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PubMed2025

A One Health perspective: Genomic insights into temporal trends of antimicrobial resistance and zoonotic transmission risks in Escherichia coli from human and swine.

Antimicrobial resistance (AMR) poses a significant challenge within the One Health framework. By integrating genomic data from 824 E. coli isolates obtained from 22 swine farms in southwestern China with 8432 publicly available genomes from human and swine sources, this study provides comprehensive insights into the temporal trends and divergence of AMR in human and swine E. coli populations, the risk of AMR transmission from swine to human, and the evolutionary mechanisms underlying the human adaptation of ST2 strains. The results revealed an overall increase in AMR until approximately 2016, followed by a subsequent decline. However, resistance to tetracyclines, quinolones, and phenicols continues to exhibit an upward trend, highlighting the urgency of enhancing regulatory measures targeting these drugs. Horizontal gene transfer play pivotal roles in shaping distinct AMR profiles in human and swine strains. ST2 E. coli was identified as a major carrier of AMR in both human and swine, and also served as the primary reservoir of blaNDM-5 within the human-associated lineage. During evolution, ST2 E. coli underwent significant genetic changes, including the enrichment of blaNDM-5 and remodeling of virulence factors, facilitating its transition from a generalist lineage colonizing both human and swine to a human-adapted lineage.

Humans↗
PubMed2025

A chromosomal-level genome assembly of Odontolabis cuvera Hope, 1842 (Coleoptera: Lucanidae).

The stag beetle (Coleoptera: Lucanidae) represents a captivating and evolutionarily significant group, regarded as one of the most basal lineages within the superfamily Scarabaeoidea. Despite their importance for studying beetle evolution and ecology, genomic resources for this family remain scarce. Here, we report a chromosome-level genome assembly of Odontolabis cuvera, generated by integrating PacBio HiFi, Illumina, and Hi-C data. The genome assembly spans 908.07 Mb, comprising 66 scaffolds (scaffold N50: 65.36 Mb) and 147 contigs (contig N50: 16.39 Mb). A total of 99.58% (904.22 Mb) of the assembly was anchored to 14 chromosomes. BUSCO analysis (insecta_odb10 dataset, n = 1,367) demonstrated high completeness, with 99.1% of conserved insect orthologs identified (98.3% single-copy, 0.8% duplicated). Repetitive elements accounted for 53.00% (281.28 Mb) of the genome, and a total of 18,332 protein-coding genes were annotated. This high-contiguity genome provides a critical foundation for uncovering the evolutionary mechanisms and ecological adaptations unique to Lucanidae.

Animals↗
PubMed2026

O'nyong-nyong virus adaptive mutations in non-structural protein 1 and 3 enhance RNA replication and overcome FHL1 requirement.

Arthritogenic alphaviruses, like o'nyong-nyong virus (ONNV), cause debilitating musculoskeletal diseases and are geographically expanding. To predict their emergence, we seek to better understand evolutionary mechanisms that enable changes in virus tropism. Here, we identify adaptive mutations in the ONNV non-structural proteins (nsPs) that arose during cellular serial passaging and enabled ONNV to infect non-permissive Lunet cells. Using shotgun proteomics, we show that this human hepatoma cell line lacks the four-and-a-half-LIM domain protein 1 (FHL1), an essential host factor in ONNV RNA replication. Individual single nucleotide mutations in the nsP1 ring-aperture membrane-binding and oligomerization domain, the nsP3 macrodomain, and the nsP3 opal stop codon overcome FHL1 deficiency in Lunet cells by enhanced RNA replication. These findings demonstrate how subtle genomic changes in nsPs can profoundly influence alphavirus replication and tropism.

LIM Domain Proteins↗
PubMed2026

Motile and non-motile Listeria species adopt distinct ecological and evolutionary strategies to achieve broad geographic ranges across soil ecosystems.

