Bisulfite sequencing detects and quantifies DNA methylation patterns, contributing to our understanding of gene expression regulation, genome stability maintenance, conservation of epigenetic ...mechanisms across divergent taxa, epigenetic inheritance and, eventually, phenotypic variation. Graphical representation of methylation data is crucial in exploring epigenetic regulation on a genome-wide scale in both plants and animals. This is especially relevant for non-model organisms with poorly annotated genomes and/or organisms where genome sequences are not yet assembled on chromosome level. Despite being a technology of choice to profile DNA methylation for many years now there are surprisingly few lightweight and robust standalone tools available for efficient graphical analysis of data in non-model systems. This significantly limits evolutionary studies and agrigenomics research. BSXplorer is a tool specifically developed to fill this gap and assist researchers in explorative data analysis and in visualising and interpreting bisulfite sequencing data more easily.
BSXplorer provides in-depth graphical analysis of sequencing data encompassing (a) profiling of methylation levels in metagenes or in user-defined regions using line plots and heatmaps, generation of summary statistics charts, (b) enabling comparative analyses of methylation patterns across experimental samples, methylation contexts and species, and (c) identification of modules sharing similar methylation signatures at functional genomic elements. The tool processes methylation data quickly and offers API and CLI capabilities, along with the ability to create high-quality figures suitable for publication.
BSXplorer facilitates efficient methylation data mining, contrasting and visualization, making it an easy-to-use package that is highly useful for epigenetic research.
Modern flax cultivars are susceptible to many diseases; arguably, the most economically damaging of these is the Fusarium wilt fungal disease. Over the past decades international flax breeding ...initiatives resulted in the development of resistant cultivars. However, much remains to be learned about the mechanisms of resistance to Fusarium infection in flax. As a first step to uncover the genetic factors associated with resistance to Fusarium wilt disease, we performed a genome-wide association study (GWAS) using 297 accessions from the collection of the Federal Research Centre of the Bast Fiber Crops, Torzhok, Russia. These genotypes were infected with a highly pathogenic
f.sp.
MI39 strain; the wilt symptoms were documented in the course of three successive years. Six different single-locus models implemented in GAPIT3 R package were applied to a selected subset of 72,526 SNPs. A total of 15 QTNs (Quantitative Trait Nucleotides) were detected during at least two years of observation, while eight QTNs were found during all three years of the experiment. Of these, ten QTNs occupied a region of 640 Kb at the start of chromosome 1, while the remaining QTNs mapped to chromosomes 8, 11 and 13. All stable QTNs demonstrate a statistically significant allelic effect across 3 years of the experiment. Importantly, several QTNs spanned regions that harbored genes involved in the pathogen recognition and plant immunity response, including the KIP1-like protein (
) and NBS-LRR protein (
). Our results provide novel insights into the genetic architecture of flax resistance to Fusarium wilt and pinpoint potential candidate genes for further in-depth studies.
Influenza A viruses pose a constant potential threat to human health. In view of the innate antiviral activity of interferons (IFNs) and their potential use as anti-influenza agents, it is important ...to know whether viral resistance to these antiviral proteins can arise. To examine the likelihood of emergence of IFN-λ1-resistant H1N1 variants, we serially passaged the A/California/04/09 (H1N1) strain in a human lung epithelial cell line (Calu-3) in the presence of increasing concentrations of recombinant IFN-λ1 protein. To monitor changes associated with adaptation of this virus to growth in Calu-3 cells, we also passaged the wild-type virus in the absence of IFN-λ1. Under IFN-λ1 selective pressure, the parental virus developed two neuraminidase (NA) mutations, S79L and K331N, which significantly reduced NA enzyme activity (↓1.4-fold) and sensitivity to IFN-λ1 (↓˃20-fold), respectively. These changes were not associated with a reduction in viral replication levels. Mutants carrying either K331N alone or S79L and K331N together induced weaker phosphorylation of IFN regulatory factor 3 (IRF3), and, as a consequence, much lower expression of the IFN genes (IFNB1, IFNL1 and IFNL2/3) and proteins (IFN-λ1 and IFN-λ2/3). The lower levels of IFN expression correlated with weaker induction of tyrosine-phosphorylated STAT1 and reduced RIG-I protein levels. Our findings demonstrate that influenza viruses can develop increased resistance to the antiviral activity of type III interferons.
A major objective of systems biology is to organize molecular interactions as networks and to characterize information flow within networks. We describe a computational framework to integrate ...protein-protein interaction (PPI) networks and genetic screens to predict the 'signs' of interactions (i.e., activation-inhibition relationships). We constructed a Drosophila melanogaster signed PPI network consisting of 6,125 signed PPIs connecting 3,352 proteins that can be used to identify positive and negative regulators of signaling pathways and protein complexes. We identified an unexpected role for the metabolic enzymes enolase and aldo-keto reductase as positive and negative regulators of proteolysis, respectively. Characterization of the activation-inhibition relationships between physically interacting proteins within signaling pathways will affect our understanding of many biological functions, including signal transduction and mechanisms of disease.
