Gc content variation. 001; Figure 3) and for GC 3 (r = 0.

Gc content variation. GC content is found to be variable with different organisms, the process of which is envisaged to be contributed to by variation in selection, mutational bias, and biased recombination-associated DNA repair. Feb 6, 2015 · Author Summary Classical population genetics models indicate that the efficiency of selection, and hence adaptation, depends on a number of non-selective factors, such as the size of a population or the intensity of recombination. Nuclear genome size and genomic DNA base composition (usually expressed as GC content, that is the relative proportion of GC base pairs) are two genomic parameters that exhibit pronounced variation among angiosperm plants (Šmarda & Bureš, 2012; Dodsworth et al. GC content is found to be variable with different organisms, the process of which is envisaged to be contributed to by variation in selection, mutational bias, and biased recombination-associated DNA repair. The recent release of high-quality genome sequences from the Darwin Tree of Life and other large-scale genome projects provides an opportunity for GC heterogeneity to be compared across a Among-genome variation. The genomic GC content was calculated among the certain bases for the 24 chromosomes and for mtDNA as detailed in Additional file 1: Additional Methods. [20] GC content variation along genomes is a key feature of genomic organization and strongly varies between species. and its ecolog ical and evol utionary mean ing attrac ted less at-tention in plants co mpared to anim al systems and is stil l large-ly unknown. e. , 2015), possibly with adaptive consequences (Bennett & Leitch, 2011; Šmarda et al. comosus genome and com- pared it with publicly available genomes of 19 other plant spe- Jun 7, 2014 · GC content variation along genomes is a key feature of genomic organization and strongly varies between species. Sep 15, 2014 · By analyzing GC content in relation to several genomic characters, a suite of life history traits, and climatic data within a well-resolved phylogenetic framework, we also explore the possible biological and ecological relevance of GC content variation in monocots and discuss the nature of the driving forces that may have contributed to it. Each genome has a preferred GC content, which promotes the variation of amino acid composition than the recruitment sequence of amino acids. Jan 10, 2012 · Background As a key parameter of genome sequence variation, the GC content of bacterial genomes has been investigated for over half a century, and many hypotheses have been put forward to explain this GC content variation and its relationship to other fundamental processes. The situation hence can become confusing when it comes to how bacteria have generated great variation in their genomic base composition (i. 001) and whole genomes (p < 0. [19] The average GC-content in human genomes ranges from 35% to 60% across 100-Kb fragments, with a mean of 41%. The dnaE1|polV group is the extreme, which appears to have no limit in GC content variation but is regulated by mutator genes. We explored the mechanisms maintaining the GC content in angiosperm plastomes, with a Variation in GC content is assumed to correlate with various processes, including mutation biases, recombination, and environmental parameters. Mar 15, 2024 · The proportions of A:T and G:C nucleotide pairs are often unequal and can vary greatly between animal species and along chromosomes. Jun 9, 2024 · We found a positive correlation between GC content and variation in GC content (measured as SD) for overall GC (r = 0. Results A comprehensive selection of 8666 species, comprising Jan 12, 2021 · Variation in GC content is assumed to correlate with various processes, including mutation biases, recombination, and environmental parameters. Sep 27, 2022 · Missing genomic regions have higher GC and repeat content. Changing the response variable of the mixed-effects regression model described above to within-genome GC content variation, referred to as GCVAR [], we found that the core genome exhibited significantly lower GCVAR than the corresponding accessory (p < 0. Jan 10, 2012 · Testing the hypothesis that GC->AT transitions cause a reduction of genomic GC content in prokaryotic genomes on an evolutionary time scale using a phylogenetic approach to analyze triplets of closely related genomes representing a wide range of the bacterial kingdom indicates that genomic GCcontent is drifting downward in bacterial genomes where GC base pairs comprise 40% or more of the total . The VGP assemblies were on average ~635-fold more contiguous in terms of contig N50, reducing from ~23,000 to ~200,000 scaffolds in the previous assemblies to hundreds in the VGP assemblies, for an expected 20 to 40 chromosomes (Additional file 1: Table S1). [20] Feb 13, 2014 · C+G content (GC content or G+C content) is known to be correlated with genome/chromosome size in bacteria but the relationship for other kingdoms remains unclear. , 1985). The advantage of the technique is that an investigator is able to study the variation of GC content in a perceivable and precise manner. , the patchwork of GC-rich and GC-poor regions alternating along the genome) because it is associated with fundamental elements It is true that GC content variation in each group varies to different extents. Genome size tends to increase during evolution in plants and animals, and the same is likely true Dec 6, 2018 · The ratio of GC content for codons influences the corresponding amino acid composition variation. 