Broad geographic ranges often reflect ecological versatility and are associated with lower extinction risk. Motility is a key physiological and ecological trait in bacteria. However, how some motile and non-motile bacteria achieve broad geographic ranges remains poorly understood. Here, we analyzed the genomes of 141 Listeria welshimeri and 90 Listeria booriae isolates systematically obtained from soils, representing widespread motile and non-motile species, respectively. We show that L. welshimeri lacks clear phylogeographic structure, suggesting minimal geographic barriers to dispersal. Its wide distribution is likely associated with enhanced motility and effective host colonization that facilitate wildlife-driven dispersal, particularly by regional-terrestrial birds. This pattern is supported by positive selection on flagellar and chemotaxis genes, strong associations with wildlife movement patterns, and close genomic relatedness between soil and wild bird isolates. In contrast, L. booriae displays clade endemism and a strong distance-decay relationship, suggesting dispersal limitation. Despite lacking a dispersal advantage, L. booriae's wide distribution appears to be linked to genomic flexibility and metabolic versatility that support adaptation to diverse environmental conditions, especially those shaped by iron concentration and precipitation. This is evidenced by its large, open pangenome characterized by abundant and diverse metabolic pathways and broad substrates utilization capacity; pronounced positive selection on genes involved in inorganic ion, amino acid, and coenzyme transport and metabolism; and strong associations between gene richness and abiotic factors as well as bacterial community composition. These findings suggest distinct genomic foundations and ecological and evolutionary mechanisms underlying the success of motile and non-motile cosmopolitan bacteria in soil ecosystems.

Soil Microbiology↗
PubMed2024

Phased telomere-to-telomere reference genome and pangenome reveal an expansion of resistance genes during apple domestication.

The cultivated apple (Malus domestica Borkh.) is a cross-pollinated perennial fruit tree of great economic importance. Earlier versions of apple reference genomes were unphased, fragmented, and lacked comprehensive insights into the apple's highly heterozygous genome, which impeded advances in genetic studies and breeding programs. In this study, we assembled a haplotype-resolved telomere-to-telomere (T2T) reference genome for the diploid apple cultivar Golden Delicious. Subsequently, we constructed a pangenome based on 12 assemblies from wild and cultivated species to investigate the dynamic changes of functional genes. Our results revealed the gene gain and loss events during apple domestication. Compared with cultivated species, more gene families in wild species were significantly enriched in oxidative phosphorylation, pentose metabolic process, responses to salt, and abscisic acid biosynthesis process. Our analyses also demonstrated a higher prevalence of different types of resistance gene analogs (RGAs) in cultivars than their wild relatives, partially attributed to segmental and tandem duplication events in certain RGAs classes. Structural variations, mainly deletions and insertions, have affected the presence and absence of TIR-NB-ARC-LRR, NB-ARC-LRR, and CC-NB-ARC-LRR genes. Additionally, hybridization/introgression from wild species has also contributed to the expansion of resistance genes in domesticated apples. Our haplotype-resolved T2T genome and pangenome provide important resources for genetic studies of apples, emphasizing the need to study the evolutionary mechanisms of resistance genes in apple breeding.

Malus↗
PubMed2025

Insights into salt adaptation from comparative genomics of Scirpus mariqueter and a related freshwater species.

The evolutionary mechanisms underlying ecological divergence between closely related species remain a central question in biology. Scirpus mariqueter is a coastal halophyte thriving in the saline intertidal zone and exhibits marked adaptive differences compared to its freshwater relative Bolboschoenus planiculmis. However, the genomic and physiological bases of its salt tolerance remain poorly understood. We generated high-quality genome assemblies for both species and investigated the anatomical and physiological innovations underpinning S. mariqueter's adaptation to extreme environments. Morphological analyses revealed that S. mariqueter evolved specialized traits-including denser leaf palisade tissues, enhanced stem aerenchyma, and compact root cortices-synergistically limiting salt intrusion. Using chromosome-level genomes, we identified lineage-specific expansions in S. mariqueter of gene families critical for salinity tolerance, including those regulating carbohydrate metabolism, photosynthetic fidelity, and reactive oxygen species (ROS) detoxification. Strikingly, germin-like protein (GLP) and wound-induced protein (WIP) families contain tandem repeats mediating ROS scavenging and cell wall integrity, underwent adaptive expansion, paralleling anatomical innovations. Physiological profiling under salt stress confirmed S. mariqueter's unique capacity to maintain photosynthetic activity and carbohydrate production, directly linking genomic adaptations to functional resilience. This study reveals an adaptive strategy whereby structural modifications, diversification of stress-responsive gene families, and metabolic stability collectively enable S. mariqueter to thrive in saline ecosystems.

