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The focus of our study is the burials of two young men who died in distant lands (Middle Volga region and Southern Urals). Whole genome sequencing revealed a remarkable genetic similarity between the individuals and their potential decent from common ancestors. Men from the excavations of the Pepkino mound (burial No. 8, bronze caster) and buried No. 3 at the settlement of Maloyuldashevo 1 (sacrificed individual) were the owners of haplogroup R1b (Z2103) with a common paternal ancestor. The search of genome fragments identical by origin (IBD method — Identity-By-Descent) showed patterns inherited from a common ancestor without recombination. In a pairwise comparison of Pepkino caster with other samples, the probability of the occurrence of at least one IBD fragment in the genomes was more than 0.9 for both the Maloyldashevo sample, as well for a female (sample POST_131) from Southern Bavaria with close AMS date. Using the PCA method, we identified the owner of a similar genotype in a burial of the Sintashta culture (Kamennyi Ambar 5 burial ground, mound 2, burial 16), for which a mixed origin was previously established with the participation of West Siberian hunter-gatherers and steppe dwellers of the Bronze Age. In addition, among other genetic outliers of the same necropolis, there were men with haplogroup of the Y chromosome R1b, which brings them closer to the individuals we studied from the Pepkino mound and Maloyuldashevo settlement. Thus, the distribution of a mobile group has been shown, which was incorporated into different cultural traditions.

To assess the genomic diversity of Fusarium oxysporum f. sp. lini strains and compile a comprehensive gene repertoire, we constructed a pangenome using 13 isolates from four different clonal lineages, each exhibiting distinct levels of virulence. Syntenic analyses of two selected genomes revealed significant chromosomal rearrangements unique to each genome. A comprehensive examination of both core and accessory pangenome content and diversity points at an open genome state. Additionally, Gene Ontology (GO) enrichment analysis indicated that non-core pangenome genes are associated with pathogen recognition and immune signaling. Furthermore, the Folini pansecterome, encompassing secreted proteins critical for fungal pathogenicity, primarily consists of three functional classes: effector proteins, CAZYmes, and proteases. These three classes account for approximately 3.5% of the pangenome. Each functional class within the pansecterome was meticulously annotated and characterized with respect to pangenome category distribution, PFAM domain frequency, and strain virulence assessment. This analysis revealed that highly virulent isolates have specific types of PFAM domains that are exclusive to them. Upon examining the repertoire of SIX genes known for virulence in other formae speciales, it was found that all isolates had a similar gene content except for two, which lacked SIX genes entirely.

Chickpea is a staple crop for many nations worldwide. Modeling genotype-by-environment interactions and assessing the genotype’s ability to contribute adaptive alleles are crucial for chickpea breeding. In this study, we evaluated 12 agronomically important traits of 159 accessions from the N.I. Vavilov All Russian Institute for Plant Genetic Resources collection. These included 145 landraces and 13 cultivars grown in different climatic conditions in Kuban (45°18′ N and 40°52′ E) in both 2016 and 2022, as well as in Astrakhan (46°06′ N and 48°04′ E) in 2022. Using the IIIVmrMLM model in multi-environmental mode, we identified 161 quantitative trait nucleotides (QTNs) with stable genetic effects across different environments. Furthermore, we have observed 254 QTN-by-environment interactions with distinct environment-specific effects. Notably, five of these interactions manifested large effects, with R2 values exceeding 10%, while the highest R2 value for stable QTNs was 4.7%. Within the protein-coding genes and their 1 Kb flanking regions, we have discerned 22 QTNs and 45 QTN-by-environment interactions, most likely tagging the candidate causal genes. The landraces obtained from the N.I Vavilov All Russian Institute for Plant Genetic Resources collection exhibit numerous favorable alleles at quantitative trait nucleotide loci, showing stable effects in the Kuban and Astrakhan regions. Additionally, they possessed a significantly higher number of Kuban-specific favorable alleles of the QTN-by-environment interaction loci compared to the Astrakhan-specific ones. The environment-specific alleles found at the QTN-by-environment interaction loci have the potential to enhance chickpea adaptation to specific climatic conditions.

