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128 results for “gene copy number”
Chemical composition, soil water content and 16S rRNA and ITS gene copy numbers of soil aggregates and bulk soil samples
<p>This repository contains all data to reproduce the analyses presented in "Distinct microbial communities are linked to organic matter properties in millimetre-sized soil aggregates", Simon et al 2024, <em>The ISME Journal </em>(DOI: 10.1093/ismejo/wrae156).</p>
High MHC gene copy number maintains diversity despite homozygosity in a Critically Endangered single-island endemic bird, but no evidence of MHC-based mate choice
<p>Raw sequence data from two amplicon libraries of MHC class I exon 3 of Raso Lark <em>Alauda razae</em>, sequenced on an Illumina Miseq. The two different libraries (two different Illumina runs) are collected in separat tar archive (.tar). Within each of those are individual sequence reads as gzipped fastq files (.fastq.gz). Each sample has two files, one for read 1 (R1) and one for read 2 (R2), with file names structured as follows. Delimited by underscore (_) are:</p> <ol> <li>sample name as referred to in the data and paper (“RingNo” in the Supporting data table);</li> <li>formal ID (also referred to in data table, often corresponding to full ring number);</li> <li>Illumina sample number (i.e. based on the order that samples are listed in the sample sheet);</li> <li>Illumina lane number (static as L001, as Miseq instruments have a single lane on their flow cells);</li> <li>read number (R1 [forward] or R2 [reverse]);</li> <li>static identifier from Illumina (001).</li> </ol> <p>Thus, the file 83304_TJ83304_S163_L001_R2_001.fastq.gz is the reverse (read 2) MHC class I exon 3 sequence of individual 83304 (ring number TJ83304).</p>
Rare Genomic Copy Number Variants Implicate New Candidate Genes for Bicuspid Aortic Valve
<p>Whole genome genotyping data in dbGAP format and copy number variant calls in dbVar format.</p> <p>dbVar data includes CNV calls from cases with early onset bicuspid aortic valve disease (EBAV), cases from the International BAV Consortium (BAVCon), and controls from the dbGAP Wisconsin Longitudinal Study on Aging dataset (WLS).</p> <p>dbGAP files are divided into 12 batches of genotypes from EBAV subjects (EBAV1-12):</p> <p>1) PLINK output files (.map and .ped)</p> <p>2) GenomeStudio Final Report files</p> <p>3) One master pedigree file</p> <p>4) dbGAP subject mapping files</p> <p> </p>
Dataset for: Ace and ace-like genes of invasive redlegged earth mite: Copy number variation, target-site mutations, and their associations with organophosphate insensitivity
<p class="MsoNormal">This repository contains the scripts and data required to replicate the analyses in Thia et al.'s, "Evolution of an acetylcholinesterase<em> </em>gene complex and its contribution toward organophosphate insensitivity in an invasive mite pest", submitted to <em>Pest Management Science</em>.</p> <p class="MsoNormal">In this work, Thia et al. use a combination of experimental selection and pool-seq genomic analyses to understand the genetic mechanisms underpinning organophosphate insensitivity in the redlegged earth mite, <em>Halotydeus destructor</em>. There is a special emphasis on disentangling the roles of copy number variation and target-site mutations in the acetylcholinesterase genes, <em>ace,</em> and radiated <em>ace</em>-like genes<span>.</span></p> <p class="MsoNormal">There are three major analyses: (1) an F<sub>ST</sub> genome scan to identify outlier loci between alive (insensitive) and dead (sensitive) mites; (2) an analysis of <em>ace </em>copy number variation between alive and dead mites; and (3) an analysis of candidate target-site mutations in the <em>ace</em> gene.</p>
Dataset for: Ace and ace-like genes of invasive redlegged earth mite: Copy number variation, target-site mutations, and their associations with organophosphate insensitivity
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Data from: Extreme copy number variation at a tRNA ligase gene affecting phenology and fitness in yellow monkeyflowers
Copy number variation (CNV) is a major part of the genetic diversity segregating within populations, but remains poorly understood relative to single nucleotide variation. Here, we report on a tRNA ligase gene (RLG1a) exhibiting unprecedented, and fitness-relevant, CNV within an annual population of the yellow monkeyflower Mimulus guttatus. Variation at RLG1a was associated with multiple traits in pooled population resequencing (PoolSeq) scans of phenotypic and phenological cohorts. Five of 35 (14%) of resequenced inbred lines carried three-copy variants of RLG1a (trip+), and trip+ lines exhibited elevated RLG1a expression. trip+ carriers, in addition to being over-represented in late-flowering and large-flowered PoolSeq populations, flowered later under stressful conditions in a greenhouse experiment (P < 0.05). In early-flowering wild cohorts, we discovered an additional rare variant (high+) that carries 250-300 copies of RLG1a totaling ~5.7Mb, equivalent to 20-40% of a chromosome. Mendelian segregation of diagnostic alleles and qPCR-based copy counts In the progeny of a high+ carrier, indicate that high+ is a single tandem array unlinked from the single copy RLG1a locus in the reference genome. In the wild, high+ carriers had highest fitness in two dry and/or hot years (2015 and 2017; both P < 0.01), while single copy individuals were twice as fecund as either CNV genotype in a lush year (2016: p < 0.005). Our results demonstrate fluctuating selection on CNVs affecting phenological traits in a wild population, suggest that plant tRNA ligases mediate stress-responsive life-history traits, and introduce a novel system for investigating the molecular mechanisms of gene amplification.
