Compositional Properties of Green-Plant Plastid Genomes

We studied variation of GC contents among plastid (Pt) genomes of green plants. In the green plants, the GC contents of the whole Pt genomes range from 42.14 to 28.81%. These values are similar to those observed in the mitochondrial (Mt) genomes of the green plants, however, the GC contents in the Pt genomes are not related to those in the Mt genomes or the nuclear (Nc) genomes. In addition, some compositional properties of the three types of genomes are different. Thus, it is suggested that the GC contents of the Pt genomes are maintained independently of the other genomes within a cell. We found that the compositional bias toward AT is strong at the third codon position and in intergenic spacer (IGS) regions in the Pt genomes, and the GC contents (GC3 and GCIGS) at these sites are generally similar within each genome. Additionally, the GC3 and GCIGS are strongly related to the whole-genome GC content. Therefore, the interspecific variation of the GC contents in the Pt genomes is suggested to be mainly caused by the variation of the GC3 and GCIGS, both of which are considered to be under weak selective constraints. Using a maximum likelihood approach, we estimated equilibrium GC3 (eqGC₃) of 12 genes in the land-plant Pt genomes. We found an increase in eqGC₃ after the divergence of liverworts. These results suggest that genome-wide factors such as GC mutational bias are important for the biased base composition in the Pt genomes.Reviewing Editor: Dr. Brian Morton     

Statistical inference of sequence-dependent mutation rates

Several lines of research are now converging towards an integrated understanding of mutational mechanisms and their evolutionary implications. Experimentally, crystal structures reveal the effect of sequence context on polymerase fidelity; large-scale sequencing projects generate vast amounts of sequence polymorphism data; and locus-specific databases are being constructed. Computationally, software and analytical tools have been developed to analyze mutational data, to identify mutational hot spots, and to compare the signatures of mutagenic agents.     

The Correlation Between Recombination Rate and Dinucleotide Bias in Drosophila melanogaster

Revealing how recombination affects genomic sequence is of great significance to our understanding of genome evolution. The present paper focuses on the correlation between recombination rate and dinucleotide bias in Drosophila melanogaster genome. Our results show that the overall dinucleotide bias is positively correlated with recombination rate for genomic sequences including untranslated regions, introns, intergenic regions, and coding sequences. The correlation patterns of individual dinucleotide biases with recombination rate are presented. Possible mechanisms of interaction between recombination and dinucleotide bias are discussed. Our data indicate that there may be a genome-wide universal mechanism acting between recombination rate and dinucleotide bias, which is likely to be neighbor-dependent biased gene conversion.     

The Rate and Molecular Spectrum of Spontaneous Mutations in the GC-Rich Multichromosome Genome of Burkholderia cenocepacia

Spontaneous mutations are ultimately essential for evolutionary change and are also the root cause of many diseases. However, until recently, both biological and technical barriers have prevented detailed analyses of mutation profiles, constraining our understanding of the mutation process to a few model organisms and leaving major gaps in our understanding of the role of genome content and structure on mutation. Here, we present a genome-wide view of the molecular mutation spectrum in Burkholderia cenocepacia, a clinically relevant pathogen with high %GC content and multiple chromosomes. We find that B. cenocepacia has low genome-wide mutation rates with insertion–deletion mutations biased toward deletions, consistent with the idea that deletion pressure reduces prokaryotic genome sizes. Unlike prior studies of other organisms, mutations in B. cenocepacia are not AT biased, which suggests that at least some genomes with high %GC content experience unusual base-substitution mutation pressure. Importantly, we also observe variation in both the rates and spectra of mutations among chromosomes and elevated G:C > T:A transversions in late-replicating regions. Thus, although some patterns of mutation appear to be highly conserved across cellular life, others vary between species and even between chromosomes of the same species, potentially influencing the evolution of nucleotide composition and genome architecture.     

Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena thermophila

Knowledge of the rate and fitness effects of mutations is essential for understanding the process of evolution. Mutations are inherently difficult to study because they are rare and are frequently eliminated by natural selection. In the ciliate Tetrahymena thermophila, mutations can accumulate in the germline genome without being exposed to selection. We have conducted a mutation accumulation (MA) experiment in this species. Assuming that all mutations are deleterious and have the same effect, we estimate that the deleterious mutation rate per haploid germline genome per generation is U = 0.0047 (95% credible interval: 0.0015, 0.0125), and that germline mutations decrease fitness by s = 11% when expressed in a homozygous state (95% CI: 4.4%, 27%). We also estimate that deleterious mutations are partially recessive on average (h = 0.26; 95% CI: –0.022, 0.62) and that the rate of lethal mutations is <10% of the deleterious mutation rate. Comparisons between the observed evolutionary responses in the germline and somatic genomes and the results from individual-based simulations of MA suggest that the two genomes have similar mutational parameters. These are the first estimates of the deleterious mutation rate and fitness effects from the eukaryotic supergroup Chromalveolata and are within the range of those of other eukaryotes.     

Fitness-dependent mutation rates in finite populations

Mutation rate may be condition dependent, whereby individuals in poor condition, perhaps from high mutation load, have higher mutation rates than individuals in good condition. Agrawal (J. Evol. Biol.15, 2002, 1004) explored the basic properties of fitness-dependent mutation rate (FDMR) in infinite populations and reported some heuristic results for finite populations. The key parameter governing how infinite populations evolve under FDMR is the curvature (k) of the relationship between fitness and mutation rate. We extend Agrawal's analysis to finite populations and consider dominance and epistasis. In finite populations, the probability of long-term existence depends on k. In sexual populations, positive curvature leads to low equilibrium mutation rate, whereas negative curvature results in high mutation rate. In asexual populations, negative curvature results in rapid extinction via 'mutational meltdown', whereas positive curvature sometimes allows persistence. We speculate that fitness-dependent mutation rate may provide the conditions for genetic architecture to diverge between sexual and asexual taxa.