How repetitive are genomes?

Background  

Genome sequences vary strongly in their repetitiveness and the causes for this are still debated. Here we propose a novel measure of genome repetitiveness, the index of repetitiveness, I _r, which can be computed in time proportional to the length of the sequences analyzed. We apply it to 336 genomes from all three domains of life.     

Where are the pseudogenes in bacterial genomes?

Most bacterial genomes have very few pseudogenes; notable exceptions include the genomes of the intracellular parasites Rickettsia prowazekii and Mycobacterium leprae. As DNA can be introduced into microbial genomes in many ways, the compact nature of these genomes suggests that the rate of DNA influx is balanced by the rate of DNA deletion. We propose that the influx of dangerous genetic elements such as transposons and bacteriophages selects for the maintenance of relatively high deletion rates in most bacteria; the sheltered lifestyle of intracellular parasites removes this threat, leading to reduced deletion rates and larger pseudogene loads.     

How big is the iceberg of which organellar genes in nuclear genomes are but the tip?

As more and more complete bacterial and archaeal genome sequences become available, the role of lateral gene transfer (LGT) in shaping them becomes more and more clear. Over the long term, it may be the dominant force, affecting most genes in most prokaryotes. We review the history of LGT, suggesting reasons why its prevalence and impact were so long dismissed. We discuss various methods purporting to measure the extent of LGT, and evidence for and against the notion that there is a core of never-exchanged genes shared by all genomes, from which we can deduce the "true" organismal tree. We also consider evidence for, and implications of, LGT between prokaryotes and phagocytic eukaryotes.     

Why are the genomes of endosymbiotic bacteria so stable?

The comparative analysis of three strains of the endosymbiotic bacterium Buchnera aphidicola has revealed high genome stability associated with an almost complete absence of chromosomal rearrangements and horizontal gene transfer events during the past 150 million years. The loss of genes involved in DNA uptake and recombination in the initial stages of endosymbiosis probably underlies this stability. Gene loss, which was extensive during the initial steps of Buchnera evolution, has continued in the different Buchnera lineages since their divergence.     

How independent are TSE agents from their hosts?

Central to understanding the nature TSE agents (or prions) is how their genetic information is distinguished from the host. Are TSEs truly infectious diseases with host-independent genomes, or are they aberrations of a host component derived from the host genome? Recent experiments tested whether glycosylation of host PrP affects TSE strain characteristics. Wild-type mice were infected with 3 TSE strains passaged through transgenic mice with PrP devoid of glycans at 1 or both N-glycosylation sites. Strain-specific characteristics of 1 TSE strain changed but did not change for 2 others. Changes resulted from the selection of mutant TSE strains in a novel replicative environment. In general the properties of established TSEs support the genetic independence of TSE agents from the host, and specifically the primary structure of PrP does not directly encode TSE agent properties. However sporadic TSEs, challenge this independency. The prion hypothesis explains emerging TSEs relatively successfully but poorly accounts for the diversity and mutability of established TSE strains, or how many different infectious conformations are sustained thermodynamically. Research on early changes in RNA expression and events at the ribosome may inform the debate on TSE agent properties and their interaction with host cell machinery.     

How has horizontal gene transfer shaped the evolution of insect genomes?

As the most diverse group of animals on Earth, insects are key organisms in ecosystems. Horizontal gene transfer (HGT) refers to the transfer of genetic material between species by non-reproductive means. HGT is a major evolutionary force in prokaryotic genome evolution, but its importance in different eukaryotic groups, such as insects, has only recently begun to be understood. Genomic data from hundreds of insect species have enabled the detection of large numbers of HGT events and the elucidation of the functions of some of these foreign genes. Although quantification of the extent of HGT in insects broadens our understanding of its role in insect evolution, the scope of its influence and underlying mechanism(s) of its occurrence remain open questions for the field.     

Diversification of Escherichia coli genomes: are bacteriophages the major contributors?

Determination of the genome sequence of enterohemorrhagic Escherichia coli O157 Sakai and genomic comparison with the laboratory strain K-12 has revealed that the two strains share a highly conserved 4.1-Mb sequence and that each also contains a large amount of strain-specific sequence. The analysis also revealed the presence of a surprisingly large number of prophages in O157, most of which are lambda-like phages that resemble each other. Based on these results, we discuss how the E. coli strains have diverged from a common ancestral strain, and how bacteriophages contributed to this process. We also describe possible mechanisms by which O157 acquired many closely related phages, and raise the possibility that such bacteria might function as 'phage factories', releasing a variety of chimeric or mosaic phages into the environment.     

How good are comparative models in the understanding of protein dynamics?