Data from: The fire ant social supergene is characterized by extensive gene and transposable element copy number variation
In the fire ant Solenopsis invicta, a supergene composed of ~600 genes and having two variants, SB and Sb, regulates colony social form. In single queen colonies all individuals carry only the SB allele, while in multiple queen colonies, some individuals carry the Sb allele. In this study we characterized genes with copy number variation between SB and Sb-carrying individuals. We showed extensive acquisition of gene duplicates in Sb genome, with some likely involved in polygyne-related phenotypes. We found 260 genes with differences in copy number between SB and Sb, of which 239 are in greater copy number in Sb. We observed TE accumulation on Sb, likely due to the accumulation of repetitive elements on the non-recombining chromosome. We found a weak correlation between TE copy number and differential expression, suggesting some TEs may still be proliferating in Sb, however many of the duplicated TEs were already silenced. Among the 115 non-TE genes with higher copy in Sb, enzymes responsible for cuticular hydrocarbon synthesis were highly represented. These include a desaturase and an elongase; both potentially responsible for differential queen odor and likely beneficial for polygyne ants. These genes seem to have translocated into the supergene from other chromosomes and proliferated by multiple duplication events. While the presence of transposable elements (TEs) in supergenes is well documented, little is known about duplication of non-TE genes and their possible adaptive role. Overall, our results suggest that gene duplications may be an important factor leading to monogyne and polygyne ant societies.
UCSC Xena Data Browser Copy Number Data - Genes (Thresholded)
<p>Downloaded by Gregory Way from the UCSC Xena data browser on 14 July 2017</p> <p>https://xenabrowser.net/datapages/?dataset=TCGA.PANCAN.sampleMap/Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes&host=https://tcga.xenahubs.net</p>
Convergent evolution and predictability of gene copy numbers associated with diets in mammals
<p>Convergent evolution, the evolution of the same or similar phenotypes in phylogenetically independent lineages, is a widespread phenomenon in nature. If the genetic basis for convergent evolution is predictable to some extent, it may be possible to infer organismic phenotypes and adaptability based on genome sequence data. While repeated amino acid changes have been studied in association with convergent evolution, relatively little is known about the potential contribution of repeated gene copy number changes. In this study, we explore whether certain gene copy number changes are linked to diet shifts in mammals and assess if trophic ecology can be inferred from the copy numbers of a specific set of genes. Using 86 mammalian genome sequences, we identified several genes with higher copy numbers in herbivores, carnivores, and omnivores, even after phylogenetic corrections. We were able to confirm previous findings on genes such as amylase, olfactory receptor, and xenobiotic metabolism genes, and identify novel genes whose copy numbers correlate with dietary patterns. For example, omnivores exhibited higher copy numbers of genes encoding gene expression regulators. We also established a discriminant function based on the copy numbers of 13 genes that can help predict trophic ecology based on genome sequence data. These findings highlight a possible association between convergent evolution and repeated copy number changes in specific genes, suggesting the potential to develop a method for predicting animal ecology and adaptability from genome sequence data.</p>
Quantitative PCR from human genomic DNA: the determination of gene copy numbers for congenital adrenal hyperplasia and RCCX copy number variation
<p>The dataset is related a study in which we aimed to simultaneously assess the performance of 7 quantitative polymerase chain reaction (qPCR) assays for the gene copy number (GCN) determination of the genetic elements of RCCX copy number variation (CNV). A single laboratory method validations of duplex qPCR assays with hydrolysis probes on <em>CYP21A1P</em> and <em>CYP21A2</em> genes, which are responsible for congenital adrenal hyperplasia, were performed using 46 human genomic DNA samples. We also performed the verifications on 5 qPCR assays for the genetic elements of RCCX CNV such as <em>C4A</em> gene, <em>C4B</em>, gene, RCCX CNV breakpoint, HERV-K(C4) CNV deletion and insertion alleles. The dataset contains the data of genomic DNA samples, the raw quantification cycle values of all qPCR experiments, the peak heights and dosage quotient of multiplex ligation-dependent probe amplification (MLPA) experiments, and the detailed GCN results based on qPCR and MLPA. All other analyses are available in our publication under the same title.</p>
Data from: The effect of copy number hemiplasy on gene family evolution
