microbiome associated plant phenotypes. In this context there in an urgent need for an approach studying the microbial community and plant complementarity traits from indigenous communities. Here we report the pattern of bacterial distributions at the Evolution Canyon (EC) in Israel to gain insight into microbiomes exposed to contrasting microclimates at the North Facing Slope (NFS) and South Facing Slope (SFS) sun and shade areas using high-throughput sequencing. While the NFS and SFS shaded areas bacterial distribution didnt differ, our results show significant differences between the NFS and the SFS sunny areas. The families Geodermatophilaceae, Beijerinckiaceae, and Pseudonocardiaceae are dominant in the NFS sun area, and the families Rubrobacteriaceae, unclassified Solirubrobacterales bacterium 67 14, unclassified Actinobacteriota, class Gaiellales dominate at the SFS sun area. Likewise, both Shannon and inverse Simpsons diversity indices are higher at the NFS sun area compared to the NFS shaded area. There was no substantial difference between diversity indices in SFS sun and shaded area. Our results advance our understanding of the bacterial distributions at what is in effect a natural laboratory of ecosystems that probably evolved 5 to 7 million years ago. The data are an important step towards using transcriptomics, metabolomic profiles and selective plating for figuring out key strains and the supporter strains that strengthen the ecological functions of the key strains. Collectively, this will enable us to assemble redundant and stable synthetic PGPR communities consisting of key and supporter strains for promoting plant health and stress tolerance under changing climates. ### Competing Interest Statement The authors have declared no competing interest.

Zokors, an Asiatic group of subterranean rodents, originated in lowlands and colonized high-elevational zones following the uplift of the Qinghai–Tibet plateau about 3.6 million years ago. Zokors live at high elevation in subterranean burrows and experience hypobaric hypoxia, including both hypoxia (low oxygen concentration) and hypercapnia (elevated partial pressure of CO 2 ). Here we report a genomic analysis of six zokor species (genus Eospalax ) with different elevational ranges to identify structural variants (deletions and inversions) that may have contributed to high-elevation adaptation. Based on an assembly of a chromosome-level genome of the high-elevation species, Eospalax baileyi , we identified 18 large inversions that distinguished this species from congeners native to lower elevations. Small-scale structural variants in the introns of EGLN1 , HIF1A , HSF1 and SFTPD of E. baileyi were associated with the upregulated expression of those genes. A rearrangement on chromosome 1 was associated with altered chromatin accessibility, leading to modified gene expression profiles of key genes involved in the physiological response to hypoxia. Multigene families that underwent copy-number expansions in E. baileyi were enriched for autophagy, HIF1 signalling and immune response. E. baileyi show a significantly larger lung mass than those of other Eospalax species. These findings highlight the key role of structural variants underlying hypoxia adaptation of high-elevation species in Eospalax .

Crop wild relatives offer natural variations of disease resistance for crop improvement. Here, we report the isolation of broad-spectrum powdery mildew resistance gene Pm36, originated from wild emmer wheat, that encodes a tandem kinase with a transmembrane domain (WTK7-TM) through the combination of map-based cloning, PacBio SMRT long-read genome sequencing, mutagenesis, and transformation. Mutagenesis assay reveals that the two kinase domains and the transmembrane domain of WTK7-TM are critical for the powdery mildew resistance function. Consistently, in vitro phosphorylation assay shows that two kinase domains are indispensable for the kinase activity of WTK7-TM. Haplotype analysis uncovers that Pm36 is an orphan gene only present in a few wild emmer wheat, indicating its single ancient origin and potential contribution to the current wheat gene pool. Overall, our findings not only provide a powdery mildew resistance gene with great potential in wheat breeding but also sheds light into the mechanism underlying broad-spectrum resistance. Powdery mildew is a fungal leaf disease that reduces yield and grain quality in susceptible wheat varieties. Here, the authors report the cloning of the wild emmer wheat originated powdery mildew resistance gene Pm36 as a membrane associated tandem kinase and its possible resistance mechanism.

Mounting theoretical and empirical studies prove that sympatric speciation is possible in nature, however, it’s commonality is still debated. Here we show genomic evidence for incipient sympatric speciation in Drosophila hydei from Evolution Canyon I in Mount Carmel Israel. First, we provide a reference genome with contig N50 of 4.72 Mb. Population genomes were clearly separated between the hot-dry savannoid African slope (AS) and cool-humid temperate European slope (ES). Genetic diversity and recombination rate was significantly higher in ES new sympatric species than that in AS. Tajima’s D is significantly higher in AS than that in ES suggesting they were under different non-random selection patterns, rejecting neutrality. We identified 137 islands and the genetic parameters were significantly different with that of the backgrounds. Putatively selected genes (GO enrichment) from ES population were enriched in higher aggression, photoreception, autophagy, temperature, neurogenetics and reproduction, and defense responses against bacteria and fungi. By contrast, in the AS, the selected genes were enriched in aging, autophagy, visual system and response to nutrient level.