The 3D structure of a protein is essential to understand protein dynamics. If experimentally determined structure is unavailable, comparative models could be used to infer dynamics. However, the effectiveness of comparative models, compared to experimental structures, in inferring dynamics is not clear. To address this, we compared dynamics features of ~800 comparative models with their crystal structures using normal mode analysis. Average similarity in magnitude, direction, and correlation of residue motions is >0.8 (where value 1 is identical) indicating that the dynamics of models and crystal structures are highly similar. Accuracy of 3D structure and dynamics is significantly higher for models built on multiple and/or high sequence identity templates (>40%). Three-dimensional (3D) structure and residue fluctuations of models are closer to that of crystal structures than to templates (TM score 0.9 vs 0.7 and square inner product 0.92 vs 0.88). Furthermore, long-range molecular dynamics simulations on comparative models of RNase 1 and Angiogenin showed significant differences in the conformational sampling of conserved active-site residues that characterize differences in their activity levels. Similar analyses on two EGFR kinase variant models highlight the effect of mutations on the functional state-specific αC helix motions and these results corroborate with the previous experimental observations. Thus, our study adds confidence to the use of comparative models in understanding protein dynamics.     

Why are plastid genomes retained in non-photosynthetic organisms?

The evolution of the plastid from a photosynthetic bacterial endosymbiont involved a dramatic reduction in the complexity of the plastid genome, with many genes either discarded or transferred to the nucleus of the eukaryotic host. However, this evolutionary process has not gone to completion and a subset of genes remains in all plastids examined to date. The various hypotheses put forward to explain the retention of the plastid genome have tended to focus on the need for photosynthetic organisms to retain a genetic system in the chloroplast, and they fail to explain why heterotrophic plants and algae, and the apicomplexan parasites all retain a genome in their non-photosynthetic plastids. Here we consider two additional explanations: the 'essential tRNAs' hypothesis and the 'transfer-window' hypothesis.     

How are the vertical migrations of copepods controlled?

Using Calanus finmarchicus (Gunnerus) as a model organism, a hypothesis is suggested to explain the diel and seasonal vertical migrations of herbivorous copepods in boreal and polar waters. The hypothesis is based on the following assumptions. Hungry copepods are assumed to react to food smell by increased swimming. High lipid content is assumed to turn the copepods upside down. Light avoidance is assumed to operate solely while the copepods are satiated. The following three major peaks in downflux of phytoplankton remains are assumed to reach 1000 m depth or more: pre- and post-spring bloom peaks and the autumn increase. A minor “afternoon peak” in short-range downflux of phytoplankton is also assumed to exist. The assumptions are used to explain the following main traits in copepod migrations. The afternoon increase in downflux of phytoplankton material induces upward swimming of hungry copepods. If satiated, light avoidance brings them down again at dawn. The late stages of many species of copepods accumulate large amounts of lipids and if the above assumptions are valid, they will be turned upside down and swim down if activated. During midsummer, the downflux does not reach deep water and the copepods are assumed to spend some time in midwater until they moult. Copepods moulting from stage V into female adults use up to half of their lipids to produce eggs, which are more anteriorly located. This is assumed to turn their bodies back into an upright position and the copepods are assumed to swim up to the surface again when they smell sinking phytoplankton remains. Fat copepods are assumed to follow the downflux of phytoplankton material down to diapause depths, especially at the end of the spring bloom and in autumn. It is assumed that enough lipids are used up during the diapause to turn the copepods into head-up position again. The smell of fast-sinking fecal pellets containing prebloom phytoplankton is assumed to bring the copepods up from diapause again in late winter. The probable implications for the survival of cod larvae are discussed.     

Genetic and karyotypic structure in the shrews of the Sorex araneus group: are they independent?

The species of the common shrew (Sorex araneus) group are morphologically very similar but exhibit high levels of karyotypic variation. Here we used genetic variation at 10 microsatellite markers in a data set of 212 individuals mostly sampled in the western Alps and composed of five karyotypic taxa (Sorex coronatus, Sorex antinorii and the S. araneus chromosome races Cordon, Bretolet and Vaud) to investigate the concordance between genetic and karyotypic structure. Bayesian analysis confirmed the taxonomic status of the three sampled species since individuals consistently grouped according to their taxonomical status. However, introgression can still be detected between S. antinorii and the race Cordon of S. araneus. This observation is consistent with the expected low karyotypic complexity of hybrids between these two taxa. Geographically based cryptic substructure was discovered within S. antinorii, a pattern consistent with the different postglaciation recolonization routes of this species. Additionally, we detected two genetic groups within S. araneus notwithstanding the presence of three chromosome races. This pattern can be explained by the probable hybrid status of the Bretolet race but also suggests a relatively low impact of chromosomal differences on genetic structure compared to historical factors. Finally, we propose that the current data set (available at http://www.unil.ch/dee/page7010_en.html#1) could be used as a reference by those wanting to identify Sorex individuals sampled in the western Alps.     

