AT/GC genome composition Dotaz Zobrazit nápovědu
BACKGROUND AND AIMS: Genome size is known to affect various plant traits such as stomatal size, seed mass, and flower or shoot phenology. However, these associations are not well understood for species with very large genomes, which are laregly represented by geophytic plants. No detailed associations are known between DNA base composition and genome size or species ecology. METHODS: Genome sizes and GC contents were measured in 219 geophytes together with tentative morpho-anatomical and ecological traits. KEY RESULTS: Increased genome size was associated with earliness of flowering and tendency to grow in humid conditions, and there was a positive correlation between an increase in stomatal size in species with extremely large genomes. Seed mass of geophytes was closely related to their ecology, but not to genomic parameters. Genomic DNA GC content showed a unimodal relationship with genome size but no relationship with species ecology. CONCLUSIONS: Evolution of genome size in geophytes is closely related to their ecology and phenology and is also associated with remarkable changes in DNA base composition. Although geophytism together with producing larger cells appears to be an advantageous strategy for fast development of an organism in seasonal habitats, the drought sensitivity of large stomata may restrict the occurrence of geophytes with very large genomes to regions not subject to water stress.
- MeSH
- délka genomu MeSH
- DNA rostlinná analýza genetika MeSH
- ekologie MeSH
- ekosystém MeSH
- genom rostlinný MeSH
- molekulární evoluce MeSH
- průduchy rostlin anatomie a histologie MeSH
- roční období MeSH
- rostliny anatomie a histologie genetika MeSH
- semena rostlinná anatomie a histologie MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
We determined the complete mitochondrial genome of the facultative entomopathogenic nematode Oscheius chongmingensis. The mitogenome length was 15,413 bp and similar to other Rhabditids contains genes for 2 rRNAs, 22 tRNAs, and 12 proteins (ATPase subunit 8 is missing). Predicted tRNAs indicated the secondary structure typical for chromadorean nematodes. Gene order is similar to that observed in the genus Caenorhabditis. The control AT-rich region is considerably large (2061 bp, 84% of AT), positioned in between tRNA(Ala) and tRNA(Pro) and has several microsatellite-like (AT)n elements.
- MeSH
- délka genomu MeSH
- fylogeneze MeSH
- genom mitochondriální * MeSH
- mitochondriální geny MeSH
- oblasti bohaté na AT MeSH
- otevřené čtecí rámce MeSH
- regulační oblasti nukleových kyselin MeSH
- Rhabditida klasifikace genetika MeSH
- sekvenční analýza DNA MeSH
- sekvenování celého genomu MeSH
- zastoupení bazí MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND AND AIMS: The genus Carex exhibits karyological peculiarities related to holocentrism, specifically extremely broad and almost continual variation in chromosome number. However, the effect of these peculiarities on the evolution of the genome (genome size, base composition) remains unknown. While in monocentrics, determining the arithmetic relationship between the chromosome numbers of related species is usually sufficient for the detection of particular modes of karyotype evolution (i.e. polyploidy and dysploidy), in holocentrics where chromosomal fission and fusion occur such detection requires knowledge of the DNA content. METHODS: The genome size and GC content were estimated in 157 taxa using flow cytometry. The exact chromosome numbers were known for 96 measured samples and were taken from the available literature for other taxa. All relationships were tested in a phylogenetic framework using the ITS tree of 105 species. KEY RESULTS: The 1C genome size varied between 0·24 and 1·64 pg in Carex secalina and C. cuspidata, respectively. The genomic GC content varied from 34·8 % to 40·6 % from C. secalina to C. firma. Both genomic parameters were positively correlated. Seven polyploid and two potentially polyploid taxa were detected in the core Carex clade. A strong negative correlation between genome size and chromosome number was documented in non-polyploid taxa. Non-polyploid taxa of the core Carex clade exhibited a higher rate of genome-size evolution compared with the Vignea clade. Three dioecious taxa exhibited larger genomes, larger chromosomes, and a higher GC content than their hermaphrodite relatives. CONCLUSIONS: Genomes of Carex are relatively small and very GC-poor compared with other angiosperms. We conclude that the evolution of genome and karyotype in Carex is promoted by frequent chromosomal fissions/fusions, rare polyploidy and common repetitive DNA proliferation/removal.
