Soybean is a leguminous plant cultivated in many countries and is considered important in the food industry due to the high levels of oil and protein content in the beans. The high demand for soybeans and its products in the industry requires the expansion of cultivation areas. Despite climatic restrictions, West Siberia is gradually expanding its area of soybean cultivation. In this study, we present the first analysis of the population structure and genetic diversity of the 175 soybean Glycine max breeding lines and varieties cultivated in West Siberia (103 accessions) and other regions of Russia (72 accessions), and we compare them with the cultivated soybean varieties from other geographical locations. Principal component analysis revealed several genetic clusters with different levels of genetic heterogeneity. Studied accessions are genetically similar to varieties from China, Japan, and the USA and are genetically distant to varieties from South Korea. Admixture analysis revealed four ancestry groups based on genetic ancestry and geographical origin, which are consistent with the regions of cultivation and origin of accessions and correspond to the principal component analysis result. Population statistics, including nucleotide diversity, Tajima’s D, and linkage disequilibrium, are comparatively similar to those observed for studied accessions of a different origin. This study provides essential population and genetic information about the unique collection of breeding lines and varieties cultivated in West Siberia and other Russian regions to foster further evolutionary, genome-wide associations and functional breeding studies.

The global spread of antibiotic resistance is forcing the scientific community to find new molecular strategies to counteract it. Deep functional profiling of microbiomes provides an alternative source for the discovery of novel antibiotic producers and probiotics. Recently, we implemented this ultrahigh-throughput screening approach for the isolation of Bacillus pumilus strains efficiently producing the ribosome-targeting antibiotic amicoumacin A (Ami). Proteomics and metabolomics revealed essential insight into the activation of Ami biosynthesis. Here, we applied omics to boost Ami biosynthesis, providing the optimized cultivation conditions for high-scale production of Ami. Ami displayed a pronounced activity against Lactobacillales and Staphylococcaceae, including methicillin-resistant Staphylococcus aureus (MRSA) strains, which was determined using both classical and massive single-cell microfluidic assays. However, the practical application of Ami is limited by its high cytotoxicity and particularly low stability. The former is associated with its self-lactonization, serving as an improvised intermediate state of Ami hydrolysis. This intramolecular reaction decreases Ami half-life at physiological conditions to less than 2 h, which is unprecedented for a terminal amide. While we speculate that the instability of Ami is essential for Bacillus ecology, we believe that its stable analogs represent attractive lead compounds both for antibiotic discovery and for anticancer drug development.

Transcription activation factors and multisubunit coactivator complexes get recruited at specific chromatin sites via protein domains that recognize histone modifications. Single PHDs (plant homeodomains) interact with differentially modified H3 histone tails. Double PHD finger (DPF) domains possess a unique structure different from PHD and are found in six proteins: histone acetyltransferases MOZ and MORF; chromatin remodeling complex BAF (DPF1–3); and chromatin remodeling complex PBAF (PHF10). Among them, PHF10 stands out due to the DPF sequence, structure, and functions. PHF10 is ubiquitously expressed in developing and adult organisms as four isoforms differing in structure (the presence or absence of DPF) and transcription regulation functions. Despite the importance of the DPF domain of PHF10 for transcription activation, its structure remains undetermined. We performed homology modeling of the human PHF10 DPF domain and determined common and distinct features in structure and histone modifications recognition capabilities, which can affect PBAF complex chromatin recruitment. We also traced the evolution of DPF1–3 and PHF10 genes from unicellular to vertebrate organisms. The data reviewed suggest that the DPF domain of PHF10 plays an important role in SWI/SNF-dependent chromatin remodeling during transcription activation.

Soybean (Glycine max) is a leguminous plant with a broad range of applications, particularly in agriculture and food production, where its seed composition—especially oil and protein content—is highly valued. Improving these traits is a primary focus of soybean breeding programs. In this study, we conducted a genome-wide association study (GWAS) to identify genetic loci linked to oil and protein content in seeds, using imputed genotype data for 180 Eurasian soybean varieties and the novel “genotypic twins” approach. This dataset encompassed 87 Russian and European cultivars and 93 breeding lines from Western Siberia. We identified 11 novel loci significantly associated with oil and protein content in seeds (p-value < 1.5 × 10⁻⁶), including one locus on chromosome 11 linked to protein content and 10 loci associated with oil content (chromosomes 1, 5, 11, 16, 17, and 18). The protein-associated locus is located near a gene encoding a CBL-interacting protein kinase, which is involved in key biological processes, including stress response mechanisms such as drought and osmotic stress. The oil-associated loci were linked to genes with diverse functions, including lipid transport, nutrient reservoir activity, and stress responses, such as Sec14p-like phosphatidylinositol transfer proteins and Germin-like proteins. These findings suggest that the loci identified not only influence oil and protein content but may also contribute to plant resilience under environmental stress conditions. The data obtained from this study provide valuable genetic markers that can be used in breeding programs to optimize oil and protein content, particularly in varieties adapted to Russian climates, and contribute to the development of high-yielding, nutritionally enhanced soybean cultivars.

Wheat is a cereal grain that plays an important role in the world’s food industry. The identification of the loci that change the concentration of elements in wheat seeds is an important challenge nowadays especially for genomic selection and breeding of novel varieties. In this study, we performed a multivariate genome-wide association study (GWAS) of the seven traits—concentrations of Zn, Mg, Mn, Ca, Cu, Fe, and K in grain—of the Russian collection of common wheat Triticum aestivum (N = 149 measured in two years in two different fields). We replicated one known locus associated with the concentration of Zn (IAAV1375). We identified four novel loci—BS00022069_51 (associated with concentrations of Ca and K), RFL_Contig6053_3082 (associated with concentrations of Fe and Mn), Kukri_rep_c70864_329 (associated with concentrations of all elements), and IAAV8416 (associated with concentrations of Fe and Mn)—three of them were located near the genes TraesCS6A02G375400, TraesCS7A02G094800, and TraesCS5B02G325400. Our result adds novel information on the loci involved in wheat grain element contents and may be further used in genomic selection.

Nonsense mutations are a type of mutations which results in a premature termination codon occurrence. In general, these mutations have been considered to be among the most harmful ones which lead to premature protein translation termination and result in shortened nonfunctional polypeptide. However, there is evidence that not all nonsense mutations are harmful as well as some molecular mechanisms exist which allow to avoid pathogenic effects of these mutations. This review addresses relevant information on nonsense mutations in eukaryotic genomes, characteristics of these mutations, and different molecular mechanisms preventing or mitigating harmful effects thereof.