Drosophila melanogaster is the oldest classic model object in developmental genetics. It may seem that various structures of the fruit fly at all developmental stages have been well studied and described. However, recently we have shown that some specialized structures of the D. melanogaster eggshell contain an amyloid fibril network. Here, we demonstrate that this amyloid network is formed by the chorionic protein s36. The s36 protein colocalizes with the amyloid-specific dyes Congo Red and Thioflavin S in the micropyle, dorsal appendages, and pillars. The fibrils of s36 obtained from the eggs demonstrate amyloid properties. In the context of the CG33223 gene deletion, the s36 protein is produced but is not detected in the eggshell. The absence of amyloid fibrils of s36 in the eggshell disrupts the endochorion morphology and blocks the development of the micropyle, dorsal appendages, and pillars, leading to sterility. Our data show for the first time that amyloid fibrils are essential for morphogenesis modulation. We suggest that attachment of follicle cells to the s36 extracellular fibrils triggers signaling to enable subsequent cellular divisions needed for building the specialized eggshell structures. [ABSTRACT FROM AUTHOR]

A collection of flax accessions maintained by the Russian Federal Research Center for Bast Fiber Crops was characterized to evaluate its resistance to Fusarium wilt. 297 samples representing different morphotypes and selection status were infected with highly virulent MI39 strain of Fusarium oxysporum f. sp. lini. Evaluation of disease symptoms was performed at the full emergence stage in a greenhouse. The experiment lasted for 3 successive years. The disease severity index (DSI) record was obtained for every genotype in each year of the experiment. The data set was produced in a framework of a project focused on both a) deciphering the mechanisms of plant immunity, and b) development of flax cultivars resistant to Fusarium wilt. The data is available via Figshare repository.

Genetic diversity in a breeding program is essential to overcome modern-day environmental challenges faced by humanity and produce robust, resilient crop cultivars with improved agronomic characteristics, as well as to trace crop domestication history. Flax (Linum usitatissimum), one of the first crops domesticated by mankind, has been traditionally cultivated for fiber as well as for medicinal purposes and as a nutritional product. The origins of fiber flax are hidden in the mists of time and can be hypothetically traced back to either the Indo-Afghan region or Fertile Crescent. To shed new light on fiber flax genetic diversity and breeding history, in this study, we presented a comprehensive analysis of the core collection of flax (306 accessions) of different morphotypes and geographic origins maintained by the Russian Federal Research Center for Bast Fiber Crops. We observed significant population differentiation between oilseed and fiber morphotypes, as well as mapped genomic regions affected by recent breeding efforts. We also sought to unravel the origins of kryazhs, Russian heritage landraces, and their genetic relatedness to modern fiber flax cultivars. For the first time, our results provide strong genetic evidence in favor of the hypothesis on kryazh’s mixed origin from both the Indo-Afghan diversity center and Fertile Crescent. Finally, we showed predominant contribution from Russian landraces and kryazhs into the ancestry of modern fiber flax varieties. Taken together, these findings may have practical implications on the development of new improved flax varieties with desirable traits that give farmers greater choice in crop management and meet the aspirations of breeders.

Abstract Background The cell-surface attachment protein (Env) of the HERV-K(HML-2) lineage of endogenous retroviruses is a potentially attractive tumour-associated antigen for anti-cancer immunotherapy. The human genome contains around 100 integrated copies (called proviruses or loci) of the HERV-K(HML-2) virus and we argue that it is important for therapy development to know which and how many of these contribute to protein expression, and how this varies across tissues. We measured relative provirus expression in HERV-K(HML-2), using enriched RNA-Seq analysis with both short- and long-read sequencing, in three Mantle Cell Lymphoma cell lines (JVM2, Granta519 and REC1). We also confirmed expression of the Env protein in two of our cell lines using Western blotting, and analysed provirus expression data from all other relevant published studies. Results Firstly, in both our and other reanalysed studies, approximately 10% of the transcripts mapping to HERV-K(HML-2) came from Env-encoding proviruses. Secondly, in one cell line the majority of the protein expression appears to come from one provirus (12q14.1). Thirdly, we find a strong tissue-specific pattern of provirus expression. Conclusions A possible dependency of Env expression on a single provirus, combined with the earlier observation that this provirus is not present in all individuals and a general pattern of tissue-specific expression among proviruses, has serious implications for future HERV-K(HML-2)-targeted immunotherapy. Further research into HERV-K(HML-2) as a possible tumour-associated antigen in blood cancers requires a more targeted, proteome-based, screening protocol that will consider these polymorphisms within HERV-K(HML-2). We include a plan (and necessary alignments) for such work.

