What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

Some notable exceptions aside, eukaryotic genomes are distinguished from those of Bacteria and Archaea in a number of ways, including chromosome structure and number, repetitive DNA content, and the presence of introns in protein-coding regions. One of the most notable differences between eukaryotic and prokaryotic genomes is in size. Unlike their prokaryotic counterparts, eukaryotes exhibit enormous (more than 60 000-fold) variability in genome size which is not explained by differences in gene number. Genome size is known to correlate with cell size and division rate, and by extension with numerous organism-level traits such as metabolism, developmental rate or body size. Less well described are the relationships between genome size and other properties of the genome, such as gene content, transposable element content, base pair composition and related features. The rapid expansion of ‘complete’ genome sequencing projects has, for the first time, made it possible to examine these relationships across a wide range of eukaryotes in order to shed new light on the causes and correlates of genome size diversity. This study presents the results of phylogenetically informed comparisons of genome data for more than 500 species of eukaryotes. Several relationships are described between genome size and other genomic parameters, and some recommendations are presented for how these insights can be extended even more broadly in the future.     

How much does the amphioxus genome represent the ancestor of chordates?

One of the main motivations to study amphioxus is its potential for understanding the last common ancestor of chordates, which notably gave rise to the vertebrates. An important feature in this respect is the slow evolutionary rate that seems to have characterized the cephalochordate lineage, making amphioxus an interesting proxy for the chordate ancestor, as well as a key lineage to include in comparative studies. Whereas slow evolution was first noticed at the phenotypic level, it has also been described at the genomic level. Here, we examine whether the amphioxus genome is indeed a good proxy for the genome of the chordate ancestor, with a focus on protein-coding genes. We investigate genome features, such as synteny, gene duplication and gene loss, and contrast the amphioxus genome with those of other deuterostomes that are used in comparative studies, such as Ciona, Oikopleura and urchin.     

Restriction fragment maps of the genome of Bacillus subtilis bacteriophage SPβ

Six different restriction endonucleases were used to generate restriction fragment maps of the genome of the temperate Bacillus subtilis phage SPβ. AvaI and SalI each had six target sites in the phage DNA, AvaII had three, BamHI had seven, PstI had twenty, and SacI had sixteen. Restriction analysis and heteroduplex analysis were used to locate a 10-kb region of DNA that is deleted in the clear-plaque mutant, spβci. Thedeletion lay approx. 50 kb from the left end of the 126-kb phage genome.     

Is RecG a general guardian of the bacterial genome?

The RecG protein of Escherichia coli is a double-stranded DNA translocase that unwinds a variety of branched DNAs in vitro, including Holliday junctions, replication forks, D-loops and R-loops. Coupled with the reported pleiotropy of recG mutations, this broad range of potential targets has made it hard to pin down what the protein does in vivo, though roles in recombination and replication fork repair have been suggested. However, recent studies suggest that RecG provides a more general defence against pathological DNA replication. We have postulated that this is achieved through the ability of RecG to eliminate substrates that the replication restart protein, PriA, could otherwise exploit to re-replicate the chromosome. Without RecG, PriA triggers a cascade of events that interfere with the duplication and segregation of chromosomes. Here we review the studies that led us to this idea and to conclude that RecG may be both a specialist activity and a general guardian of the genome.     

The Escherichia coli genome sequence: the end of an era or the start of the FUN?

Our dream of determining the entire Escherichia coli K12 genome sequence has been realized. This calls for new approaches for the analysis of gene expression and function in biology's best-understood organism. Comparison of the E. coli genome sequence with others will provide important taxonomic insights and have implications for the study of bacterial virulence. Approximately 20% of E. coli genes have been designated FUN genes, because they have no known function or homologies to sequence databases. FUN genes promise to have an exciting impact on bacterial research. The post-genome era requires novel strategies that address gene regulation at the level of the entire cell. These strategies need to supersede the reductionist approach to genetic analysis. Only then will the genome sequence lead us to an understanding of how a bacterial cell really works.     

Structure–function analysis of the barley genome: the gene-rich region of chromosome 2HL

A major gene-rich region on the end of the long arm of Triticeae group 2 chromosomes exhibits high recombination frequencies, making it an attractive region for positional cloning. Traits known to be controlled by this region include chasmogamy/cleistogamy, frost tolerance at flowering, grain yield, head architecture, and resistance to Fusarium head blight and rusts. To assist these cloning efforts, we constructed detailed genetic maps of barley chromosome 2H, including 61 polymerase chain reaction markers. Colinearity with rice occurred in eight distinct blocks, including five blocks in the terminal gene-rich region. Alignment of rice sequences from the junctions of colinear chromosome segments provided no evidence for the involvement of long (>2.5 kb) inverted repeats in generating inversions. However, reuse of some junction sequences in two or three separate evolutionary breakage/fusion events was implicated, suggesting the presence of fragile sites. Sequencing across 91 gene fragments totaling 107 kb from four barley genotypes revealed the highest single nucleotide substitution and insertion–deletion polymorphism levels in the terminal regions of the chromosome arms. The maps will assist in the isolation of genes from the chromosome 2L gene-rich region in barley and wheat by providing markers and accelerating the identification of the corresponding points in the rice genome sequence. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Metabolomics platforms for genome wide association studies—linking the genome to the metabolome

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Highlights► Genome-wide association studies with metabolomics constitute mGWAS. ► mGWAS provide insights into genetic and environmental impact on metabolic processes. ► We review essential strategies for mGWAS. ► Examples of mGWAS in large cohort studies are discussed.     

Evolution of genome size in Drosophila. is the invader's genome being invaded by transposable elements?

Genome size varies considerably between species, and transposable elements (TEs) are known to play an important role in this variability. However, it is far from clear whether TEs are involved in genome size differences between populations within a given species. We show here that in Drosophila melanogaster and Drosophila simulans the size of the genome varies among populations and is correlated with the TE copy number on the chromosome arms. The TEs embedded within the heterochromatin do not seem to be involved directly in this phenomenon, although they may contribute to differences in genome size. Furthermore, genome size and TE content variations parallel the worldwide colonization of D. melanogaster species. No such relationship exists for the more recently dispersed D. simulans species, which indicates that a quantitative increase in the TEs in local populations and fly migration are sufficient to account for the increase in genome size, with no need for an adaptation hypothesis.     

Sulphur islands in the Escherichia coli genome: markers of the cell's architecture?

Two highly contrasted images depict genomes: at first sight, genes appear to be distributed randomly along the chromosome. In contrast, their organisation into operons (or pathogenicity islands) suggests that, at least locally, related functions are in physical proximity. Analysis of the codon usage bias in orthologous genes in the genome of bacteria which diverged a long time ago suggested that some physical (architectural) selection pressure organised the distribution of genes along the chromosome. The metabolism of highly reactive species such as sulphur-containing molecules must be compartmentalised to escape the deleterious actions of diffusible reagents such as gases or radicals. We analysed the distribution of sulphur metabolism genes in the genome of Escherichia coli and found a number of them to be clustered into statistically significant islands. Another interesting feature of these genes is that the proteins they encode are significantly deprived of cysteine and methionine residues, as compared to the bulk proteins. We speculate that this clustering is associated to the organisation of sulphur metabolism proteins into islands where the sensitive sulphur-containing molecules are protected from reacting with elements in the environment such as dioxygen, nitric oxide or radicals.