How do we compare hundreds of bacterial genomes?

The genomic revolution is fully upon us in 2006 and the pace of discovery is set to accelerate with the emergence of ultra-high-throughput sequencing technologies. Our complete genome collection of bacteria and archaea continues to grow in number and diversity, as genome sequencing is applied to an array of new problems, from the characterization of the pan-genome to the detection of mutation after experimentation and the exploration of microbial communities in unprecedented detail. The benefits of large-scale comparative genomic analyses are driving the community to think about how to manage our public collections of genomes in novel ways.     

How old are the extant lineages of Toxoplasma gondii?

Most known isolates of Toxoplasma gondii belong to one of only three lineages, which are presumed to be clonal. Three models have been proposed for the evolutionary relationship of these lineages to the other extant lineages: Model (a) proposing that all lineages are derived from a most recent common ancestor (MRCA) in the distant past, Model (b) that all lineages are derived from a MRCA in the very recent past, and Model (c) that the clonal lineages share a recent MRCA but are related to the other lineages only in the distant past. Here, I test these models using DNA intron and coding-sequence data for loci at 14 genes, using three different methods to calculate the time of the MRCA. All of the calculations agree that the MRCA of the clonal lineages was > 70% of the age of the MRCA of all lineages, thus favouring Model (a). The MRCA may have existed approximately 150,000 years ago, with the clonal lineages expanding in prevalence approximately 10,000 years ago.     

Why are estimates of the terrestrial carbon balance so different?

The carbon balance of the world's terrestrial ecosystems is uncertain. Both top‐down (atmospheric) and bottom‐up (forest inventory and land‐use change) approaches have been used to calculate the sign and magnitude of a net terrestrial flux. Different methods often include different processes, however, and comparisons can be misleading. Differences are not necessarily the result of uncertainties or errors, but often result from incomplete accounting inherent in some of the methods. Recent estimates are reviewed here. Overall, a northern mid‐latitude carbon sink of approximately 2 Pg C yr^?1 appears robust, although the mechanisms responsible are uncertain. Several lines of evidence point to environmentally enhanced rates of carbon accumulation. Other lines suggest that recovery from past disturbances is largely responsible for the sink. The tropics appear to be a small net source of carbon or nearly neutral, and the same uncertainties of mechanism exist. In addition, studies in the tropics do not permit an unequivocal choice between two alternatives: large emissions of carbon from deforestation offset by large sinks in undisturbed forests, or moderate emissions from land‐use change with essentially no change in the carbon balance in undisturbed forests. Resolution of these uncertainties is most likely to result from spatially detailed historical reconstructions of land‐use change and disturbance in selected northern mid‐latitude regions where such data are available, and from systematic monitoring of changes in the area of tropical forests with satellite data of high spatial resolution collected over the last decades and into the future.     

How heterogeneous are the cloud forest communities in the mountains of central Veracruz, Mexico?

The montane forest in central Veracruz, Mexico is a hotspot of biodiversity. We asked whether lower and upper montane forests could be distinguished in this ecoregion. Variables of vegetation and seasonality in precipitation were tested across 14 sites between 1,250- and 2,550-m elevations. A total of 1,639 individuals and 128 tree species was recorded. There was a unimodal pattern in the richness of species, genera, and families; their richness was positively correlated with precipitation in the wettest quarter of the year, though there were no differences in the basal area and density. Rarefaction, species turnover, nonmetric multidimensional scaling, and a cluster histogram suggest two major groups: lower elevation forests that are less diverse, have low beta diversity and are more similar in composition, with Clethra macrophylla, Liquidambar styraciflua, and Quercus lancifolia as indicator species; and higher elevation forests that are more diverse, have high species turnover, and include forests with Quercus corrugata and Prunus rhamnoides, and forests with Fagus grandifolia, Persea americana, and Ternstroemia sylvatica as indicator species. However, other communities (an Oreomunnea mexicana at the upper site, and a limestone site in the lower forests), exemplify the high regional heterogeneity. We conclude that elevation and seasonality in precipitation produce a directional change in richness and indicator species, but not in vegetation structure. Lower montane forests differed from cloud forests at upper elevations. However, other factors should be included—mainly biogeographic affinities, historic and recent anthropogenic disturbance—to conclusively distinguish them. Montane forest can still be considered very heterogeneous and very high in beta diversity.