GC-content
Dotaz
Zobrazit nápovědu
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.
Genomic DNA base composition (GC content) is predicted to significantly affect genome functioning and species ecology. Although several hypotheses have been put forward to address the biological impact of GC content variation in microbial and vertebrate organisms, the biological significance of GC content diversity in plants remains unclear because of a lack of sufficiently robust genomic data. Using flow cytometry, we report genomic GC contents for 239 species representing 70 of 78 monocot families and compare them with genomic characters, a suite of life history traits and climatic niche data using phylogeny-based statistics. GC content of monocots varied between 33.6% and 48.9%, with several groups exceeding the GC content known for any other vascular plant group, highlighting their unusual genome architecture and organization. GC content showed a quadratic relationship with genome size, with the decreases in GC content in larger genomes possibly being a consequence of the higher biochemical costs of GC base synthesis. Dramatic decreases in GC content were observed in species with holocentric chromosomes, whereas increased GC content was documented in species able to grow in seasonally cold and/or dry climates, possibly indicating an advantage of GC-rich DNA during cell freezing and desiccation. We also show that genomic adaptations associated with changing GC content might have played a significant role in the evolution of the Earth's contemporary biota, such as the rise of grass-dominated biomes during the mid-Tertiary. One of the major selective advantages of GC-rich DNA is hypothesized to be facilitating more complex gene regulation.
- MeSH
- aklimatizace genetika MeSH
- chromozomy rostlin genetika MeSH
- DNA rostlinná chemie genetika MeSH
- ekosystém MeSH
- fylogeneze MeSH
- genetická variace MeSH
- genom rostlinný MeSH
- lipnicovité chemie klasifikace genetika MeSH
- Magnoliopsida chemie klasifikace genetika MeSH
- molekulární evoluce * MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
• Knowledge of the phylogenetic pattern and biological relevance of the base composition of large eukaryotic genomes (including those of plants) is poor. With the use of flow cytometry (FCM), the amount of available data on the guanine + cytosine (GC) content of plants has nearly doubled in the last decade. However, skepticism exists concerning the reliability of the method because of uncertainty in some input parameters. • Here, we tested the reliability of FCM for estimating GC content by comparison with the biochemical method of DNA temperature melting analysis (TMA). We conducted measurements in 14 plant species with a maximum currently known GC content range (33.6-47.5% as measured by FCM). We also compared the estimations of the GC content by FCM with genomic sequences in 11 Oryza species. • FCM and TMA data exhibited a high degree of correspondence which remained stable over the relatively wide range of binding lengths (3.39-4.09) assumed for the base-specific dye used. A high correlation was also observed between FCM results and the sequence data in Oryza, although the latter GC contents were consistently lower. • Reliable estimates of the genomic base composition in plants by FCM are comparable with estimates obtained using other methods, and so wider application of FCM in future plant genomic research, although it would pose a challenge, would be supported by these findings.
- MeSH
- Bacteria genetika MeSH
- denaturace nukleových kyselin MeSH
- DNA rostlinná genetika MeSH
- druhová specificita MeSH
- genom rostlinný genetika MeSH
- průtoková cytometrie metody MeSH
- reprodukovatelnost výsledků MeSH
- sekvence nukleotidů MeSH
- teplota MeSH
- zastoupení bazí genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
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.
Liquid transportation fuels in the middle distillate range contain thousands of hydrocarbons making the predictions and calculations of properties from composition a challenging process. We present a new approach of hydrogen content determination by comprehensive two-dimensional gas chromatography with flame ionization detector (GC×GC-FID) using a weighted average method. GC×GC-FID hydrogen determination precision was excellent (0.005 wt% repeatability). The method accuracy was evaluated by high-resolution nuclear magnetic resonance (NMR) technique, which is non-biased, measures the H signal directly and was independently validated by controls in the current study. The hydrogen content (in the range of 12.72-15.54 wt%) in 28 fuel samples were determined using GC×GC-FID. Results were within ± 2% of those obtained via NMR. Owing to the fact that NMR is accepted as an accurate technique for hydrogen content determination, the GC×GC method proposed in this study can be considered precise and accurate.
- Publikační typ
- časopisecké články MeSH
Our novel Python-based tool EVANGELIST allows the visualization of GC and repeats percentages along chromosomes in sequenced genomes and has enabled us to perform quantitative large-scale analyses on the chromosome level in fish and other vertebrates. This is a different approach from the prevailing analyses, i.e., analyses of GC% in the coding sequences that make up not more than 2% in human. We identified GC content (GC%) elevations in microchromosomes in ancient fish lineages similar to avian microchromosomes and a large variability in the relationship between the chromosome size and their GC% across fish lineages. This raises the question as to what extent does the chromosome size drive GC% as posited by the currently accepted explanation based on the recombination rate. We ascribe the differences found across fishes to varying GC% of repetitive sequences. Generally, our results suggest that the GC% of repeats and proportion of repeats are independent of the chromosome size. This leaves an open space for another mechanism driving the GC evolution in vertebrates.
- MeSH
- chromozomy genetika MeSH
- cytogenetika * MeSH
- genom genetika MeSH
- molekulární evoluce * MeSH
- obratlovci klasifikace genetika MeSH
- ptáci klasifikace genetika MeSH
- rekombinace genetická genetika MeSH
- repetitivní sekvence nukleových kyselin MeSH
- ryby klasifikace genetika MeSH
- zastoupení bazí genetika MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Four bacterial isolates, which produced polyunsaturated fatty acids (PUFA), were isolated from water samples of radioactive springs collected from Jáchymov spa. Jáchymov (Sankt Joachimsthal) is a city in northwestern Bohemia, where Marie and Pierre Curie isolated radium in 1898 from the mineral uraninite. To date, four springs (Agricola, Behounek, C1, and Curie) have been used for spa purposes, that is for the treatment of nervous and rheumatic disorders by constantly produced radioactive gas radon (222 Rn) dissolved in the water. The radioactivity reaches 24 kBq/L. Using 16S rRNA gene sequence analysis, all four isolates were identified as members of the genus Kocuria, with two isolates designated 208 and 401 affiliated with Kocuria kristinae, while isolates 101 and 301 most likely with K. rhizophila. The content of fatty acids in polar lipids was determined by gas chromatography-mass spectrometry (GC-MS) and two PUFA, that is arachidonic and eicosapentaenoic, were identified. The position of double bonds was confirmed by GC-MS of 3-pyridylcarbinol (formerly picolinyl) esters. We assume that all four isolates of Kocuria produce PUFA to increase the stability of cell membranes, which may be impaired by the reaction of the reactive oxygen species. These can arise, for example, because of α radiation during 222 Rn decay.
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