Chickpea is a staple crop for many nations worldwide. Modeling genotype-by-environment interactions and assessing the genotype's ability to contribute adaptive alleles are crucial for chickpea breeding. In this study, we evaluated 12 agronomically important traits of 159 accessions from the N.I. Vavilov All Russian Institute for Plant Genetic Resources collection. These included 145 landraces and 13 cultivars grown in different climatic conditions in Kuban (45°18′ N and 40°52′ E) in both 2016 and 2022, as well as in Astrakhan (46°06′ N and 48°04′ E) in 2022. Using the IIIVmrMLM model in multi-environmental mode, we identified 161 quantitative trait nucleotides (QTNs) with stable genetic effects across different environments. Furthermore, we have observed 254 QTN-by-environment interactions with distinct environment-specific effects. Notably, five of these interactions manifested large effects, with R2 values exceeding 10%, while the highest R2 value for stable QTNs was 4.7%. Within the protein-coding genes and their 1 Kb flanking regions, we have discerned 22 QTNs and 45 QTN-by-environment interactions, most likely tagging the candidate causal genes. The landraces obtained from the N.I Vavilov All Russian Institute for Plant Genetic Resources collection exhibit numerous favorable alleles at quantitative trait nucleotide loci, showing stable effects in the Kuban and Astrakhan regions. Additionally, they possessed a significantly higher number of Kuban-specific favorable alleles of the QTN-by-environment interaction loci compared to the Astrakhan-specific ones. The environment-specific alleles found at the QTN-by-environment interaction loci have the potential to enhance chickpea adaptation to specific climatic conditions. [ABSTRACT FROM AUTHOR]

To assess the genomic diversity of Fusarium oxysporum f. sp. lini strains and compile a comprehensive gene repertoire, we constructed a pangenome using 13 isolates from four different clonal lineages, each exhibiting distinct levels of virulence. Syntenic analyses of two selected genomes revealed significant chromosomal rearrangements unique to each genome. A comprehensive examination of both core and accessory pangenome content and diversity points at an open genome state. Additionally, Gene Ontology (GO) enrichment analysis indicated that non-core pangenome genes are associated with pathogen recognition and immune signaling. Furthermore, the Folini pansecterome, encompassing secreted proteins critical for fungal pathogenicity, primarily consists of three functional classes: effector proteins, CAZYmes, and proteases. These three classes account for approximately 3.5% of the pangenome. Each functional class within the pansecterome was meticulously annotated and characterized with respect to pangenome category distribution, PFAM domain frequency, and strain virulence assessment. This analysis revealed that highly virulent isolates have specific types of PFAM domains that are exclusive to them. Upon examining the repertoire of SIX genes known for virulence in other formae speciales, it was found that all isolates had a similar gene content except for two, which lacked SIX genes entirely. [ABSTRACT FROM AUTHOR]

At least 50% of factors predisposing to alcohol dependence (AD) are genetic and women affected with this disorder present with more psychiatric comorbidities, probably indicating different genetic factors involved. We aimed to run a genome-wide association study (GWAS) followed by a bioinformatic functional annotation of associated genomic regions in patients with AD and eight related clinical measures. A genome-wide significant association of rs220677 with AD (p-value = 1.33 × 10−8 calculated with the Yates-corrected χ2 test under the assumption of dominant inheritance) was discovered in female patients. Associations of AD and related clinical measures with seven other single nucleotide polymorphisms listed in previous GWASs of psychiatric and addiction traits were differently replicated in male and female patients. The bioinformatic analysis showed that regulatory elements in the eight associated linkage disequilibrium blocks define the expression of 80 protein-coding genes. Nearly 68% of these and of 120 previously published coding genes associated with alcohol phenotypes directly interact in a single network, where BDNF is the most significant hub gene. This study indicates that several genes behind the pathogenesis of AD are different in male and female patients, but implicated molecular mechanisms are functionally connected. The study also reveals a central role of BDNF in the pathogenesis of AD.

A collection of flax accessions from Russian Federal Research Center for Bast Fiber Crops was characterised to evaluate its phenotypic diversity. 406 samples representing different morphotypes were selected for thorough quantitative assessment of various agronomic traits. We measured height, length of technical part of the stem, technical part weight, inflorescence length, number of bolls and seeds per plant, 1000 seed weight, the diameter of the stem, the number of internodes and finally, distance between internodes. The fiber quality was estimated by calculating stem slenderness, stem taperingness and elementary fiber length. The dataset was produced in a framework of a project focused on characterization of diversity of flax genotypes and phenotypes, as well as on identification of genomic regions associated with various traits, it is hosted on Figshare.

