Mapping of antibody responses to the protective antigen of Bacillus anthracis by flow cytometric analysis

BACKGROUND: Different plant species vary as to the ratio of nucleotide base pairs of genomic DNA. A correlation between genome size and base pair ratio has been claimed. Base composition can be analyzed by base-specific dyes. METHODS: Genome size is determined by flow cytometry of suspensions of nuclei stained by the base independent dye, PI. For estimation of the AT frequency, the AT-specific dyes 4,6-diamidino-2-phenylindole, dihydrochloride (DAPI) and Hoechst 33342 (HO) were used. We define a dye factor (DF) as the ratio of the two estimates (peak ratios) of nuclear fluorescence intensities of sample relative to reference plant nuclei using a given dye and an intercalating fluorochrome. RESULTS: No significant correlation between genome size and the DF for DAPI was found when 54 plant species were investigated. However, similarities within and differences among the plant families were shown. The comparison of DAPI and HO DFs gave no consistent differences as would be predicted from the model of different binding site length of dyes. This result may be explained by the nonrandom distribution of base pairs. CONCLUSIONS: There is no general correlation between genome size and AT/GC ratio in higher plants. Similar AT/GC ratios within a plant family result from the general similarity of the DNA sequences within a family. The fluorescence of base-specific dyes is influenced by the nonrandom distribution of bases in the DNA molecule.     

GC-biased gene conversion and selection affect GC content in the Oryza genus (rice)

Base composition varies among and within eukaryote genomes. Although mutational bias and selection have initially been invoked, more recently GC-biased gene conversion (gBGC) has been proposed to play a central role in shaping nucleotide landscapes, especially in yeast, mammals, and birds. gBGC is a kind of meiotic drive in favor of G and C alleles, associated with recombination. Previous studies have also suggested that gBGC could be at work in grass genomes. However, these studies were carried on third codon positions that can undergo selection on codon usage. As most preferred codons end in G or C in grasses, gBGC and selection can be confounded. Here we investigated further the forces that might drive GC content evolution in the rice genus using both coding and noncoding sequences. We found that recombination rates correlate positively with equilibrium GC content and that selfing species (Oryza sativa and O. glaberrima) have significantly lower equilibrium GC content compared with more outcrossing species. As recombination is less efficient in selfing species, these results suggest that recombination drives GC content. We also detected a positive relationship between expression levels and GC content in third codon positions, suggesting that selection favors codons ending with G or C bases. However, the correlation between GC content and recombination cannot be explained by selection on codon usage alone as it was also observed in noncoding positions. Finally, analyses of polymorphism data ruled out the hypothesis that genomic variation in GC content is due to mutational processes. Our results suggest that both gBGC and selection on codon usage affect GC content in the Oryza genus and likely in other grass species.     

DNA base composition of planktonic species of Anabaena (Cyanobacteria) and its taxonomic value

Fifty axenic strains of planktonic Anabaena, including 24 strains of the straight form and 26 strains of the coiled form, were examined for their DNA base composition (GC content). The taxonomic value of their GC content at species level was evaluated by comparing their morphological, physiological and biochemical properties. The DNA base composition determined for all fifty strains ranged from 35.9 to 56.4 mol% GC. The straight-form strains were in the range of 35.9-56.4 mol% GC, while coiled forms were in the range of 38.1-50.3 mol% GC. In general, strains assigned to the same species showed similar DNA base composition. However, of three strains of A. affinis Lemmermann that were separated into two categories, two had 40.6-40.9 mol% GC, and the third strain 45.6 mol% GC. It is noteworthy that the DNA base composition of the newly established species A. eucompacta Li et Watanabe was 45.5 mol% GC, which differed from 39.5 mol% GC of the morphologically close species, A. compacta (Nygarrd) Hickel.     

Deoxyribonucleic Acid Base Composition in the Taxonomy of Staphylococcus

Twenty-four strains of Staphylococcus aureus, including eight known mutants of S. aureus and strains growing under a variety of environmental conditions or exposed to a number of physical and chemical agents, maintained a remarkably narrow range of guanine plus cytosine (GC) content (32.4 to 35.1%). The wide range of GC content (30.7 to 40%) reported in the literature was due to the variety of methods and calculations used rather than to any substantial variation in base composition. The UV-2 "mutant" (ATCC 13680) with a GC content of 67.6% reported to be derived from S. aureus (ATCC 13679) was a species of Corynebacterium. The data presented were consistent with the concept that base composition changes only to a very slight degree by mutation.     