Salt Tolerance↗
PubMed2025

Advances in tumor subclone formation and mechanisms of growth and invasion.

Tumor subclones refer to distinct cell populations within the same tumor that possess different genetic characteristics. They play a crucial role in understanding tumor heterogeneity, evolution, and therapeutic resistance. The formation of tumor subclones is driven by several key mechanisms, including the inherent genetic instability of tumor cells, which facilitates the accumulation of novel mutations; selective pressures from the tumor microenvironment and therapeutic interventions, which promote the expansion of certain subclones; and epigenetic modifications, such as DNA methylation and histone modifications, which alter gene expression patterns. Major methodologies for studying tumor subclones include single-cell sequencing, liquid biopsy, and spatial transcriptomics, which provide insights into clonal architecture and dynamic evolution. Beyond their direct involvement in tumor growth and invasion, subclones significantly contribute to tumor heterogeneity, immune evasion, and treatment resistance. Thus, an in-depth investigation of tumor subclones not only aids in guiding personalized precision therapy, overcoming drug resistance, and identifying novel therapeutic targets, but also enhances our ability to predict recurrence and metastasis risks while elucidating the mechanisms underlying tumor heterogeneity. The integration of artificial intelligence, big data analytics, and multi-omics technologies is expected to further advance research in tumor subclones, paving the way for novel strategies in cancer diagnosis and treatment. This review aims to provide a comprehensive overview of tumor subclone formation mechanisms, evolutionary models, analytical methods, and clinical implications, offering insights into precision oncology and future translational research.

Humans↗
PubMed2023

Diverse evolutionary rates and gene duplication patterns among families of functional olfactory receptor genes in humans.

In humans, odors are detected by ~400 functional olfactory receptor (OR) genes. The superfamily of functional OR genes can be further divided into tens of families. In large part, the OR genes have experienced extensive tandem duplications, which have led to gene gains and losses. However, whether different OR gene families have experienced distinct modes of gene duplication has yet to be reported. We conducted comparative genomic and evolutionary analyses for human functional OR genes. Based on analysis of human-mouse 1-1 orthologs, we found that human functional OR genes show higher-than-average evolutionary rates, and there are significant differences among families of functional OR genes. Via comparison with seven vertebrate outgroups, families of human functional OR genes show different extents of gene synteny conservation. Although the superfamily of human functional OR genes is enriched in tandem and proximal duplications, there are particular families which are enriched in segmental duplications. These findings suggest that human functional OR genes may be governed by different evolutionary mechanisms and that large-scale gene duplications have contributed to the early evolution of human functional OR genes.

Humans↗
PubMed2025

Lytic coelomocyte death is tuned by cleavage but not phosphorylation of MLKL in echinoderms.

Lytic cell death including necroptosis and pyroptosis is induced by mixed lineage kinase domain-like protein (MLKL) phosphorylation and inflammatory caspase specific cleavage Gasdermins in higher mammals, respectively. In this study, we identified a novel MLKL homolog containing a tetrapeptide recognition motif (14-LVAD-17) of inflammatory caspase from Apostichopus japonicus,which was absent of Gasdermins member by genome screening. Functional analysis revealed that AjMLKL was involved in the regulation of Vibrio splendidus AJ01 infection induced lytic coelomocyte death in a cleavage-dependent manner, but not through RIPK3-dependent phosphorylation as mammals. Mechanistically, the activated form of cysteine-aspartic specific proteases-1 (AjCASP-1) bound to the tetrapeptide site of AjMLKL and cleaved it at Asp17. Cleaved AjMLKL18-491 displayed higher binding affinities towards phosphatidylinositol phosphate and cardiolipin compared to those of un-cleaved form. In addition, cleaved AjMLKL18-491 exerted stronger ability in disrupting the membrane integrity of liposome. More importantly, AjMLKL18-491 caused a large non-selective ionic coelomocyte pore and could directly kill the invasive AJ01. Moreover, activation of inflammatory AjCASP-1 was further found to be dependent on forming an inflammasome-like complex via CASc domain of AjCASP-1 and the N-terminal Ig domains of internalized AjNLRC4. All our results proved first evidence that lytic cell death was activated through MLKL cleavage, not MLKL phosphorylation in echinoderm, which offered insights into the functional, evolutionary mechanisms of lytic cell death in invertebrates.