BackgroundVariant annotation is a crucial step in the analysis of genome sequencing data. Functional annotation results can have a strong influence on the ultimate conclusions of disease studies. Incorrect or incomplete annotations can cause researchers both to overlook potentially disease-relevant DNA variants and to dilute interesting variants in a pool of false positives. Researchers are aware of these issues in general, but the extent of the dependency of final results on the choice of transcripts and software used for annotation has not been quantified in detail.MethodsThis paper quantifies the extent of differences in annotation of 80 million variants from a whole-genome sequencing study. We compare results using the RefSeq and Ensembl transcript sets as the basis for variant annotation with the software Annovar, and also compare the results from two annotation software packages, Annovar and VEP (Ensembl's Variant Effect Predictor), when using Ensembl transcripts.ResultsWe found only 44% agreement in annotations for putative loss-of-function variants when using the RefSeq and Ensembl transcript sets as the basis for annotation with Annovar. The rate of matching annotations for loss-of-function and nonsynonymous variants combined was 79% and for all exonic variants it was 83%. When comparing results from Annovar and VEP using Ensembl transcripts, matching annotations were seen for only 65% of loss-of-function variants and 87% of all exonic variants, with splicing variants revealed as the category with the greatest discrepancy. Using these comparisons, we characterised the types of apparent errors made by Annovar and VEP and discuss their impact on the analysis of DNA variants in genome sequencing studies.ConclusionsVariant annotation is not yet a solved problem. Choice of transcript set can have a large effect on the ultimate variant annotations obtained in a whole-genome sequencing study. Choice of annotation software can also have a substantial effect. The annotation step in the analysis of a genome sequencing study must therefore be considered carefully, and a conscious choice made as to which transcript set and software are used for annotation.

Many individuals with multiple or large colorectal adenomas or early-onset colorectal cancer (CRC) have no detectable germline mutations in the known cancer predisposition genes. Using whole-genome sequencing, supplemented by linkage and association analysis, we identified specific heterozygous POLE or POLD1 germline variants in several multiple-adenoma and/or CRC cases but in no controls. The variants associated with susceptibility, POLE p.Leu424Val and POLD1 p.Ser478Asn, have high penetrance, and POLD1 mutation was also associated with endometrial cancer predisposition. The mutations map to equivalent sites in the proofreading (exonuclease) domain of DNA polymerases ɛ and δ and are predicted to cause a defect in the correction of mispaired bases inserted during DNA replication. In agreement with this prediction, the tumors from mutation carriers were microsatellite stable but tended to acquire base substitution mutations, as confirmed by yeast functional assays. Further analysis of published data showed that the recently described group of hypermutant, microsatellite-stable CRCs is likely to be caused by somatic POLE mutations affecting the exonuclease domain.

In development, the switch from pluripotency to differentiation is important but it is often unclear how it is regulated. Here, the authors show that the tumour suppressor RASSF1A mediates this switch by promoting YAP-p73 transcription, which in turn enables differentiation.

Transposons are genomic elements that can relocate within a host genome using a ‘cut’- or ‘copy-and-paste’ mechanism. They make up a significant part of many genomes, serve as a driving force for genome evolution, and are linked with Mendelian diseases and cancers. Interactions between two specific retrotransposon types, autonomous (e.g., LINE1/L1) and nonautonomous (e.g., Alu), may lead to fluctuations in the number of these transposons in the genome over multiple cell generations. We developed and examined a simple model of retrotransposon dynamics under conditions where transposon replication machinery competed for cellular resources: namely, free ribosomes and available energy (i.e., ATP molecules). Such competition is likely to occur in stress conditions that a malfunctioning cell may experience as a result of a malignant transformation. The modeling revealed that the number of actively replicating LINE1 and Alu elements in a cell decreases with the increasing competition for resources; however, stochastic effects interfere with this simple trend. We stochastically simulated the transposon dynamics in a cell population and showed that the population splits into pools with drastically different transposon behaviors. The early extinction of active Alu elements resulted in a larger number of LINE1 copies occurring in the first pool, as there was no competition between the two types of transposons in this pool. In the other pool, the competition process remained and the number of L1 copies was kept small. As the level of available resources reached a critical value, both types of dynamics demonstrated an increase in noise levels, and both the period and the amplitude of predator–prey oscillations rose in one of the cell pools. We hypothesized that the presented dynamical effects associated with the impact of the competition for cellular resources inflicted on the dynamics of retrotransposable elements could be used as a characteristic feature to assess a cell state, or to control the transposon activity.

The genome expression pattern is strongly modified during the heat shock response (HSR) to form an adaptive state. This may be partly achieved by modulating microRNA levels that control the expression of a great number of genes that are embedded within the gene circuitry. Here, we investigated the cross-talk between two highly conserved and universal house-keeping systems, the HSR and microRNA machinery, in Drosophila melanogaster. We demonstrated that pronounced interstrain differences in the microRNA levels are alleviated after heat shock (HS) to form a uniform microRNA pattern. However, individual strains exhibit different patterns of microRNA expression during the course of recovery. Importantly, HS-regulated microRNAs may target functionally similar HS-responsive genes involved in the HSR. Despite the observed general downregulation of primary microRNA precursor expression as well as core microRNA pathway genes after HS, the levels of many mature microRNAs are upregulated. This indicates that the regulation of miRNA expression after HS occurs at transcriptional and post-transcriptional levels. It was also shown that deletion of all hsp70 genes had no significant effect on microRNA biogenesis but might influence the dynamics of microRNA expression during the HSR.