- MeSH
- Carex (rostlina) genetika MeSH
- chromozomy rostlin genetika MeSH
- délka genomu genetika MeSH
- fylogeneze MeSH
- genom rostlinný genetika MeSH
- Markovovy řetězce MeSH
- metoda Monte Carlo MeSH
- molekulární evoluce * MeSH
- polyploidie MeSH
- zastoupení bazí genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND AND AIMS: Studies in the carnivorous family Lentibulariaceae in the last years resulted in the discovery of the smallest plant genomes and an unusual pattern of genomic GC content evolution. However, scarcity of genomic data in other carnivorous clades still prevents a generalization of the observed patterns. Here the aim was to fill this gap by mapping genome evolution in the second largest carnivorous family, Droseraceae, where this evolution may be affected by chromosomal holokinetism in Drosera METHODS: The genome size and genomic GC content of 71 Droseraceae species were measured by flow cytometry. A dated phylogeny was constructed, and the evolution of both genomic parameters and their relationship to species climatic niches were tested using phylogeny-based statistics. KEY RESULTS: The 2C genome size of Droseraceae varied between 488 and 10 927 Mbp, and the GC content ranged between 37·1 and 44·7 %. The genome sizes and genomic GC content of carnivorous and holocentric species did not differ from those of their non-carnivorous and monocentric relatives. The genomic GC content positively correlated with genome size and annual temperature fluctuations. The genome size and chromosome numbers were inversely correlated in the Australian clade of Drosera CONCLUSIONS: Our results indicate that neither carnivory (nutrient scarcity) nor the holokinetism have a prominent effect on size and DNA base composition of Droseraceae genomes. However, the holokinetic drive seems to affect karyotype evolution in one of the major clades of Drosera Our survey confirmed that the evolution of GC content is tightly connected with the evolution of genome size and also with environmental conditions.
A spectrogram reflects the arrangement of nucleotides through the whole chromosome or genome. Our previous study suggested that the spectrogram of whole genome DNA sequences is a suitable tool for the determination of relationships among bacteria. Related bacteria have similar spectrograms, and similarity in spectrograms was measured using a color layout descriptor. Several parameters, such as the mapping of four bases into a spectrogram, the number of considered elements in the color layout descriptor, the color model of the image and the building tree method, can be changed. This study addresses the use of parameter selection to ensure the best classification results. The quality of the classification was measured by Matthew's correlation coefficient (MCC). The proposed method with optimal parameters (called SpectCMP-Spectrogram CoMParison method) achieved an average MCC of 0.73 at the phylum level. The SpectCMP method was also tested at the order level; the average MCC in the classification of class Gammaproteobacteria was 0.76. The success of a classification with respect to the correct phyla was compared to three methods that are used in bacterial phylogeny: the CVTree method, OGTree method and moment vector method. The results show that the SpectCMP method can be used in bacterial classification at various taxonomic levels.
In angiosperms, genome size and nucleobase composition (GC content) exhibit pronounced variation with possible adaptive consequences. The hyperdiverse orchid family possessing the unique phenomenon of partial endoreplication (PE) provides a great opportunity to search for interactions of both genomic traits with the evolutionary history of the family. Using flow cytometry, we report values of both genomic traits and the type of endoreplication for 149 orchid species and compare these with a suite of life-history traits and climatic niche data using phylogeny-based statistics. The evolution of genomic traits was further studied using the Brownian motion (BM) and Ornstein-Uhlenbeck (OU) models to access their adaptive potential. Pronounced variation in genome size (341-54 878 Mb), and especially in GC content (23.9-50.5%), was detected among orchids. Diversity in both genomic traits was closely related to the type of endoreplication, plant growth form and climatic conditions. GC content was also associated with the type of dormancy. In all tested scenarios, OU models always outperformed BM models. Unparalleled GC content variation was discovered in orchids, setting new limits for plants. Our study indicates that diversity in both genome size and GC content has adaptive consequences and is tightly linked with evolutionary transitions to PE.