Animals↗
PubMed2026

Chromosome-Level Genome Assembly of Solanum carolinense.

Horsenettle (Solanum carolinense L.) is a noxious weed widely distributed across North America and increasingly invasive in other regions. Its strong environmental adaptability, complex defense strategies, and distinctive reproductive traits make it an important model for studying plant-herbivore coevolution. However, the absence of high-quality genomic resources has limited deeper investigation into its adaptive evolutionary mechanisms. In this study, we generated a chromosome-level reference genome assembly for S. carolinense using an integrated approach combining PacBio HiFi long-read sequencing, Illumina second-generation sequencing, and Hi-C chromatin interaction scaffolding. The final genome assembly had a total length of 915.40 Mb, with a contig N50 of 51.06 Mb and a scaffold N50 of 73.17 Mb; 96.05% of the sequences were successfully anchored onto 12 pseudochromosomes. The genome was characterized by a high proportion of repetitive sequences (73.64%) and substantial heterozygosity (1.13%), consistent with a highly repetitive and moderately high heterozygous genome. BUSCO analysis indicated that the chromosome-level genome assembly of S. carolinense reached a completeness score of 94.8%. A total of 32,206 protein-coding genes were annotated, of which 97.95% received functional annotations. The evaluation of the annotated protein-coding gene set returned a completeness value of 94.9%. This reference genome provides a valuable resource for advancing research on the adaptive evolution of weedy Solanaceae species, supports the development of more effective management strategies for this troublesome species, and offers a technical reference for assembling other highly heterozygous weed genomes.

Solanum carolinense↗
PubMed2026

Performance Profiles of Short DNA Barcode Segments for Family Level Detection of Asteraceae Within Asterales.

Short DNA barcodes may facilitate sequence recovery from degraded material, but their ability to retain target-family identity while excluding related taxa varies among genomic regions. We computationally evaluated 16 nuclear, plastid, and mitochondrial marker regions from 11 Asterales families using 279,956 NCBI locus-record matches and an accession-disjoint discovery/test design. Thirty-one candidate segments of 50-200 bp (mean, 98.55 bp) were screened in discovery data and evaluated for within-Asteraceae sequence recall, differentiation from non-Asteraceae Asterales, in silico primer behavior, phylogenetic placement, and exploratory matching across 808 metadata-defined metagenomic samples. Conserved regions such as matR and rbcL showed high within-Asteraceae identity, whereas ITS1, ITS, and trnH-psbA showed larger differences from related-family backgrounds; ITS2 and ycf1 showed intermediate profiles. Candidate segments were placed within or immediately adjacent to Asteraceae reference branches in segment-specific maximum-likelihood analyses, although support and topology varied among regions. Metadata-defined target-containing groups had higher mean query coverage and identity than background groups; because target presence was not independently verified and no classifier was fitted, these comparisons were descriptive and did not estimate diagnostic accuracy. Definitionally linked sequence statistics were interpreted as structural associations rather than evidence of causal evolutionary mechanisms. These results provide a family-level computational comparison of candidate short segments for Asteraceae detection within Asterales. Species identification, operational marker combinations, threshold robustness, and laboratory performance require validation using taxonomically dense, voucher-linked, and experimentally characterized datasets.

Asteraceae↗
PubMed2026

[Genomic evolution and epidemiological patterns of respiratory syncytial virus and their implications for surveillance and early warning].

Respiratory syncytial virus (RSV) is an important respiratory pathogen in infants, young children and older adults. Based on global RSV genomic surveillance data, this review systematically summarizes the geographic distribution, seasonal epidemic patterns, and long-term evolutionary trends of RSV, with particular emphasis on the sustained circulation and evolutionary mechanisms of dominant genotypes such as ON1 in RSV-A and BA9 in RSV-B. Current evidence indicates that RSV transmission dynamics are tightly coupled with viral evolution. The G gene evolves relatively rapidly and contains multiple positively selected sites, suggesting an important role in immune escape and population adaptation. In recent years, changes in social behavior patterns and population immunity have further disrupted the seasonal rhythm of RSV and may have influenced the spread of dominant genotypes. Under routine respiratory infectious disease surveillance, strengthened genomic monitoring and integration of multi-source data are needed to improve early warning of abnormal RSV epidemics and variant-associated risks, thereby providing prospective evidence for protecting high-risk populations and informing public health decision-making.