Tibetan sheep were introduced to the Qinghai Tibet plateau roughly 3,000 B.P., making this species a good model for investigating genetic mechanisms of high-altitude adaptation over a relatively short timescale. Here, we characterize genomic structural variants (SVs) that distinguish Tibetan sheep from closely related, low-altitude Hu sheep, and we examine associated changes in tissue-specific gene expression. We document differentiation between the two sheep breeds in frequencies of SVs associated with genes involved in cardiac function and circulation. In Tibetan sheep, we identified high-frequency SVs in a total of 462 genes, including EPAS1 , PAPSS2 , and PTPRD . Single-cell RNA-Seq data and luciferase reporter assays revealed that the SVs had cis -acting effects on the expression levels of these three genes in specific tissues and cell types. In Tibetan sheep, we identified a high-frequency chromosomal inversion that exhibited modified chromatin architectures relative to the noninverted allele that predominates in Hu sheep. The inversion harbors several genes with altered expression patterns related to heart protection, brown adipocyte proliferation, angiogenesis, and DNA repair. These findings indicate that SVs represent an important source of genetic variation in gene expression and may have contributed to high-altitude adaptation in Tibetan sheep.

The subterranean blind mole rat, Spalax, has evolved significantly over 47 million years to thrive in its underground habitat. A key enzyme in this adaptation is heparanase, which degrades heparan sulfate (HS) in the extracellular matrix (ECM), facilitating angiogenesis and releasing growth factors for endothelial cells. Spalax heparanase has various splice variants influencing tumor growth and metastasis differently. We report a novel splice variant from a hypoxia-exposed kidney sample resulting from exon 12 skipping. This variant maintains the translation frame but lacks enzymatic activity, offering insights into Spalax’s unique adaptations.

Both homeologous exchanges and homeologous expression bias are generally found in most allopolyploid species. Whether homeologous exchanges and homeologous expression bias differ between repeated allopolyploid speciation events from the same progenitor species remains unknown. Here, we detected a third independent and recent allotetraploid origin for the model grass Brachypodium hybridum. Our homeologous exchange with replacement analyses indicated the absence of significant homeologous exchanges in any of the three types of wild allotetraploids, supporting the integrity of their progenitor subgenomes and the immediate creation of the amphidiploids. Further homeologous expression bias tests did not uncover significant subgenomic dominance in different tissues and conditions of the allotetraploids. This suggests a balanced expression of homeologs under similar or dissimilar ecological conditions in their natural habitats. We observed that the density of transposons around genes was not associated with the initial establishment of subgenome dominance; rather, this feature is inherited from the progenitor genome. We found that drought response genes were highly induced in the two subgenomes, likely contributing to the local adaptation of this species to arid habitats in the third allotetraploid event. These findings provide evidence for the consistency of subgenomic stability of parental genomes across multiple allopolyploidization events that led to the same species at different periods. Our study emphasizes the importance of selecting closely related progenitor species genomes to accurately assess homeologous exchange with replacement in allopolyploids, thereby avoiding the detection of false homeologous exchanges when using less related progenitor species genomes.

Oats (Avena sativa L.) are mostly used as a germplasm resource for forage. This experiment showed the differences in the nutrient composition and the forage quality of five wild leather oat populations from Israel and one cultivated leather oat population from China. It also showed the correlation of the indicators with the geo-environmental factors in the places of origin of the six populations that were analysed. Three replicated experiments were conducted during a three-year period from 2018.10 to 2020.03, mainly from 11 indicators of nutrient composition and forage quality. In this experiment, Spearman’s correlation was used to analyse the differences between different groups (p < 0.05), the relationship between components was analysed by principal component analysis (PCA), and the kinship relationship between six groups was also analysed based on the data of 11 components. In terms of nutrient content, the cultivated group Hu had significantly lower ash (8.92%), crude protein (11.96%), and soluble sugar content (10.51%) than the wild oat groups. In terms of forage quality, the lignin content (3.31%) of the Hu population was 2.3 times higher than that of Evolution Canyon, and the fibre content was 8 times higher than that of Sede Boqer. This indicates that wild oats have better nutritional value and palatability. Following the correlation analysis, it was found that the environmental factors of the origin had a significant effect on the indexes of ash, crude protein, and soluble sugar of oat straw, but had less effect on the content of crude fat, total phosphorus, and total potassium. Meanwhile, the annual rainfall and the number of rainfall days in the origin had a significant effect on the fibre content. In conclusion, the higher variability of wild oat populations due to the influence of different environmental and geographical factors may be a new possibility brought by forage oats.