Protein arginine methyltransferase (PRMT) 5 is over-expressed in a variety of cancers and the master transcription regulator E2F1 is an important methylation target. We have explored the role of ...PRMT5 and E2F1 in regulating the non-coding genome and report here a striking effect on long non-coding (lnc) RNA gene expression. Moreover, many MHC class I protein-associated peptides were derived from small open reading frames in the lncRNA genes. Pharmacological inhibition of PRMT5 or adjusting E2F1 levels qualitatively altered the repertoire of lncRNA-derived peptide antigens displayed by tumour cells. When presented to the immune system as either ex vivo-loaded dendritic cells or expressed from a viral vector, lncRNA-derived peptides drove a potent antigen-specific CD8 T lymphocyte response, which translated into a significant delay in tumour growth. Thus, lncRNA genes encode immunogenic peptides that can be deployed as a cancer vaccine.
The Genetic Landscape of Fiber Flax Duk, Maria; Kanapin, Alexander; Rozhmina, Tatyana ...
Frontiers in plant science,
12/2021, Letnik:
12
Journal Article
Recenzirano
Odprti dostop
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 (
), 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.
Here we characterize the expression of the full system of genes which control the segmentation morphogenetic field of
Drosophila at the protein level in one dimension. The data used for this ...characterization are quantitative with cellular resolution in space and about 6 min in time. We present the full quantitative profiles of all 14 segmentation genes which act before the onset of gastrulation. The expression patterns of these genes are first characterized in terms of their average or typical behavior. At this level, the expression of all of the genes has been integrated into a single atlas of gene expression in which the expression levels of all genes in each cell are specified. We show that expression domains do not arise synchronously, but rather each domain has its own specific dynamics of formation. Moreover, we show that the expression domains shift position in the direction of the cephalic furrow, such that domains in the anlage of the segmented germ band shift anteriorly while those in the presumptive head shift posteriorly. The expression atlas of integrated data is very close to the expression profiles of individual embryos during the latter part of the blastoderm stage. At earlier times gap gene domains show considerable variation in amplitude, and significant positional variability. Nevertheless, an average early gap domain is close to that of a median individual. In contrast, we show that there is a diversity of developmental trajectories among pair-rule genes at a variety of levels, including the order of domain formation and positional accuracy. We further show that this variation is dynamically reduced, or canalized, over time. As the first quantitatively characterized morphogenetic field, this system and its behavior constitute an extraordinarily rich set of materials for the study of canalization and embryonic regulation at the molecular level.
We applied an in vitro selection approach using two different plant lectins that bind to α2,3- or α2,6-linked sialic acids to determine which genetic changes of the A/California/04/09 (H1N1) virus ...alter hemagglutinin (HA) receptor binding toward α2,3- or α2,6-linked glycans. Consecutive passages of the A/California/04/09 virus with or without lectins in human lung epithelial Calu-3 cells led to development of three HA1 amino acid substitutions, N129D, G155E, and S183P, and one mutation in the neuraminidase (NA), G201E. The S183P mutation significantly increased binding to several α2,6 SA-linked glycans, including YDS, 6'SL(N), and 6-Su-6'SLN, compared to the wild-type virus (↑3.6-fold, P < 0.05). Two other HA1 mutations, N129D and G155E, were sufficient to significantly increase binding to α2,6-linked glycans, 6'SLN and 6-Su-6'SLN, compared to S183P (↑4.1-fold, P < 0.05). These HA1 mutations also increased binding affinity for 3'SLN glycan compared to the wild-type virus as measured by Biacore surface plasmon resonance method. In addition, the HA1 N129D and HA1 G155E substitutions were identified as antigenic mutations. Furthermore, the G201E mutation in NA reduced the NA enzyme activity (↓2.3-fold). These findings demonstrate that the A/California/04/09 (H1N1) virus can acquire enhanced receptor affinity for both α2,3- and α2,6-linked sialic receptors under lectin-induced selective pressure. Such changes in binding affinity are conferred by selection of beneficial HA1 mutations that affect receptor specificity, antigenicity, and/or functional compatibility with the NA protein.
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 (
L.) is a major grain legume and a good source of plant-based protein. However, comprehensive knowledge of flowering time control in
is lacking. In this study, we acquire high-throughput ...transcriptome sequencing data and analyze changes in gene expression during floral transition in the early flowering cultivar ICCV 96029, later flowering
accessions, and two wild species,
and
. We identify
orthologs of
flowering time genes and analyze differential expression of 278 genes between four species/accessions, three tissue types, and two conditions. Our results show that the differences in gene expression between ICCV 96029 and other cultivated chickpea accessions are vernalization-dependent. In addition, we highlight the role of
, an ortholog of
in
, in the vernalization response of cultivated chickpea. A common set of differentially expressed genes was found for all comparisons between wild species and cultivars. The direction of expression change for different copies of the
gene was variable in different comparisons, which suggests complex mechanisms of FT protein transport. Our study makes a contribution to the understanding of flowering time control in
, and can provide genetic strategies to further improve this important agronomic trait.
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