Humans↗
PubMed2025

Unraveling evolutionary pathways: allopolyploidization and introgression in polyploid Prunus (Rosaceae).

Allopolyploidization, resulting from hybridization and subsequent whole-genome duplication (WGD), is a fundamental mechanism driving evolutionary diversification across various lineages within the Tree of Life. The polyploid Prunus (Rosaceae), significant for its economic and agricultural value, provides an ideal model for investigating the evolutionary dynamics associated with allopolyploidy. In this study, we utilized deep genome skimming (DGS) data to demonstrate a comprehensive analytical framework for elucidating the underlying allopolyploidy that includes a newly adapted tool (DGS-Tree2GD) tailored explicitly for accurately detecting WGD events. Additionally, we introduced two methods to evaluate the contribution of incomplete lineage sorting (ILS) to lineage diversification. Phylogenomic discordance analyses revealed that allopolyploidization, rather than ILS, played a dominant role in the origin and dynamics of polyploid Prunus. Moreover, we inferred that the uplift of the Himalayas from the Middle to Late Miocene was a key driver in the rapid diversification of the Maddenia clade, an endemic group in East Asia. This geological event facilitated extensive hybridization and allopolyploidization, particularly the introgression between the Himalayas-Hengduan and Central-Eastern China clades. This case study demonstrates the robustness and efficacy of our analytical approach in precisely identifying WGD events and elucidating the evolutionary mechanisms underlying allopolyploidization in polyploid Prunus.

Polyploidy↗
PubMed2025

Genomic signatures of innovation and selection in the extremotolerant yeast Kluyveromyces marxianus.

Extremophiles can be the product of millions of years of evolutionary engineering and refinement. The underlying mechanisms can be quite distinct from the ones operating at earlier stages of trait innovation. In this work, we have developed the compost yeast Kluyveromyces marxianus, which diverged from its closest relative >20 million years ago, as a model for interspecies comparative biology and genomics. We applied a battery of growth assays to species of the Kluyveromyces genus and found that K. marxianus outperformed its relatives in a battery of heat and chemical stress conditions. We then generated and analyzed genomes from across the genus, to find derived genetic features associated with, and potentially causal for, K. marxianus traits. We found robust expansions in gene families in the K. marxianus genome, most notably among genes annotated as transmembrane transporters and in metabolism. In molecular-evolution tests, we identified adaptive protein variants at hundreds of genes, among which plasma membrane transporters were over-represented. Together, these signals enable a model for the molecular mechanisms and evolutionary pressures underlying K. marxianus traits, including gains in transporter function mediating stress resistance, and metabolic variants contributing to its capacity for rapid growth in challenging conditions. Such oligogenic architectures may be the rule rather than the exception in phenotypes that have evolved over long timescales.

Journal Article↗
PubMed2026

Genome-Wide Identification and Bioinformatics Analysis of the FAD Gene Family in Walnut (Juglans regia L.).

Fatty acid desaturase (FAD) is a core catalytic enzyme in plants for the synthesis of unsaturated fatty acids, profoundly affecting plant growth, development, and adaptability to various environmental stresses. The walnut (Juglans regia L.) is an important woody oil tree species, and its kernel is rich in unsaturated fatty acids. Systematic identification of the walnut FAD gene family and analysis of its function are of great significance for revealing the molecular mechanisms underlying unsaturated fatty acid metabolism in the walnut. Based on walnut whole-genome data, this study used homology alignment and hidden Markov model search methods to identify the JrFAD gene family members. Subsequently, a variety of bioinformatics tools were used to systematically analyze their structural characteristics, evolutionary expansion mechanism, expression regulation, and function. A total of 21 JrFAD gene family members were identified and classified into five subfamilies. The family genes were unevenly distributed on nine chromosomes. WGD/segmental duplication was the main expansion method, and the duplicated gene pairs experienced strong purification selection. The family gene promoter sequence is rich in regulatory elements that respond to light, plant hormones, and various stresses. The expression pattern analysis showed that JrFAD3.1 and JrFAD2.3 showed high expression specifically during the rapid accumulation of walnut kernel oil. This study clarified the composition and evolutionary characteristics of the FAD gene family in the walnut, which provides useful information for in-depth analyses of its functional mechanism in the regulation of lipid metabolism, and also identified potential candidate gene resources for the genetic improvement of walnut varieties with high amounts of unsaturated fatty acids.

