Chromatin-associated non-coding RNAs play important roles in various cellular processes by targeting genomic loci. Two types of genome-wide NGS experiments exist to detect such targets: ‘one-to-all’, which focuses on targets of a single RNA, and ‘all-to-all’, which captures targets of all RNAs in a sample. As with many NGS experiments, they are prone to biases and noise, so it becomes essential to detect ‘peaks’—specific interactions of an RNA with genomic targets. Here, we present BaRDIC—Binomial RNA–DNA Interaction Caller—a tailored method to detect peaks in both types of RNA–DNA interaction data. BaRDIC is the first tool to simultaneously take into account the two most prominent biases in the data: chromatin heterogeneity and distance-dependent decay of interaction frequency. Since RNAs differ in their interaction preferences, BaRDIC adapts peak sizes according to the abundances and contact patterns of individual RNAs. These features enable BaRDIC to make more robust predictions than currently applied peak-calling algorithms and better handle the characteristic sparsity of all-to-all data. The BaRDIC package is freely available at https://github.com/dmitrymyl/BaRDIC.

Naturally transgenic plants are plants that have undergone Agrobacterium-mediated transformation under natural conditions without human involvement. Among Arachis hypogaea L., A. duranensis Krapov. & W.C. Greg, A. ipaensis Krapov. & W.C. Greg, A. monticola Krapov. & Rigoni, and A. stenosperma Krapov. & W.C. Greg are known to contain sequences derived from the T-DNA of “Agrobacterium”. In the present study, using molecular genetics and bioinformatic methods, we characterized natural transgenes in 18 new species from six sections of the genus Arachis. We found that small fragments of genes for enzymes of the agropine synthesis pathway were preserved only in some of the studied samples and were lost in the majority of the species during evolution. At the same time, genes, similar to cucumopine synthases (cus-like), remained intact in almost all of the investigated species. In cultivated peanuts, they are expressed in a tissue-specific manner. We demonstrated the intraspecific variability of the structure and expression of the cus-like gene in cultivated peanuts. The described diversity of gene sequences horizontally transferred from Agrobacterium to plants helps to shed light on the phylogeny of species of the genus Arachis and track possible hybridization events. Data on the ability of certain species to hybridize are useful for planning breeding schemes aimed at transferring valuable traits from wild species into cultivated peanuts.

Chromatin-associated non-coding RNAs play important roles in various cellular processes by targeting genomic loci. Two types of genome-wide NGS experiments exist to detect such targets: “one-to-all”, which focuses on targets of a single RNA, and “all-to-all”, which captures targets of all RNAs in a sample. As with many NGS experiments, they are prone to biases and noise, so it becomes essential to detect “peaks” – specific interactions of an RNA with genomic targets. Here we present BaRDIC – Binomial RNA-DNA Interaction Caller – a tailored method to detect peaks in both types of RNA-DNA interaction data. BaRDIC is the first tool to simultaneously take into account the two most prominent biases in the data: chromatin heterogeneity and distance-dependent decay of interaction frequency. Since RNAs differ in their interaction preferences, BaRDIC adapts peak sizes according to the abundances and contact patterns of individual RNAs. These features enable BaRDIC to make more robust predictions than currently applied peak-calling algorithms and better handle the characteristic sparsity of all-to-all data. BaRDIC package is freely available at https://github.com/dmitrymyl/BaRDIC .

Cultivated peanut is an allotetraploid species that received the A and B genomes from Arachis duranensis and A. ipaensis. Homologs of the agrobacterial cucumopine synthase gene were previously found in both genomes as a result of horizontal transfer [1]. These sequences are found both in ancestral species and in cultivated peanuts. In addition to them, natural GMOs are A. monticola and A. stenosperma. How widespread natural GMOs are within the genus Arachis is currently unknown. The aim of our study was to search for natural GMOs within the genus Arachis and to analyze the polymorphism of natural transgenes out the studied species. METHODS: Gene sequencing for various Arachis species was determined using the bwa [2], GATK [3] and samtools [4] packages based on NGS data aggregated in the SRA NCBI database. RESULTS: We have found homologues of the cucumopine synthase gene in the genomes of A. appressipila, A. batizocoi, A. cardenasii, A. correntina, A. diogoi, A. duranensis, A. glandulifera, A. helodes, A. hoehnei, A. ipaensis, A. macedoi, A. magna, A. monticola, A. paraguariensis, A. pintoi, A. pusilla, A. rigonii, A. stenophylla, A. stenosperma, A. trinitensis, A. valida, A. villosa, and also characterized the intraspecific variability of the gene in cultivated peanuts. In 16 of the 22 species studied, the gene is full-length. The report will consider the possibility of using the cucumopine synthase gene in peanut phylogenetic studies. CONCLUSION: The list of species of natural GMOs within the genus Arachis today includes 23 species.

The two-spotted spider mite, Tetranychus urticae Koch, is a major agricultural pest with a rapid propensity for developing acaricide resistance. Bifenazate targets mitochondrial cytochrome b (CYTB). While the G126S mutation is associated with resistance, its independent role remains unclear, as it often occurs with other SNPs. This study explores the molecular basis of bifenazate resistance in a Russian laboratory strain derived from a St. Petersburg greenhouse population. Disruptive selection with increasing bifenazate concentrations generated resistant and susceptible isofemale lines. AlphaFold2 structural modeling of CYTB indicated that G126S causes a steric clash, leading to conformational destabilization, whereas other reported mutations primarily affect the ligand-binding pocket. Oxford Nanopore sequencing revealed a low initial frequency of the G126S allele (<1%; 226/35,895 reads) in the unselected population. After one year of stepwise selection (0.00005–0.031% a.i.), the mutant allele frequency surged to 90% (7272/8056 reads). No other resistance-associated mutations were found in the analyzed cytb fragment. We report the first identification of the G126S mutation in a Russian T. urticae population and demonstrate rapid fixation under bifenazate selection. Within this genetic background, G126S alone appears sufficient to confer high-level resistance, emphasizing the population-specific nature of resistance evolution and the critical need for local monitoring.