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50 results for “gene conversion”
Chicken Immunoglobulin Gene Conversion Full Dataset
<p>Full dataset containing PacBio sequencing data and gene conversion information output from Brepconvert, for the immunoglobulin heavy and light chain of six 3 week old Rhode Island Red chickens studied as part of the publication Diversification of Antibodies by Gene Conversion in the Domestic Chicken (Gallus gallus domesticus). </p>
Supplemental data for: Increased mutation and gene conversion within human segmental duplications
<p>Data used for figure generation and analysis in: <strong>Increased mutation and gene conversion within human segmental duplications</strong></p> <ol> <li>new-assemblies.zip contains all the new assemblies added in this work beyond the HPRC assemblies (Clint PTR, CHM1, HG00514, NA12878, HG03125). All other assemblies used in this analysis are available through the HPRC: <a href="https://github.com/human-pangenomics/HPP_Year1_Assemblies/blob/main/assembly_index/Year1_assemblies_v2_genbank.index">assembly_index/Year1_assemblies_v2_genbank.index</a>.</li> <li>all-sample.vcf is a vcf file with all the variant calls used in this analysis. </li> <li>alignments.zip contains all the syntenic alignments used for analysis. </li> <li>data.zip contains annotation data and other information used in analysis and figure making. </li> <li>Online tables 1-4 (Online-tables.xlsx)</li> </ol> <p>Code used in figure making and analysis is on <a href="https://github.com/mrvollger/sd-divergence-and-igc-figures">GitHub</a>.</p> <p>Snakemake pipelines used in the analysis are also on GitHub:</p> <ul> <li>Assembly alignment and IGC calling: https://github.com/mrvollger/asm-to-reference-alignment</li> <li>Variant calling from assembly alignments: https://github.com/mrvollger/sd-divergence</li> <li>Analysis of the triplet content of SNVs: https://github.com/mrvollger/mutyper_workflow</li> </ul>
Data from: Evolutionary variation in gene conversion at the avian MHC is explained by fluctuating selection, gene copy numbers, and life history
<p>The Major Histocompatibility Complex (MHC) multigene family encodes key pathogen-recognition molecules of the vertebrate adaptive immune system. Hyper-polymorphism of MHC genes is <em>de novo</em> generated by point mutations, but new haplotypes may also arise by re-shuffling of existing variation through intra- and inter-locus gene conversion. Although the occurrence of gene conversion at the MHC has been known for decades, we still have limited understanding of its functional importance. Here, I took advantage of extensive genetic resources (~9000 sequences) to investigate a broad scale macroevolutionary patterns in gene conversion processes at the MHC across nearly 200 avian species. Gene conversion was found to constitute a universal mechanism in birds, as 83% of species showed footprints of gene conversion at either MHC class and 25% of all allelic variants were attributed to gene conversion. Gene conversion processes were stronger at MHC-II than MHC-I, but inter-specific variation at both MHC classes was explained by similar evolutionary scenarios, reflecting fluctuating selection towards different optima and drift. Gene conversion showed uneven phylogenetic distribution across birds and was driven by gene copy number variation, supporting significant role of inter-locus gene conversion processes in the evolution of the avian MHC. Finally, MHC gene conversion was stronger in species with fast life histories (high fecundity) and in long-distance migrants, likely reflecting variation in population sizes and host-pathogen coevolutionary dynamics. The results provide a robust comparative framework for understanding macroevolutionary variation in gene conversion at the avian MHC and reinforce important contribution of this mechanism to functional MHC diversity.</p>
Data from: Evolutionary variation in gene conversion at the avian MHC is explained by fluctuating selection, gene copy numbers, and life history
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VCF-file for: The effects of GC-biased gene conversion on patterns of genetic diversity among and across butterfly genomes
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Data from: Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure
PREMISE OF THE STUDY: There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements. METHODS: We used Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences to characterize repeat structure in the plastome of Monsonia emarginata L'Hér. (Geraniaceae). We used OrgConv and inspected nucleotide alignments to infer ancestral nucleotides and identify gene conversion among repeats and mapped long (>1 kb) SMRT reads against the unit-genome assembly to identify alternative sequence arrangements. RESULTS: Although M. emarginata lacks the canonical IR, we found that large repeats (>1 kilobase; kb) represent ~22% of the plastome nucleotide content. Among the largest repeats (>2 kb) we identified GC-biased gene conversion and mapping filtered, long SMRT reads to the M. emarginata unit-genome assembly revealed alternative, substoichiometric sequence arrangements. CONCLUSION: We offer a model based on RDR and gene conversion between long repeated sequences in the M. emarginata plastome, and provide support that both intra-and intermolecular recombination between large repeats, particularly in repeat-rich plastomes, varies unit-genome structure while homogenizing the nucleotide sequence of repeats.
