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View article: Dynamic patterns of repeats and retrotransposons in the centromeres of <i>Humulus lupulus</i> L.
Dynamic patterns of repeats and retrotransposons in the centromeres of <i>Humulus lupulus</i> L. Open
Summary The centromere has a conserved function across eukaryotes; however, the associated DNA sequences exhibit remarkable diversity in both size and structure. In plants, some species possess well‐defined centromeres dominated by tandem …
View article: Factors determining chromosomal localization of transposable elements in plants
Factors determining chromosomal localization of transposable elements in plants Open
Transposable elements (TEs) constitute a significant part of plant genomes and shape their genomic landscape. While some TEs are ubiquitously dispersed, other elements specifically occupy discrete genomic loci. The evolutionary forces behi…
View article: The <i>Silene latifolia</i> genome and its giant Y chromosome
The <i>Silene latifolia</i> genome and its giant Y chromosome Open
In many species with sex chromosomes, the Y is a tiny chromosome. However, the dioecious plant Silene latifolia has a giant ~550-megabase Y chromosome, which has remained unsequenced so far. We used a long- and short-read hybrid approach t…
View article: Correction: Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning
Correction: Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning Open
View article: Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning
Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning Open
View article: Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning
Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning Open
Background Long terminal repeats (LTRs) represent important parts of LTR retrotransposons and retroviruses found in high copy numbers in a majority of eukaryotic genomes. LTRs contain regulatory sequences essential for the life cycle of th…
View article: Sexy ways: approaches to studying plant sex chromosomes
Sexy ways: approaches to studying plant sex chromosomes Open
Sex chromosomes have evolved in many plant species with separate sexes. Current plant research is shifting from examining the structure of sex chromosomes to exploring their functional aspects. New studies are progressively unveiling the s…
View article: The<i>Silene latifolia</i>genome and its giant Y chromosome
The<i>Silene latifolia</i>genome and its giant Y chromosome Open
In some species, the Y is a tiny chromosome but the dioecious plant Silene latifolia has a giant ∼550 Mb Y chromosome, which has remained unsequenced so far. Here we used a hybrid approach to obtain a high-quality male S. latifolia genome.…
View article: Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus
Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus Open
View article: Telomeric retrotransposons show propensity to form G-quadruplexes in various eukaryotic species
Telomeric retrotransposons show propensity to form G-quadruplexes in various eukaryotic species Open
View article: Additional file 5 of Telomeric retrotransposons show propensity to form G-quadruplexes in various eukaryotic species
Additional file 5 of Telomeric retrotransposons show propensity to form G-quadruplexes in various eukaryotic species Open
Additional file 5.
View article: Additional file 2 of Telomeric retrotransposons show propensity to form G-quadruplexes in various eukaryotic species
Additional file 2 of Telomeric retrotransposons show propensity to form G-quadruplexes in various eukaryotic species Open
Additional file 2: Table S1. Sequences used for Fig. 5. The scheme is based on the sequences and description in corresponding references. Table S2. Evaluation of G-forming potential of telomeric LINE elements. Table S3. Sequences of D. mel…
View article: Additional file 7 of Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus
Additional file 7 of Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus Open
Additional file 7: Supplementary Table S7. GO terms enrichment analysis of genes co-expressed in a specific module according to WGCNA analysis. Significantly enriched terms (adjusted p-value < 0.05) are sorted according to the GO terms gro…
View article: Additional file 6 of Telomeric retrotransposons show propensity to form G-quadruplexes in various eukaryotic species
Additional file 6 of Telomeric retrotransposons show propensity to form G-quadruplexes in various eukaryotic species Open
Additional file 6.
View article: Additional file 3 of Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus
Additional file 3 of Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus Open
Additional file 3: Supplementary Table S3. GO terms enrichment analysis in DEGs. Significantly enriched terms (adjusted p-value < 0.05) are sorted according to the GO terms group (P, Biological Process; F, Molecular Function; C, Cellular C…
View article: Additional file 6 of Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus
Additional file 6 of Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus Open
Additional file 6: Supplementary Table S6. List of genes co-expressed in specific modules.