普通野生稻线粒体蛋白质编码基因密码子使用偏好性的分析

以普通野生稻(Oryza rufipogon Griff.)线粒体基因组为对象,分析其蛋白质编码基因的密码子使用特征及与亚洲栽培稻(O. sativa L.)的差异,探讨其密码子偏性形成的影响因素和进化过程。结果显示:普通野生稻线粒体基因组编码序列第1、第2和第3位碱基的GC含量依次为49.18%、42.67%和40.86%;有效密码子数(Nc)分布于45.32～61.00之间,其密码子偏性较弱; Nc值仅与GC_3呈显著相关,密码子第3位的碱基组成对密码子偏性影响较大;第1向量轴上显示9.91%的差异,其与GC_3s、Nc、密码子偏好指数(CBI)和最优密码子使用频率(Fop)的相关性均达到显著水平;而GC_3和GC₁₂的相关性未达到显著水平。因此,普通野生稻线粒体基因组密码子的使用偏性主要受自然选择压力影响而形成。本研究确定了21个普通野生稻线粒体基因组的最优密码子,大多以A或T结尾,与叶绿体密码子具有趋同进化,但是与核基因组具有不同的偏好性。同义密码子相对使用度(RSCU)、PR2偏倚分析和中性绘图分析显示,普通野生稻线粒体基因功能和其密码子使用密切相关,且线粒体密码子使用在普通野生稻、粳稻(O. sativa L. subsp. japonica Kato)和籼稻(O. sativa L. subsp.indica Kato)内具有同质性。     

A thermal denaturation study of genomic DNAs from North American minnows (Cyprinidae: Teleostei)

Base compositions and differential melting rate profiles of genomic DNAs from twenty species of North American cyprinid fishes were generated via thermal denaturation. Base pair composition expressed as % GC values ranged among the twenty species from 36.1–41.3%. This range is considerably broader than that observed at comparable taxonomic levels in other vertebrate groups. Both the range and average difference in base pair composition between species in the diverse and rapidly evolving genus Notropis were considerably greater than those between species in other North American cyprinid genera. This may indicate that genomic changes at the level of base pair composition are frequent and possibly important events in cyprinid evolution. Compositional heterogeneity and asymmetry values among the twenty species were uniform and low, respectively, suggesting that most of the species lacked DNA components in their genomes which differed substantially from their main-band DNAs in base pair composition. The melting rate profiles revealed a prominent and distinct heavy or GC-rich DNA component in the genomes of three species belonging to the subgenus Cyprinella of Notropis. These and other data suggest that the heavy melting component may reflect a large, comparatively GC-rich family of highly repeated or satellite DNA sequences common to all three genomes.     

Genome-wide comparative analysis of the codon usage patterns in plants

Codon usage analysis has been a classical area of study for decades and is important for evolution, mRNA translation, and new gene discovery. Recently, genome sequencing has made it possible to perform studies of the entire genome in plant kingdoms. The base composition of the coding sequence, codon usage pattern, codon pairs, and related indicators of relative synonymous codon usage (RSCU), including the Fop, Nc, RSCU, CAI and GC contents, were analyzed. We found that the GC content of single-celled algae is the highest, whereas dicotyledons are the lowest. Moreover, the base composition of plants is similar within the same family. In addition, the GC content of the second base of the codon is lower than the first and third base. In conclusion, the codon usage characteristics are opposite in Gramineae, single-celled algae, fern and dicotyledon, moss, and Pinaceae. Furthermore, the degree of codon usage bias is decreasing with evolution. Therefore, we hypothesize that the lower the plants, the more that they must optimize codons and that higher plants no longer need to optimize codons.     

Genome size and DNA base composition of geophytes: the mirror of phenology and ecology?

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.     