Data from: Gene conversion yields novel gene combinations in paralogs of GOT1 in the copepod Tigriopus californicus
Background: Gene conversion of duplicated genes can slow the divergence of paralogous copies over time but can also result in other interesting evolutionary patterns. Islands of genetic divergence that persist in the face of gene conversion can point to gene regions undergoing selection for new functions. Novel combinations of genetic variation that differ greatly from the original sequence can result from the transfer of genetic variation between paralogous genes by rare gene conversion events. Genetically divergent populations of the copepod Tigriopus californicus provide an excellent model to look at the patterns of divergence among paralogs across multiple independent evolutionary lineages. Results: In this study the evolution of a set of paralogous genes encoding putative aspartate transaminase proteins (called GOT1 here) are examined in populations of the copepod T. californicus. One pair of duplicated genes, GOT1p1 and GOT1p2, has regions of high divergence between the copies in the face of apparent on-going gene conversion. The GOT1p2 gene also has unique haplotypes in two populations that appear to have resulted from a transfer of genetic variation via inter-paralog gene conversion. A second pair of duplicated genes GOT1Sr and GOT1Sd also shows evidence of gene conversion, but this gene conversion does not appear to have maintained each as a functional copy in all populations. Conclusions: The patterns of conservation and sequence divergence across this set of paralogous genes among populations of T. californicus suggest that some interesting evolutionary patterns are occurring at these loci. The results for the GOT1p1/GOT1p2 paralogs illustrate how gene conversion can factor in the creation of a mosaic pattern of regions of high divergence and low divergence. When coupled with rare gene conversion events of divergent regions, this pattern can result in the formation of novel proteins differing substantially from either original protein. The evolutionary patterns across these paralogs show how gene conversion can both constrain and facilitate diversification of genetic sequences.
Data from: Gene conversion yields novel gene combinations in paralogs of GOT1 in the copepod Tigriopus californicus
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Data from: Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure
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Data from: Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion
We used whole-genome resequencing data from a population of Drosophila melanogaster to investigate the causes of the negative correlation between the within-population synonymous nucleotide site diversity (πS) of a gene and its degree of divergence from related species at nonsynonymous nucleotide sites (KA). By using the estimated distributions of mutational effects on fitness at nonsynonymous and UTR sites, we predicted the effects of background selection at sites within a gene on πS and found that these could account for only part of the observed correlation between πS and KA. We developed a model of the effects of selective sweeps that included gene conversion as well as crossing over. We used this model to estimate the average strength of selection on positively selected mutations in coding sequences and in UTRs, as well as the proportions of new mutations that are selectively advantageous. Genes with high levels of selective constraint on nonsynonymous sites were found to have lower strengths of positive selection and lower proportions of advantageous mutations than genes with low levels of constraint. Overall, background selection and selective sweeps within a typical gene reduce its synonymous diversity to ∼75% of its value in the absence of selection, with larger reductions for genes with high KA. Gene conversion has a major effect on the estimates of the parameters of positive selection, such that the estimated strength of selection on favorable mutations is greatly reduced if it is ignored.
Gene conversion facilitates the adaptive evolution of self-resistance in highly toxic newts
<p>Reconstructing the histories of complex adaptations and identifying the evolutionary mechanisms underlying their origins are two of the primary goals of evolutionary biology. <i>Taricha </i>newts, which contain high concentrations of the deadly toxin tetrodotoxin (TTX) as an antipredator defense, have evolved resistance to self-intoxication, which is a complex adaptation requiring changes in six paralogs of the voltage-gated sodium channel (Na<sub>v</sub>) gene family, the physiological target of TTX. Here, we reconstruct the origins of TTX self-resistance by sequencing the entire Na<sub>v</sub> gene family in newts and related salamanders. We show that moderate TTX resistance evolved early in the salamander lineage in three of the six Na<sub>v</sub><i> </i>paralogs, preceding the proposed appearance of tetrodotoxic newts by ~100 million years. TTX-bearing newts possess additional unique substitutions across the entire Na<sub>v</sub> gene family that provide physiological TTX resistance. These substitutions coincide with signatures of positive selection and relaxed purifying selection, as well as gene conversion events, that together likely facilitated their evolution. We also identify a novel exon duplication within Na<sub>v</sub>1.4<i> </i>encoding an expressed TTX-binding site. Two resistance-conferring changes within newts appear to have spread via nonallelic gene conversion: in one case, one codon was copied between paralogs, and in the second, multiple substitutions were homogenized between the duplicate exons of Na<sub>v</sub>1.4. Our results demonstrate that gene conversion can accelerate the coordinated evolution of gene families in response to a common selection pressure.</p>
Gene conversion facilitates the adaptive evolution of self-resistance in highly toxic newts
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Data from: Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion
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Use of the B cell transcription program results in hypomethylation and overexpression of key genes in EBV-mediated conversion of resting to proliferative B cells
GEO Series GSE41957. Homo sapiens. 12 samples. Type: Methylation profiling by array.
Gene expression profiling on C3H/10T1/2 fibroblasts during their myogenic conversion in case of Six4 ablation
GEO Series GSE66319. Mus musculus. 12 samples. Type: Expression profiling by array.
A NeuroD1 AAV-Based Gene Therapy For Functional Brain Repair After Ischemic Injury Through In Vivo Astrocyte-To-Neuron Conversion
GEO Series GSE135981. Mus musculus. 7 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq analysis of gene expression in cells during Ascl1 mediated astrocyte-to-neuron conversion.
GEO Series GSE132674. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
A computational systems approach for identification of synergistic specification genes facilitates lineage conversion to prostate tissue
GEO Series GSE83298. Mus musculus. 19 samples. Type: Expression profiling by high throughput sequencing.
Fate Erasure Logic of Gene Networks Underlying Direct Neuronal Conversion of Somatic Cells by MicroRNAs III
GEO Series GSE283008. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
Attenuation of PTBP2 facilitates fibroblast to neuron conversion by promoting alternative splicing of neuronal genes
GEO Series GSE210131. Homo sapiens. 36 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.