View article: Additional file 4 of Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus
Additional file 4 of Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus Open
Additional file 4: Supplementary Table 4. KEGG pathways [20] enrichment analysis in DEGs. Significantly enriched pathways (adjusted p-value < 0.05) are shown for each tissue and cultivar.
View article: Additional file 8 of Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus
Additional file 8 of Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus Open
Additional file 8: Supplementary Table S8. Top 20 hub genes in WGCNA modules.
View article: Additional file 5 of Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus
Additional file 5 of Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus Open
Additional file 5: Supplementary Table S5. GO terms and KEGG pathways [20] enrichment analysis of DEGs specific for Topas and for sensitive cultivars DH12075 and Westar.
View article: Additional file 2 of Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus
Additional file 2 of Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus Open
Additional file 2: Supplementary Table S2. DEGs (21°C vs. 34°C) with |log2 (fold change)| >1 and adjusted p-value < 0.05 in all studied cultivars and tissues. lfcSE, standard error of the log2FoldChange; baseMean, mean of normalized counts…
View article: Additional file 4 of Telomeric retrotransposons show propensity to form G-quadruplexes in various eukaryotic species
Additional file 4 of Telomeric retrotransposons show propensity to form G-quadruplexes in various eukaryotic species Open
Additional file 4.
View article: Additional file 3 of Telomeric retrotransposons show propensity to form G-quadruplexes in various eukaryotic species
Additional file 3 of Telomeric retrotransposons show propensity to form G-quadruplexes in various eukaryotic species Open
Additional file 3.
View article: Additional file 1 of Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus
Additional file 1 of Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus Open
Additional file 1: Supplementary Table S1. Overview of the RNA sequencing data.
View article: Additional file 9 of Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus
Additional file 9 of Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus Open
Additional file 9: Supplementary Table S9. List of primers used for RT-qPCR.
View article: Unique peptidic agonists of a juvenile hormone receptor with species-specific effects on insect development and reproduction
Unique peptidic agonists of a juvenile hormone receptor with species-specific effects on insect development and reproduction Open
Juvenile hormones (JHs) control insect metamorphosis and reproduction. JHs act through a receptor complex consisting of methoprene-tolerant (Met) and taiman (Tai) proteins to induce transcription of specific genes. Among chemically diverse…
View article: Telomeric retrotransposons show high propensity to form G-quadruplexes in various species
Telomeric retrotransposons show high propensity to form G-quadruplexes in various species Open
Background: Drosophila melanogaster telomeres are composed of three retrotransposons - Het-A, TART and TAHRE (HTT), which jump at the chromosome ends in orientation specific manner. Canonical telomeres, extended by telomerase, contain G-ri…
View article: Motion Capture 3D Sign Language Resources
Motion Capture 3D Sign Language Resources Open
The new 3D motion capture data corpus expands the portfolio of existing language resources by a corpus of 18 hours of Czech sign language. This helps alleviate the current problem, which is a critical lack of quality data necessary for res…
View article: HiC-TE: a computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization
HiC-TE: a computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization Open
Motivation The role of repetitive DNA in the 3D organization of the interphase nucleus is a subject of intensive study. In studies of 3D nucleus organization, mutual contacts of various loci can be identified by Hi-C sequencing. Typical an…
View article: Additional files for Lexa et al. HiC-TE publication
Additional files for Lexa et al. HiC-TE publication Open
Additional files for Lexa et al. HiC-TE publication Additional file 1 Suplementary Figure — Flow chart of the Nextflow HiC-TE pipeline (output from running Nextflow with the -graph switch) Additional file 2
View article: Additional files for Lexa et al. HiC-TE publication
Additional files for Lexa et al. HiC-TE publication Open
Additional files for Lexa et al. HiC-TE publication Suplementary Figures HiC-TE manual Suplementary Tables PDF files with 6 complete sets of outputs, numbered by SRR ID and the name of output