Analysis of the Relationship between Genomic GC Content and Patterns of Base Usage,Codon Usage and Amino Acid Usage in Prokaryotes: Similar GC Content Adopts Similar Compositional Frequencies Regardless of the Phylogenetic Lineages

The GC contents of 2670 prokaryotic genomes that belong to diverse phylogenetic lineages were analyzed in this paper. These genomes had GC contents that ranged from 13.5% to 74.9%. We analyzed the distance of base frequencies at the three codon positions, codon frequencies, and amino acid compositions across genomes with respect to the differences in the GC content of these prokaryotic species. We found that although the phylogenetic lineages were remote among some species, a similar genomic GC content forced them to adopt similar base usage patterns at the three codon positions, codon usage patterns, and amino acid usage patterns. Our work demonstrates that in prokaryotic genomes: a) base usage, codon usage, and amino acid usage change with GC content with a linear correlation; b) the distance of each usage has a linear correlation with the GC content difference; and c) GC content is more essential than phylogenetic lineage in determining base usage, codon usage, and amino acid usage. This work is exceptional in that we adopted intuitively graphic methods for all analyses, and we used these analyses to examine as many as 2670 prokaryotes. We hope that this work is helpful for understanding common features in the organization of microbial genomes.     

The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists

Rice is not only a major food staple for the world's population but it also is a model species for a major group of flowering plants, the monocotyledonous plants. Draft genomic sequence of two subspecies of rice, Oryza sativa spp. japonica and indica ssp. are publicly available. To provide the community with a resource to data-mine the rice genome, we have constructed an annotation resource for rice (http://www.tigr.org/tdb/e2k1/osa1/). In this resource, we have annotated the rice genome for gene content, identified motifs/domains within the predicted genes, constructed a rice repeat database, identified related sequences in other plant species, and identified syntenic sequences between rice and maize. All of the data is available through web-based interfaces, FTP downloads, and a Distributed Annotation System.     

Deoxyribonucleic Acid Base Composition in Yeasts

The deoxyribonucleic acid base composition of 15 species of yeasts was determined to obtain further clues to or supporting evidence for their taxonomic position. Species examined belonged to the genera Saccharomyces, Debaryomyces, Lodderomyces, Metschnikowia, and Candida. The range of moles per cent guanine plus cytosine (GC content) for all yeasts examined extended from 34.9 to 48.3%. The sporogenous species and the asporogenous yeasts spanned the range with 36.6 to 48.3% GC and 34.9 to 48% GC, respectively. Three Saccharomyces species (S. rosei and related species) exhibited significantly higher GC contents than S. cerevisiae, whereas the fermentative species D. globosus revealed a%GC more aligned to the S. rosei group than to the nonfermentative D. hansenii. Similar GC contents were demonstrated by L. elongasporus and its proposed imperfect form C. parapsilosis. The range of GC contents of various strains of three Metschnikowia species studied was 6.1%, with the type strain of M. pulcherrima having the highest GC content (48.3%) of all of the yeasts examined.     

Base Composition Skews, Replication Orientation, and Gene Orientation in 12 Prokaryote Genomes

Variation in GC content, GC skew and AT skew along genomic regions was examined at third codon positions in completely sequenced prokaryotes. Eight out of nine eubacteria studied show GC and AT skews that change sign at the origin of replication. The leading strand in DNA replication is G-T rich at codon position 3 in six eubacteria, but C-T rich in two Mycoplasma species. In M. genitalium the AT and GC skews are symmetrical around the origin and terminus of replication, whereas its GC content variation has been shown to have a centre of symmetry elsewhere in the genome. Borrelia burgdorferi and Treponema pallidum show extraordinary extents of base composition skew correlated with direction of DNA replication. Base composition skews measured at third codon positions probably reflect mutational biases, whereas those measured over all bases in a sequence (or at codon positions 1 and 2) can be strongly affected by protein considerations due to the tendency in some bacteria for genes to be transcribed in the same direction that they are replicated. Consequently in some species the direction of skew for total genomic DNA is opposite to that for codon position 3. Received: 2 February 1998 / Accepted: 15 June 1998     