6% in the smallest bacterial genome (Candidatus Carsonella ruddii; Nakabachi et al are likely to play different roles in GC content variation. One is the fact that there are boundaries or specific spectra in compositional variability. better view of the evolutionary trends in GC content variation. , 2011). The causes and consequences of this variation are incompletely understood. 61, P ⩽ . What we are emphasizing here are two concepts. 001; Figure 3). To date, most genomic studies exploring the evolution of GC content have focused on nuclear genomes, but relatively few have concentrated on organelle genomes. The abundant sequence data available for the ITS2, a commonly employed phylogenetic marker in plants, offers an exceptional resource for exploring the GC variation across angiosperms. This huge variation was first noted by the pioneering work of Barbu et al. To date, most genomic studies exploring the evolution of GC content have focused on nuclear genomes, but relatively few have concentrated on organelle genom … Feb 10, 2017 · GC content variation differences between genetic regions. 70, P ⩽ . 001). This study analyzed genome size, chromosome size, and base composition in most of the available sequenced genomes in various kingdoms. We analyzed and compared the GC contents of 20 selected plant Feb 27, 2019 · The genomic GC content was calculated among the certain bases for the 24 chromosomes and for mtDNA as detailed in Additional file 1: Additional Methods. Bacteria are usually supposed to be subject to a high level of purifying selection in light of huge effective population sizes (). The “Transcriptomic GC Analysis” (TGCA) software was developed here to study the possible variation of GC content in the expression of whole transcriptomes. Dec 1, 2023 · Background Despite GC variation constitutes a fundamental element of genome and species diversity, the precise mechanisms driving it remain unclear. We analyzed the GC content of A. Sep 1, 2016 · GC content variation. It shows that GC-Profile would be an appropriate starting point for analyzing the isochore structures of higher eukaryotic genomes, and an intuitive tool for identifying genomic islands in prokaryotic genomes. Among species, the average genomic GC-content ranges from 13 to 75% (Pagani et al. dnaE2, a well-known mutator gene, strongly correlates with high GC content (Figure 1). Jun 19, 2019 · Introduction. The less complex genome organization of prokaryotes and direct association with their external environment results in a wide range in GC content of prokaryotic genomes, with a GC content as low as 16. , genomic GC content [GC content]) during their adaptive evolution (). Species with higher GC content have significantly more variation across their genes, whereas those that are more GC-poor seem to have a more consistent Jan 12, 2018 · An important unanswered question in evolutionary genomics is the source of considerable variation of genomic base composition (GC content) even among organisms that share one habitat. Identifying the driving force that shaped the GC content and deciphering the biological meaning of variations in the GC content will help us to understand genome evolution. Much work has focused on the so-called ‘isochore structure’ (see Glossary ) of mammalian genomes (i. 001; Figure 3) and for GC 3 (r = 0. Previously, we classified eubacteria into dnaE-based groups (the dimeric combination of DNA polymerase III alpha subunits Jul 1, 2014 · GC content variation along genomes is a key feature of genomic organization and strongly varies between species. Old residuals have high levels of usage in all proteins, and new ones have rather low level of usage. , 2014). , the patchwork of GC-rich and GC-poor regions alternating along the genome) because it is associated with fundamental elements of genome organization [1]. polV is also assumed to be heavily involved in GC content variation because its presence in the two groups lackingdnaE2 is closely related to either GC content variability (in the dnaE1| Jul 1, 2006 · It shows that GC-Profile would be an appropriate starting point for analyzing the isochore structures of higher eukaryotic genomes, and an intuitive tool for identifying genomic islands in prokaryotic genomes. Sep 9, 2010 · Although, genomic GC content shows a fair level of phylogenetic inertia , most classes of bacteria show substantial variation in genomic GC content; one of the most dramatic examples is afforded by the α-proteobacteria, which have genomic GC-contents ranging from less than 30% to greater than 60% . Nov 12, 2022 · Prokaryotes, that is Bacteria and Archaea, display the widest variation in genomic GC content among living organisms, and can vary widely from ≈ 13 to ≈ 75% (for a recent review see Bohlin and Pettersson, 2019). , Belozersky and Spirin and Sueoka Apr 12, 2016 · The GC content, one of the important compositional features of the genome, varies significantly among different genomes and different regions within a genome. In the last 10 years, evidence has accumulated that another mechanism called GC-Biased Gene Conversion (gBGC) can interfere with selection and even mimic its effects Feb 15, 2017 · As a consequence of variation in this subtle balance, it has been observed that GC-content varies considerably at two levels: (i) among genomes from different species and (ii) along chromosomes of a single species (Bernardi et al. Evolution Jan 1, 2012 · The most complete knowledge of GC content comes from bacteria, with >1,000 complete genomes already sequenced. Much work has focused on the so-called ‘isochore structure’ (see Glossary) of mammalian genomes (i.

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