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1,293 results for “gene sequencing”
Repeatome turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets
<p>The present repository provides zipped archives containing the results of the RepeatExplorer2 runs of individual as well as comparative repeat analyses in beet genomes.</p> <p> </p> <p>Sugar beet (<em>Beta vulgaris</em> subsp. <em>vulgaris</em>) and its crop wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNA sequences represent the fastest evolving parts of the genome, they likely impact genomic variability and contribute to the separation of beet gene pools. Hence, we investigated if innovations and losses in the repeatome can be linked to chromosomal differentiation and speciation.</p> <p>We traced genome- and chromosome-wide evolution across sugar beet and twelve wild beets comprising all sections of the beet genera <em>Beta </em>and <em>Patellifolia</em>. For this, we combined data from short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive data framework for our beet panel that spans the complete scale from DNA sequence to chromosome up to the genome. Genome sizes and repeat profiles reflect the separation of the beet species into three gene pools. These gene pools harbor repeats with contrasting evolutionary patterns: We identified section- and species-specific repeat emergences and losses, e.g. of the retrotransposons causal for genome expansions in the section <em>Corollinae</em>/<em>Nanae</em>. Since most genomic variability was found in the satellite DNAs, we focused on tracing the 19 beetSat families across the three beet sections/genera. These taxa harbor evidence for contrasting strategies in repeat evolution, leading to contrasting satellite DNA profiles and fundamentally different centromere architectures, ranging from chromosomal uniformity in <em>Beta</em> and <em>Patellifolia</em> species to the formation of patchwork chromosomes in <em>Corollinae/Nanae</em> species. </p> <p>We show that repetitive DNA sequences are causal for genome size expansion and contraction across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably among beet taxa, leading to the evolution of distinct chromosomal setups. These differences likely contribute to the barriers in beet breeding between the three gene pools. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genome variability, and chromosomal differentiation/evolution and provide a theoretical basis for understanding barriers in crop breeding.</p>
Fig. 7 in Transcriptome sequencing of the apricot (Prunus armeniaca L.) and identification of differentially expressed genes involved in drought stress
Fig. 7. Effects of control and drought stress on leaf microstructure of apricot. a, c, e, represent the leaf stomata, vertical section, and cuticle in the control group, respectively. b, d, f, represent the leaf stomata, vertical section, and cuticle in the drought stress group, respectively.
Fig. 4 in Transcriptome sequencing of the apricot (Prunus armeniaca L.) and identification of differentially expressed genes involved in drought stress
Fig. 4. KEGG enrichment of annotated DEGs in Treat versus Control. The Y-axis shows the KEGG pathway and the X-axis shows the Rich factor. This q value goes from purple to red, which means from 1 to 0. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3 in Transcriptome sequencing of the apricot (Prunus armeniaca L.) and identification of differentially expressed genes involved in drought stress
Fig. 3. GO classifications of DEGs for Treat versus Control. The Y-axis represents the number of DEGs in a category. The BP, CC and MF represent biological process, cellular component and molecular function respectively.
Fig. 5. SSR motifs distribution. The X in Transcriptome sequencing of the apricot (Prunus armeniaca L.) and identification of differentially expressed genes involved in drought stress
Fig. 5. SSR motifs distribution. The X-axis is SSR type, the Y-axis value is the coordinate, the specific number of repetitions should correspond to the legend according to the color, and the Z-axis is the number of SSR. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1 in Transcriptome sequencing of the apricot (Prunus armeniaca L.) and identification of differentially expressed genes involved in drought stress
Fig. 1. Gene Function Classification of the assembled unigenes. Unigenes with BLAST hits were classified into three major categories and 56 sub-categories in GO. The Y-axis shows the number of genes in each sub-category.
Fig. 3. a in Sequencing and variation of terpene synthase gene (TPS2) as the major gene in biosynthesis of thymol in different Thymus species
Fig. 3. a. Maximum likelihood tree of Thymus species based on 16 sequences of the TPS of cDNA. Numbers above branches are support values from bootstrap resembling. Accession numbers of TPS2 sequences obtained from the NCBI GenBank are shown in parentheses (Accession numbers starting with MH were obtained through this study). For the studied species, the main monoterpenes in the essential oil are included T: Thymol; C: Carvacrol; PC: p-Cymene; AT: α-Terpineol; L: Linalool. b. Dendrogram of nine studied Thymus species using Ward clustering method based on Tohidi et al. (2017).
Fig. 2 in Sequencing and variation of terpene synthase gene (TPS2) as the major gene in biosynthesis of thymol in different Thymus species
Fig. 2. Amino acid alignment of Ttps2 sequences of nine studied Thymus species. The four motifs, conserved in all species terpene synthases, are indicated in red (top). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1 in Sequencing and variation of terpene synthase gene (TPS2) as the major gene in biosynthesis of thymol in different Thymus species
Fig. 1. Predicted biosynthetic pathway of terpene synthases in Thymus genus leading to the formation of α-terpineol and γ-terpinene, the precursor of thymol and carvacrol Adapted from Lima et al. (2013).
Testing of NBIA Genes: Analysis of Genetic Heterogeneity and Validation of Mitochondrial Markers for Assessing Causality of Sequence Variants.
ClinicalTrials.gov study NCT05615571. IPD Sharing: NO. Countries: 1. Publications: 1.
Sequencing to Identify Gene Variants in Familial Colorectal Cancer
ClinicalTrials.gov study NCT01904630. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Using 16S rRNA Gene Sequencing Analysis Intestinal Microbiota in Constipation Patients
ClinicalTrials.gov study NCT02984969. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Comprehensive Gene Sequencing in Guiding Treatment Recommendations Patients With Metastatic or Recurrent Solid Tumors
ClinicalTrials.gov study NCT01987726. IPD Sharing: NO. Countries: 1. Publications: 1.
Breast Cancer Risk After Diagnostic Gene Sequencing
ClinicalTrials.gov study NCT04145817. IPD Sharing: Not stated. Countries: 2. Publications: 3.
Non-invasive Tumor Immunoglobulin Gene Next Generation Sequencing (IgNGS) in Diffuse Large B Cell Lymphoma (DLBCL)
ClinicalTrials.gov study NCT04237168. IPD Sharing: NO. Countries: 1. Publications: 5.
Genome Medical Sequencing for Gene Discovery
ClinicalTrials.gov study NCT01087320. IPD Sharing: NO. Countries: 1. Publications: 3.
Sequence alignment for 7 gene regions for new Phytophthora species in clade 2a
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Data from: Targeted re-sequencing of five Douglas-fir provenances reveals population structure and putative target genes of positive selection
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Data from: Whole genome sequencing reveals absence of recent gene-flow and separate demographic histories for Anopheles punctulatus mosquitoes in Papua New Guinea
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Data from: Utility of internally transcribed spacer region of rDNA (ITS) and β-tubulin gene sequences to infer genetic diversity and migration patterns of Colletotrichum truncatum infecting Capsicum spp.
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Allen Brain Atlas
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
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