Juglans↗
PubMed2026

Heterokairic Genes and the Eco-Evo-Devo of Timing.

Concepts of developmental timing have traditionally been framed under heterochrony as evolved (genetically based) differences in timing, while environmentally induced shifts in timing within genotypes have been treated more loosely. In this article, heterokairy is presented as plasticity in the timing of developmental events, and the term "heterokairic genes" is proposed for environmentally modulated heterochronic genes that underlie this plasticity. Evidence from nematodes, insects, plants, and vertebrates is assembled, with emphasis placed on systems where environmental cues are relayed through endocrine or metabolic pathways to known timing modules/genes. On this basis, a distinction is drawn between validated heterokairic genes, supported by direct mechanistic data, and a broader set of candidates inferred from gene-environment interactions in developmental timing. The eco-evolutionary consequences of such genes are considered, and experimental and genomic strategies for their identification are outlined. It is argued that heterokairic genes provide a useful bridge between environmental variation, developmental mechanisms, and evolutionary change in timing.

Animals↗
PubMed2026

Selection of GhTT2-A07 promoter enhances fiber quality in improved cotton varieties.

Modern cultivated cotton fibers are predominantly white with enhanced quality compared to their wild ancestors. However, the molecular mechanisms and evolutionary drivers linking fiber color to quality remain least focused. In this study, we identified FQC1 (Fiber Quality and Color 1), a major quantitative trait locus (QTL) on chromosome A07 that concurrently regulates both fiber quality and pigmentation. Through map-based cloning, we revealed that Gossypium hirsutum TRANSPARENT TESTA2-A07 (GhTT2-A07), an R2R3-MYB transcription factor, resides within this locus. GhTT2-A07 modulates fiber development by directly activating genes in the general phenylpropanoid pathway, thereby promoting the metabolic flux toward downstream secondary metabolites. Variations in the GhTT2-A07 promoter led to its reduced expression in modern white cotton cultivars. This down-regulation suppresses the accumulation of S/G/H-type lignin monomers and proanthocyanidins, resulting in altered secondary cell wall composition and ultimately enhancing the quality of mature white fibers. Population genetic analyses further indicate that the white-fiber allele GhTT2-A07W has been fixed in modern breeding genotypes, underscoring the impact of artificial selection during cotton domestication. Overall, our study elucidates the biochemical and molecular mechanisms underlying fiber quality and pigmentation in cotton, clarifies the selection criteria for high-quality white fibers in modern cultivars, and provides a theoretical basis for future targeted genetic improvement of cotton fibers.

Alleles↗
PubMed2026

Genomic distribution characteristics and interspecific differences of microsatellite landscapes in Felidae.

BACKGROUND: Microsatellites within genomes play crucial roles in regulating gene expression, DNA replication, and chromosomal structure and function. Analyzing the composition and distribution patterns of microsatellites in closely related species not only reveals their evolutionary dynamics and adaptive mechanisms but also provides essential technical support for applications in genetic breeding, species conservation, and disease research. As one of the world's most captivating animal groups, the landscape patterns of microsatellites across feline genomes remain to be systematically characterized. RESULTS: This study utilized high-quality genomic data to conduct a systematic comparative analysis of microsatellite landscape distribution patterns across the genomes of 13 felid species. The findings revealed that microsatellite abundance and distribution exhibit species-specific characteristics, with a non-random genomic distribution and a negative correlation between microsatellite abundance and repeat length. The predominant distribution pattern followed the sequence: single > double > quadruple > triple > quintuple > sextuple nucleotide repeats. Microsatellite abundance peaked in intergenic regions, whereas trinucleotide repeats were more prevalent within exons. Coding regions showed a marked preference for trinucleotide and hexanucleotide repeats. Enrichment analysis of GO and KEGG pathways indicated that coding sequences containing microsatellites were primarily involved in transcription and translation processes. CONCLUSIONS: Our study elucidates the distribution patterns and characteristics of microsatellites across diverse feline species, providing significant insights into their evolutionary mechanisms and functional roles. Furthermore, these findings establish a valuable reference and foundational dataset for the future development of high-quality, species-specific microsatellite markers in felids.

Animals↗