<p>The evolution of gene families is complex, involving gene-level evolutionary events such as gene duplication, horizontal gene transfer, and gene loss (DTL), and other processes such as incomplete lineage sorting (ILS). Because of this, topological differences often exist between gene trees and species trees. A number of models have been recently developed to explain these discrepancies, the most realistic of which attempt to consider both gene-level events and ILS. When unified in a single model, the interaction between ILS and gene-level events can cause polymorphism in gene copy number, which we refer to as copy number hemiplasy (CNH).</p> <p>In this paper we extend the Wright-Fisher process to include duplications and losses over several species, and show that the probability of CNH for this process can be significant. We study how well two unified models --- MLMSC (MultiLocus MultiSpecies Coalescent), which models CNH, and DLCoal (Duplication, Loss, and Coalescence), which does not --- approximate the Wright-Fisher process with duplication and loss.</p> <p>We then study the effect of CNH on gene family evolution by comparing MLMSC and DLCoal. We generate comparable gene trees under both models, showing significant differences in various summary statistics; most importantly, CNH reduces the number of gene copies greatly. If this is not taken into account, the traditional method of estimating duplication rates (by counting the number of gene copies) becomes inaccurate. The simulated gene trees are also used for species tree inference with the summary methods ASTRAL and ASTRAL-Pro, demonstrating that their accuracy, based on CNH-unaware simulations calibrated on real data, may have been overestimated.}</p>
Accumulation of gene copy number variations during the early phase of free-spawning abalone speciation
<p><span>The g</span><span>enetic basis of speciation in free-spawning marine invertebrates is poorly understood. Although gene copy number variations (GCNVs) as well as nucleotide variations possibly trigger the speciation of these organisms, empirical evidence for such </span><span>a hypothesis</span><span> is limited. In this study, we searched for genomic signatures of GCNVs that may contribute to the speciation of Western Pacific abalone species. Whole-genome sequencing data suggested the existence of significant amounts of GCNVs in closely related abalones, <em>Haliotis discus</em> and <em>H. madaka</em>, in the early phase of speciation. In addition, the degree of interspecies genetic differentiation in the genes where GCNVs were estimated was higher than </span><span>that </span><span>in other genes, suggesting that nucleotide divergence also accumulate</span><span>s in the genes with GCNVs.</span><span> GCNVs in some genes were also detected in other related abalone species, suggesting that these GCNVs are derived from both ancestral and <em>de novo</em> mutations.</span> <span>Our findings </span><span>suggest that GCNVs have been accumulated in </span><span>the early phase</span><span> of free-spawning abalone speciation.</span></p>
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: Higher evolutionary dynamics of gene copy number for Drosophila glue genes located near short repeat sequences
<p><strong>Background</strong></p> <p>During evolution, genes can experience duplications, losses, inversions and gene conversions. Why certain genes are more dynamic than others is poorly understood. Here we examine how several <em>Sgs</em> genes encoding glue proteins, which make up a bioadhesive that sticks the animal during metamorphosis, have evolved in <em>Drosophila</em> species.</p> <p><strong>Results</strong></p> <p>We examined high-quality genome assemblies of 24 <em>Drosophila</em> species to study the evolutionary dynamics of four glue genes that are present in <em>D. melanogaster</em> and are part of the same gene family <em>–</em> <em>Sgs1, Sgs3, Sgs7 and Sgs8 –</em> across approximately 30 millions of years. We annotated a total of 102 <em>Sgs</em> genes and grouped them into 4 subfamilies. We present here a new nomenclature for these <em>Sgs</em> genes based on protein sequence conservation, genomic location and presence/absence of internal repeats. Two types of glue genes were uncovered. The first category (<em>Sgs1, Sgs3x, Sgs3e</em>) showed a few gene losses but no duplication, no local inversion and no gene conversion. The second group (<em>Sgs3b, Sgs7, Sgs8</em>) exhibited multiple events of gene losses, gene duplications, local inversions and gene conversions. Our data suggest that the presence of short "new glue" genes near the genes of the latter group may have accelerated their dynamics.</p> <p><strong>Conclusions</strong></p> <p>Our comparative analysis suggests that the evolutionary dynamics of glue genes is influenced by genomic context. Our molecular, phylogenetic and comparative analysis of the four glue genes <em>Sgs1, Sgs3, Sgs7</em> and <em>Sgs8 </em>provides the foundation for investigating the role of the various glue genes during <em>Drosophila</em> life.</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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Data from: The fire ant social supergene is characterized by extensive gene and transposable element copy number variation
Open the record for dataset details and reuse information.
Accumulation of gene copy number variations during the early phase of free-spawning abalone speciation
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Data from: The effect of copy number hemiplasy on gene family evolution
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Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy
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Data from: Extreme copy number variation at a tRNA ligase gene affecting phenology and fitness in yellow monkeyflowers
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Allen Brain Atlas
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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.