Although the samples were primarily isolated from anthropogenic environments, H. uvarum exhibited an open pangenome, indicating substantial adaptive potential to diverse stresses and establishes a genomic foundation for future ecological and industrial research on this yeast.
Abstract
Hanseniaspora uvarum is a representative non-Saccharomyces species that plays a significant role in fermentation processes such as winemaking. In recent years, this species has gained attention in food engineering and evolutionary biology. However, the population genomic signatures in this species remain poorly understood. In this study, a population genomics analysis was conducted on 151 H. uvarum strains (45 from Ningxia, China; 21 from other regions of China; 67 from Australia; and 18 from other regions or of unspecified origin), and a pangenome analysis was performed on 159 strains, incorporating eight additional genome assemblies. Phylogenetic analysis, ancestry coefficient analysis, and principal component analysis generally distinguished Chinese strains from those sampled on other continents. However, substantial post-divergence gene flow and introgression were inferred between intercontinentally paired clades. Positively selected candidate genes exhibited region-specific patterns: GO terms related to the positive regulation of filamentous growth in response to external stimuli were significantly enriched in the Ningxia strains; the stress-related GO term “cytoplasmic stress granule” was significantly enriched in both the Ningxia and Australian strains, but with distinct sets of associated genes. Although the samples were primarily isolated from anthropogenic environments, H. uvarum exhibited an open pangenome, indicating substantial adaptive potential to diverse stresses. This study advances our understanding of the evolutionary dynamics of H. uvarum and establishes a genomic foundation for future ecological and industrial research on this yeast.
It is demonstrated that homologous recombination, genome plasticity, and lineage-specific diversification are major drivers of adaptation, ecological fitness, and pathogenic evolution in this emerging phytopathogen P. jejuense across diverse hosts and geographic regions.
Dario Arizala, S. Dobhal, Gamze Boluk et al.· bioRxiv· 0 citations
Quinoa (Chenopodium quinoa Willd.) is an allotetraploid crop with extraordinary environmental adaptability. To explore its genetic diversity, evolutionary dynamics, and altitudinal differentiation, we constructed a gene-based pangenome using 11 genomes (7 highland and 4 lowland accessions), comprising 51,298 orthologous groups with 19,653 core pan-genes, suggesting a near-closed pangenome architecture within the sampled accessions. Evolutionary analysis revealed that core pan-genes experienced the strongest purifying selection, whereas private pan-genes exhibited the weakest purifying selection, though the difference was not statistically significant compared to the other three pan-gene sets. Subgenomic asymmetry analysis showed that subgenome A retained fewer single-copy genes than subgenome B, with dosage-sensitive two-copy genes enriched in biotic stress-related domains and tandemly duplicated genes associated with abiotic stress adaptation. Presence/absence variation (PAV) analysis identified 7,477 orthologous groups enriched in highland accessions and 3,549 enriched in lowland accessions. We caution that these counts may be substantially inflated by the uneven sample size (7 highland vs. 4 lowland accessions) and should be interpreted as descriptive enrichment patterns rather than definitive evidence of ecotype divergence. Highland-enriched genes were enriched in transposon-related families and FAR1 domains potentially enhancing genomic plasticity and light signaling, whereas lowland-enriched genes were enriched in nitrogen metabolism and defense-related families. Copy number variation of betalain biosynthetic genes (CqCYP76AD, CqDODA, CqDOPA5-GT) was not the primary driver of seed coat color divergence between highland and lowland ecotypes. Four positively selected genes, including NADH-quinone oxidoreductase and MT-A70, harbor population-specific amino acid substitutions that may contribute to differential adaptation, potentially optimizing photosynthetic metabolism, RNA epigenetic modification, and protein homeostasis. These findings provide insights into the genomic basis of quinoa’s environmental adaptation and altitudinal differentiation, offering a genomic resource for molecular breeding.
Y. Pu, Li-Wen Wang, Yong-Chao Gong et al.· Frontiers in Plant Science· 0 citations
Abstract Over the last decades, the yeast Saccharomyces cerevisiae has emerged as a key model for studying microbial domestication, particularly in the context of winemaking. The recent surge of population genomic data, encompassing thousands of genomes, has profoundly reshaped our understanding of the evolutionary history and adaptive potential of wine yeasts. Despite arising from a domestication bottleneck, wine yeasts form a well-structured population and display striking genome dynamism. Extensive variation in heterozygosity, aneuploidy, structural variations, and gene content may provide a reservoir of genomic variation that contributes to adaptive potential in the harsh winemaking environment. While some genetic variation and genome restructuring contribute to adaptation, gene flow through hybridization, introgression and especially horizontal gene transfer has emerged as a major driver of functional innovation. These findings establish wine yeasts as a powerful model to link genome evolution with adaptation to anthropogenic environments. They also provide a foundation for the rational improvement of industrial strains through approaches such as quantitative trait locus mapping, adaptive laboratory evolution and genome-wide association studies. Extending these frameworks to non-Saccharomyces species and integrating genomic, functional and ecological data will be key to understanding and engineering microbial communities, to face the modern winemaking challenges.
Carmen Becerra-Rodríguez, H. Devillers, J. Legras et al.· FEMS Yeast Research· 0 citations
Collectively, the NY strain achieves strong salinity tolerance by integrating genetic variation, transcriptional reprogramming and metabolic remodeling, synergistically maintaining ion homeostasis, osmotic balance and energy supply.
Jiahua Zhang, Min Zhang, Chungui Huang et al.· Marine Biotechnology· 0 citations
ABSTRACT Streptomyces sampsonii is a promising biocontrol bacterium, but its genomic basis of adaptation and secondary metabolism remains unclear. Here, we present a chromosome‐level genome assembly of S. sampsonii (7.20 Mb, 6015 protein‐coding genes) and perform comparative analyses with 95 related Streptomyces species. Phylogenomic and synteny analyses revealed its closest relationship with S. albidoflavus , while extensive structural variations distinguished more distant lineages. Pangenome analysis uncovered 84,178 gene clusters, with pan_shell and pan_cloud genes predominantly enriched in xenobiotic biodegradation, metabolism, and antibiotic biosynthesis, highlighting their roles in ecological adaptation and biocontrol potential. Biosynthetic gene cluster (BGC) analysis identified numerous NRPS, PKS, and terpene pathways, many of which belong to pan_shell and pan_cloud regions, suggesting dynamic evolutionary origins. We further detected 66,260 horizontally transferred (HGT) genes, including 438 in BGCs, underscoring HGT as a major driver of metabolic innovation. Together, these findings provide novel insights into the genomic diversity, adaptive capacity, and secondary metabolic potential of S. sampsonii and its close relatives.
Bo-Yang Zhang, Shuo Ji· Ecology and Evolution· 0 citations
The findings elucidate the genomic basis underlying the strong invasiveness of this nematode, clarify its global dispersal routes, and identify putative loci associated with adaptive evolution after invasion.
Xiong Xiong, Jing Ning, Jie Li et al.· Pest Management Science· 0 citations
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