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128 results for “gene copy number”
Data from: Higher evolutionary dynamics of gene copy number for Drosophila glue genes located near short repeat sequences
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Convergent evolution and predictability of gene copy numbers associated with diets in mammals
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Postprandial Effect of High-starch Meals in Individuals With Low and High Copy Number of the Salivary Amylase Gene
ClinicalTrials.gov study NCT03974126. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Data from: Copy number variation and expression analysis reveals a nonorthologous pinta gene family member involved in butterfly vision
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Data from: High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure
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Table S1.- Occurrence analysis in alpha-proteobacteria, represented by number of copies of each gene on strain genome.
<p>Data set of 204 alphaproteobacteria to analyze for the presence and absence of 12 proteins related to the pantothenate synthesis and transport. The protein FASTA files (faa) for each of the genomes were downloaded from the RefSeq NCBI database. Protein sequences with an expectation value (E) of 10<sup>-3</sup>or less were considered as putative homologues. We used Proteinortho v5.15 to obtain the clusters of orthologous proteins from the 204 protein FASTA files. Next, we used the Pfam v31.0 database to determine which protein ortho clusters represent the 12 proteins of interest analyzed in this work. The proteins we searched for were: PYD1, PYD2, PYD3, GAD, KPHMT, PS, ADC, KPR, MRF, KAR, Aam and GabT.</p>
Data from: Gene copy number variations as signatures of adaptive evolution in the parthenogenetic, plant-parasitic nematode Meloidogyne incognita
Adaptation to changing environmental conditions represents a challenge to parthenogenetic organisms and until now, how phenotypic variants are generated in clones in response to the selection pressure of their environment remains poorly known. The obligatory parthenogenetic root-knot nematode species Meloidogyne incognita has a worldwide distribution and is the most devastating plant-parasitic nematode. Despite its asexual reproduction, this species exhibits an unexpected capacity of adaptation to environmental constraints, e.g., resistant hosts. Here we used a genome-wide comparative hybridization strategy to evaluate variations in gene copy numbers between genotypes of M. incognita resulting from two parallel experimental evolution assays on a susceptible vs. resistant host plant. We detected gene copy number variations (CNVs) associated with the ability of the nematodes to overcome resistance of the host plant, and this genetic variation may reflect an adaptive response to host resistance in this parthenogenetic species. The CNV distribution throughout the nematode genome is not random and suggests the occurrence of genomic regions more prone to undergo duplications and losses in response to the selection pressure of the host resistance. Furthermore, our analysis revealed an outstanding level of gene loss events in nematode genotypes that have overcome the resistance. Overall, our results support the view that gene loss could be a common class of adaptive genetic mechanism in response to a challenging new biotic environment in clonal animals.
Data from: Evolution of the leucine-rich repeat receptor-like protein kinase gene family: Ancestral copy number and functional divergence of BAM1 and BAM2 in Brassicaceae
Gene duplication allows for functional divergence and innovation that provide selective advantages. However, in flowering plants genetic studies have revealed that single-gene mutations affecting one of two or more closely related paralogs often fail to cause detectable morphological defects, suggesting functional redundancy. Flowering plants have hundreds of genes encoding leucine-rich repeat receptor-like protein kinases (LRR-RLKs), several of which play important roles in anther development but little is known about their evolutionary history and possible functional divergence. We investigated the evolutionary relationship of the LRR-RLK gene family by phylogenetic analysis and found that these closely related paralogs resulted from multiple duplication events, such as the one resulting in BAM1 and BAM2. We further used qRT-PCR to verify gene expression changes in immature anthers from the bam1/bam2 single and double mutants compared with wild type providing strong evidence that the BAM1 and BAM2 genes have evolved different functions, with differential effects on anther gene expression. Moreover, careful examination of anther development in bam1 and bam2 single mutants revealed previously unrecognized extra cell division in tapetum cell layers. Thus our results from phylogenetic, molecular and morphological analyses uncover sequence and functional differences between paralogs whose single mutants lack obvious fertility defects, effectively revealing functional divergence of duplicate genes.
Gene copy number is associated with phytochemistry in Cannabis sativa
<p>Gene copy number variation is known to be important in nearly every species where it has been examined. Alterations in gene copy number may provide a fast way of acquiring diversity, allowing rapid adaptation under strong selective pressures, and may also be a key component of standing genetic variation within species. <i>Cannabis sativa </i>plants produce a distinguishing set of secondary metabolites, the cannabinoids, many of which have medicinal utility. Two major cannabinoids -THCA and CBDA - are products of a three-step biochemical pathway. Using whole genome shotgun sequence data for 69 <i>Cannabis</i> cultivars from diverse lineages within the species, we found that genes encoding the synthases in this pathway vary in copy number. Transcriptome sequence data shows that the cannabinoid paralogs are differentially expressed among lineages within the species. We also found that copy number partially explains variation in cannabinoid content levels among <i>Cannabis</i> plants. Our results demonstrate that biosynthetic genes found at multiple points in the pathway could be useful for breeding purposes, and suggest that natural and artificial selection have shaped copy number variation. Truncations in specific paralogs are associated with lack of production of particular cannabinoids, showing how phytochemical diversity can evolve through a complex combination of processes.</p>
Supplementary material 2 from: Martin JL, Santi I, Pitta P, John U, Gypens N (2022) Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias. Metabarcoding and Metagenomics 6: e85794. https://doi.org/10.3897/mbmg.6.85794
Supplementary Data 2
Supplementary material 1 from: Martin JL, Santi I, Pitta P, John U, Gypens N (2022) Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias. Metabarcoding and Metagenomics 6: e85794. https://doi.org/10.3897/mbmg.6.85794
Supplementary Data 1
Supplementary material 3 from: Martin JL, Santi I, Pitta P, John U, Gypens N (2022) Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias. Metabarcoding and Metagenomics 6: e85794. https://doi.org/10.3897/mbmg.6.85794
Supplementary Data 3
Supplementary material 4 from: Martin JL, Santi I, Pitta P, John U, Gypens N (2022) Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias. Metabarcoding and Metagenomics 6: e85794. https://doi.org/10.3897/mbmg.6.85794
Tables S1–S4, Figures S1–S4
Dataset for "Association between Amylase Alpha 1 Gene (AMY1) Copy Number Variation and Dental Caries Experience in Turkish Population"
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Data from: Evolution of the leucine-rich repeat receptor-like protein kinase gene family: Ancestral copy number and functional divergence of BAM1 and BAM2 in Brassicaceae
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Gene copy number is associated with phytochemistry in Cannabis sativa
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Data from: Copy number polymorphism in the α-globin gene cluster of European rabbit (Oryctolagus cuniculus).
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Data from: Gene copy number variations as signatures of adaptive evolution in the parthenogenetic, plant-parasitic nematode Meloidogyne incognita
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Integrative analysis of DNA copy number, DNA methylation and gene expression in multiple myeloma reveals alterations related to relapse [DNA copy number]
GEO Series GSE77536. Homo sapiens. 38 samples. Type: Genome variation profiling by SNP array.
RNA polymerase I activators count and adjust ribosomal RNA gene copy number
GEO Series GSE116661. Saccharomyces cerevisiae BY4741. 25 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing.
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