Patterns of plant diversity at high altitudes on the Qinghai-Tibetan Plateau

Aims To describe the biodiversity patterns of plants along an altitudinal gradient on the Qinghai-Tibetan Plateau and to clarify the bias in plant specimen records at high altitude.Methods We conducted a large-scale investigation of vegetation at a wide range of altitudes, focusing on a high-altitudinal range (3?200–5?200 m) at different locations on the Qinghai-Tibetan Plateau. We then compared the altitudinal distribution of plant species obtained from our field investigation with that in plant specimen records from published sources and an online database.Important findings Our data provide evidence that altitude plays a large role in regulating species composition on the Qinghai-Tibetan Plateau. We could not, however, detect a clear relationship between altitude and species richness, although a weak monotonically increasing trend of richness was detected with increasing altitude. According to specimen records, most species have been sampled at a wide range of altitudes, and the average range of 145 species is>2?000 m. Despite this wide range, more than half of the species we observed were at higher altitudes than the specimen records indicate. High-altitude areas have probably been so poorly sampled that only a small fraction of the resident species has been recorded. This study clearly shows the regional bias of specimen records in the Qinghai-Tibetan Plateau.     

Impact of shrub canopies on understorey vegetation in western Eurasian tundra

Question: How does the composition and species richness of understorey vegetation associate with changing abundance of deciduous shrub canopies? What are the species‐specific associations between shrubs and understorey plants? Location: Tundra habitats along an over 1000‐km long range, spanning from NW Fennoscandia to the Yamal Peninsula in northwest Russia. Methods: The data from 758 vegetation sample plots from 12 sites comprised cover estimates of all plant species, including bryophytes and lichens, and canopy height of deciduous shrubs. The relationships between shrub volume and cover of plant groups and species richness of vegetation were investigated. In addition, species‐specific associations between understorey species and shrub volume were analysed. Results: Shrub abundance was shown to be associated with the composition of understorey vegetation, and the association patterns were consistent across the study sites. Increased forb cover was positively associated with shrub volume, whereas bryophyte, lichen, dwarf shrub and graminoid cover decreased in association with increasing volume of deciduous shrubs. The total species richness of vegetation declined with increasing shrub volume. Conclusions: The results suggest that an increase of shrubs – due to climatic warming or a decrease in grazing pressure – is likely to have strong effects on plant–plant interactions and lead to a decrease in the diversity of understorey vegetation.     

Complex mutation and weak selection together determined the codon usage bias in bryophyte mitochondrial genomes

Mutation and selection are two major forces causing codon usage biases. How these two forces influence the codon usages in green plant mitochondrial genomes has not been well investigated. In the present study, we surveyed five bryophyte mitochondrial genomes to reveal their codon usage patterns as well as the determining forces. Three interesting findings were made. First, comparing to Chara vulgaris, an algal species sister to all extant land plants, bryophytes have more G, C-ending codon usages in their mitochondrial genes. This is consistent with the generally higher genomic GC content in bryophyte mitochondria, suggesting an increased mutational pressure toward GC. Second, as indicated by Wright's Nc-GC3s plot, mutation, not selection, is the major force affecting codon usages of bryophyte mitochondrial genes. However, the real mutational dynamics seem very complex. Context-dependent analysis indicated that nucleotide at the 2nd codon position would slightly affect synonymous codon choices. Finally, in bryophyte mitochondria, tRNA genes would apply a weak selection force to fine-tune the synonymous codon frequencies, as revealed by data of Ser4-Pro-Thr-Val families. In summary, complex mutation and weak selection together determined the codon usages in bryophyte mitochondrial genomes.     

Evidence of Selection upon Genomic GC-Content in Bacteria

The genomic GC-content of bacteria varies dramatically, from less than 20% to more than 70%. This variation is generally ascribed to differences in the pattern of mutation between bacteria. Here we test this hypothesis by examining patterns of synonymous polymorphism using datasets from 149 bacterial species. We find a large excess of synonymous GC→AT mutations over AT→GC mutations segregating in all but the most AT-rich bacteria, across a broad range of phylogenetically diverse species. We show that the excess of GC→AT mutations is inconsistent with mutation bias, since it would imply that most GC-rich bacteria are declining in GC-content; such a pattern would be unsustainable. We also show that the patterns are probably not due to translational selection or biased gene conversion, because optimal codons tend to be AT-rich, and the excess of GC→AT SNPs is observed in datasets with no evidence of recombination. We therefore conclude that there is selection to increase synonymous GC-content in many species. Since synonymous GC-content is highly correlated to genomic GC-content, we further conclude that there is selection on genomic base composition in many bacteria.