Actinobacteria of the acI lineage are the most abundant microbes in freshwater systems, but there are so far no pure living cultures of these organisms, possibly because of metabolic dependencies on other microbes. This, in turn, has hampered an in-depth assessment of the genomic basis for their success in the environment. Here we present genomes from 16 axenic cultures of acI Actinobacteria. The isolates were not only of minute cell size, but also among the most streamlined free-living microbes, with extremely small genome sizes (1.2-1.4 Mbp) and low genomic GC content. Genome reduction in these bacteria might have led to auxotrophy for various vitamins, amino acids and reduced sulphur sources, thus creating dependencies to co-occurring organisms (the 'Black Queen' hypothesis). Genome analyses, moreover, revealed a surprising degree of inter- and intraspecific diversity in metabolic pathways, especially of carbohydrate transport and metabolism, and mainly encoded in genomic islands. The striking genotype microdiversification of acI Actinobacteria might explain their global success in highly dynamic freshwater environments with complex seasonal patterns of allochthonous and autochthonous carbon sources. We propose a new order within Actinobacteria ('Candidatus Nanopelagicales') with two new genera ('Candidatus Nanopelagicus' and 'Candidatus Planktophila') and nine new species.
- MeSH
- Actinobacteria klasifikace genetika izolace a purifikace MeSH
- biodiverzita MeSH
- DNA bakterií chemie MeSH
- fylogeneze MeSH
- genom bakteriální * MeSH
- metabolické sítě a dráhy genetika MeSH
- sladká voda mikrobiologie MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The structure of the Aneura pinguis mitochondrial genome (GenBank accession no. NC_026901) is similar to that of closely related Metzgeriales species: it has a total length of 165 603 bp, the base composition of the mitogenome is the following: A (26.2%), C(23.6%), G(23.8%), and T(26.4%). The A. piguis mitochondrial genome contains 69 genes. A complete mitochondrial genome sequence of A. pinguis will help better to understand mitogenome structure and content among Metzgeriales order.
- MeSH
- délka genomu MeSH
- DNA rostlinná MeSH
- fylogeneze * MeSH
- genom mitochondriální * MeSH
- genom rostlinný MeSH
- genomika MeSH
- Marchantiophyta genetika MeSH
- mitochondriální DNA MeSH
- mitochondriální geny * MeSH
- sekvence nukleotidů MeSH
- sekvenční analýza DNA MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Pseudomonas prosekii is a recently described species isolated exclusively from James Ross Island close to the Antarctic Peninsula at 64° south latitude. Here, we present two P. prosekii genome sequences and their analyses with respect to phylogeny, low temperature adaptation, and potential biotechnological applications. The genome of P. prosekii P2406 comprised 5,896,482 bp and 5324 genes (GC content of 59.71%); the genome of P. prosekii P2673 consisted of 6,087,670 bp and 5511 genes (GC content of 59.50%). Whole genome sequence comparisons confirmed a close relationship between both investigated strains and strain P. prosekii LMG 26867T. Gene mining revealed the presence of genes involved in stress response, genes encoding cold shock proteins, oxidative stress proteins, osmoregulation proteins, genes for the synthesis of protection molecules, and siderophores. Comparative genome analysis of P. prosekii and P. aeruginosa PAO1 highlighted differences in genome content between extremophile species and a mesophilic opportunistic pathogen.
- MeSH
- aklimatizace MeSH
- bakteriální proteiny genetika MeSH
- fylogeneze MeSH
- fyziologická adaptace MeSH
- genom bakteriální * MeSH
- mapování chromozomů MeSH
- nadmořská výška MeSH
- Pseudomonas genetika izolace a purifikace fyziologie MeSH
- sekvence nukleotidů MeSH
- sekvenování celého genomu MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Antarktida MeSH
