WRKYs are a multigenic family of transcription factors that are plant-specific and involved in the regulation of plant development and various stress response processes. However, the evolution of WRKY genes is not fully understood. This family has also been incompletely studied in grapevine, and WRKY genes have been named with different numbers in different studies, leading to great confusion. In this work, 62 Vitis vinifera WRKY genes were identified based on six genomes of different cultivars. All WRKY genes were numbered according to their chromosomal location, and a complete revision of the numbering was performed. Amino acid variability between different cultivars was assessed for the first time and was greater than 5% for some WRKYs. According to the gene structure, all WRKYs could be divided into two groups: more exons/long length and fewer exons/short length. For the first time, some chimeric WRKY genes were found in grapevine, which may play a specific role in the regulation of different processes: VvWRKY17 (an N-terminal signal peptide region followed by a non-cytoplasmic domain) and VvWRKY61 (Frigida-like domain). Five phylogenetic clades A–E were revealed and correlated with the WRKY groups (I, II, III). The evolution of WRKY was studied, and we proposed a WRKY evolution model where there were two dynamic phases of complexity and simplification in the evolution of WRKY.

Peach (Prunus persica (L.)) is one of the major commercial stone fruit crops. A genetic analysis of peach collections around the world is essential for effective breeding programmes, and the development of genomic and marker-assisted selection. This study focuses on research on peach collection at the Nikita Botanical Garden and aims to identify single-nucleotide polymorphisms (SNPs) at the genome level and analyse the genetic diversity, population structure, and the linkage disequilibrium (LD) pattern among 161 cultivars and hybrids. A total of 288,784 SNPs were identified using the genotyping-by-sequencing (GBS) approach and, after filtering, 7803 high-quality SNPs were used in the analyses. The 161 accessions were clustered into two groups using principal component analyses (PCoA) and seven populations by ADMIXTURE v.1.3 software, which was confirmed using phylogenetic analyses. The distribution of the genotypes within subpopulations reflected any fruit-related traits. A low level of genetic diversity and medium linkage disequilibrium was detected in peach cultivars. The observed heterozygosity was lower than expected and varied from 0.11 to 0.22 in genotypes with different origins. Our results based on 7803 SNPs were compared with those based on 12 microsatellite markers and differences in clustering, observed heterozygosity, and phylogeny were identified. This highlights the need to analyse collections using whole-genome approaches.

Peach is one of the most common stone fruit crops, but it is also the most thermophilic. One of the main problems in peach cultivation is frost up to −8 °C in spring during pollen development, budding, and flowering. The adaptation of the plant to low temperatures could be related to the activation of the antioxidant system under cold stress. The aim of this work was to test the hypothesis of distinct adaptation mechanisms to cold stress in Prunus persica L. cultivars with various cold tolerances. The difference between this study and the previous ones is that previously, only contrasting varieties (resistant and sensitive) were studied. For the first time, we studied the effect of cold stress on cold-resistant varieties but with different degrees of resistance, such as “Loadel” and “Springold” (medium resistant) and “Podarok Like” and “Temisovskij” (highly resistant). The experiment was designed to simulate the effects of short-term cold snaps, which are a common occurrence during February and March in the south of Crimea. A series of tests were conducted on annual shoots that were frozen at −12 °C. The activity and gene expression of two major antioxidant enzymes, catalase and peroxidase, were studied by spectrophotometry and RT-qPCR, respectively. The experiment showed that these enzymes responded differently to cold stress in varieties with different cold tolerances. Catalase responded similarly in all four varieties. After frost, there was an increase in activity (7-fold in “Temisovskij” and 3-fold in “Podarok Like”) and a decrease in expression. In contrast to catalase, peroxidase showed an opposite response to cold stress in medium-tolerant and highly tolerant cultivars. Peroxidase activity after exposure to low temperatures increased in highly tolerant cultivars (1.5-fold in “Temisovskij”), while it decreased in medium-tolerant cultivars (1.5–2 fold in “Springold” and “Loadel”, respectively). The change in peroxidase expression was the opposite. It decreased in highly resistant varieties and increased in medium-resistant varieties. Thus, our results revealed the opposite response of one of the major antioxidant enzymes (peroxidase) in moderately resistant and highly resistant cultivars. The data obtained show that varieties with a high degree of resistance could have other adaptation mechanisms involved, which may be useful for selecting resistant varieties.

The intraspecific structure of the European anchovy (Engraulis encrasicolus) was studied on the basis of mitochondrial cytochrome b gene (cytb) fragment variability in 84 individuals from seven localities of the Black Sea and the Sea of Azov. The data on haplotype and nucleotide diversity and the values of neutrality tests suggested expansive growth of anchovy populations in the Azov-Black Sea basin. All samples from anchovy populations demonstrated a high level of haplotype diversity (Hd = 0.962). Two dominant haplotypes were identified, the frequencies of which were not directional, and they were present in all localities. Sequence analysis of the mitochondrial cytb gene fragment showed no differentiation between the Sea of Azov and the Black Sea subspecies.

Class III peroxidases are plant-specific and play a key role in the response to biotic and abiotic stresses, as well as in plant growth and development. In this study, we investigated 60 POD genes from Prunus persica based on genomic and transcriptomic data available in NCBI and analysed the expression of individual genes with qPCR. Peroxidase genes were clustered into five subgroups using the phylogenetic analysis. Their exon–intron structure and conserved motifs were analysed. Analysis of the transcriptomic data showed that the expression of PpPOD genes varied significantly in different tissues, at different developmental stages and under different stress treatments. All genes were divided into low- and high-expressed genes, and the most highly expressed genes were identified for individual tissues (PpPOD12 and PpPOD42 in flower buds and PpPOD73, PpPOD12, PpPOD42, and PpPOD31 in fruits). The relationship between cold tolerance and the level of peroxidase expression was revealed. These studies were carried out for the first time in the peach and confirmed that chilling tolerance may be related to the specificity of antioxidant complex gene expression.

A wealth of genome and transcriptome data obtained using new generation sequencing (NGS) technologies for whole organisms could not answer many questions in oncology, immunology, physiology, neurobiology, zoology and other fields of science and medicine. Since the cell is the basis for the living of all unicellular and multicellular organisms, it is necessary to study the biological processes at its level. This understanding gave impetus to the development of a new direction – the creation of technologies that allow working with individual cells (single-cell technology). The rapid development of not only instruments, but also various advanced protocols for working with single cells is due to the relevance of these studies in many fields of science and medicine. Studying the features of various stages of ontogenesis, identifying patterns of cell differentiation and subsequent tissue development, conducting genomic and transcriptome analyses in various areas of medicine (especially in demand in immunology and oncology), identifying cell types and states, patterns of biochemical and physiological processes using single cell technologies, allows the comprehensive research to be conducted at a new level. The first RNA-sequencing technologies of individual cell transcriptomes (scRNA-seq) captured no more than one hundred cells at a time, which was insufficient due to the detection of high cell heterogeneity, existence of the minor cell types (which were not detected by morphology) and complex regulatory pathways. The unique techniques for isolating, capturing and sequencing transcripts of tens of thousands of cells at a time are evolving now. However, new technologies have certain differences both at the sample preparation stage and during the bioinformatics analysis. In the paper we consider the most effective methods of multiple parallel scRNA-seq using the example of 10XGenomics, as well as the specifics of such an experiment, further bioinformatics analysis of the data, future outlook and applications of new high-performance technologies.