Genomes of uncultured eukaryotes: sorting FACS from fiction

A recent study explores the genome content of uncultured unicellular marine eukaryotes and provides insights about interactions between uncultured eukaryotes and other biological entities.     

Natural Recombination among Plant Virus Genomes: Evidence from Tobraviruses

RNA recombination in plants was first identified by the repairin vivoof a deleted genomic RNA of brome mosaic virus. Subsequently, evidence of recombination has been detected not only in experimental systems but also among an increasing number of naturally occurring isolates of plant viruses. This article discusses the different recombinants that have been found among viruses in the genusTobravirusand describes other examples of recombination among plant viruses and between the genomes of viruses and their hosts.     

Chronology of Deep Nodes in the Neotropical Primate Phylogeny: Insights from Mitochondrial Genomes

The evolution of Neotropical Primates (NP) is permeated by factors associated with the pattern of diversification and the biogeography of the major lineages. These questions can be better understood by providing a robust estimate of the chronological scenario of NP evolution, a reason why molecular dating methods have been widely applied. One aspect of especial interest is the timing of diversification of the major NP lineages (pitheciids, atelids and cebids), which may have resulted from rapid episodes of adaptive radiation, a question that requires NP divergence time estimates with accurate statistical certainty. In this study, we evaluated the primate timescale focused on the age of nodes of NP radiation. We investigated the performance of complete primate mitochondrial genomes as traditional molecular markers of primate evolution and further including original mitochondrial data from the endangered muriqui, Brachyteles arachnoides (Accession No. {"type":"entrez-nucleotide","attrs":{"text":"JX262672","term_id":"403488686","term_text":"JX262672"}}JX262672). Comparisons of the age estimates at NP nodes based on mitochondrial genomes with those obtained from a nuclear supermatrix showed similar degrees of uncertainty. Further molecular data and more informative calibration priors are required for a more precise understanding of the early NP diversification.     

Simulation of Genomes: A Review

There is an increasing role of population genetics in human genetic research linking empirical observations with hypotheses about sequence variation due to historical and evolutionary causes. In addition, the data sets are increasing in size, with genome-wide data becoming a common place in many empirical studies. As far as more information is available, it becomes clear that simplest hypotheses are not consistent with data. Simulations will provide the key tool to contrast complex hypotheses on real data by generating simulated data under the hypothetical historical and evolutionary conditions that we want to contrast. Undoubtedly, developing tools for simulating large sequences that at the same time allow simulate natural selection, recombination and complex demography patterns will be of great interest in order to better understanding the trace left on the DNA by different interacting evolutionary forces. Simulation tools will be also essential to evaluate the sampling properties of any statistics used on genome-wide association studies and to compare performance of methods applied at genome-wide scales. Several recent simulation tools have been developed. Here, we review some of the currently existing simulators which allow for efficient simulation of large sequences on complex evolutionary scenarios. In addition, we will point out future directions in this field which are already a key part of the current research in evolutionary biology and it seems that it will be a primary tool in the future research of genome and post-genomic biology.     

Inference of the Properties of the Recombination Process from Whole Bacterial Genomes

Patterns of linkage disequilibrium, homoplasy, and incompatibility are difficult to interpret because they depend on several factors, including the recombination process and the population structure. Here we introduce a novel model-based framework to infer recombination properties from such summary statistics in bacterial genomes. The underlying model is sequentially Markovian so that data can be simulated very efficiently, and we use approximate Bayesian computation techniques to infer parameters. As this does not require us to calculate the likelihood function, the model can be easily extended to investigate less probed aspects of recombination. In particular, we extend our model to account for the bias in the recombination process whereby closely related bacteria recombine more often with one another. We show that this model provides a good fit to a data set of Bacillus cereus genomes and estimate several recombination properties, including the rate of bias in recombination. All the methods described in this article are implemented in a software package that is freely available for download at http://code.google.com/p/clonalorigin/.     

Performance of genotype imputations using data from the 1000 Genomes Project

Genotype imputations based on 1000 Genomes (1KG) Project data have the advantage of imputing many more SNPs than imputations based on HapMap data. It also provides an opportunity to discover associations with relatively rare variants. Recent investigations are increasingly using 1KG data for genotype imputations, but only limited evaluations of the performance of this approach are available. In this paper, we empirically evaluated imputation performance using 1KG data by comparing imputation results to those using the HapMap Phase II data that have been widely used. We used three reference panels: the CEU panel consisting of 120 haplotypes from HapMap II and 1KG data (June 2010 release) and the EUR panel consisting of 566 haplotypes also from 1KG data (August 2010 release). We used Illumina 324,607 autosomal SNPs genotyped in 501 individuals of European ancestry. Our most important finding was that both 1KG reference panels provided much higher imputation yield than the HapMap II panel. There were more than twice as many successfully imputed SNPs as there were using the HapMap II panel (6.7 million vs. 2.5 million). Our second most important finding was that accuracy using both 1KG panels was high and almost identical to accuracy using the HapMap II panel. Furthermore, after removing SNPs with MACH Rsq <0.3, accuracy for both rare and low frequency SNPs was very high and almost identical to accuracy for common SNPs. We found that imputation using the 1KG-EUR panel had advantages in successfully imputing rare, low frequency and common variants. Our findings suggest that 1KG-based imputation can increase the opportunity to discover significant associations for SNPs across the allele frequency spectrum. Because the 1KG Project is still underway, we expect that later versions will provide even better imputation performance.     

Genomes: epigenomics and the future of genome sciences

Emerging data from diverse organisms indicate that we are only at the threshold of our understanding of the genome-wide implications of epigenetics. This relatively new field, entitled epigenomics, will be advanced by the recently completed sequence of the Tetrahymena thermophila macronuclear genome.     

Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes

Flowering plants have strikingly distinct genomes, although they contain a similar suite of expressed genes. The diversity of genome structures and organization is largely due to variation in transposable elements (TEs) and whole-genome duplication (WGD) events. We review evidence that chromatin modifications and epigenetic regulation are intimately associated with TEs and likely play a role in mediating the effects of WGDs. We hypothesize that the current structure of a genome is the result of various TE bursts and WGDs and it is likely that the silencing mechanisms and the chromatin structure of a genome have been shaped by these events. This suggests that the specific mechanisms targeting chromatin modifications and epigenomic patterns may vary among different species. Many crop species have likely evolved chromatin-based mechanisms to tolerate silenced TEs near actively expressed genes. These interactions of heterochromatin and euchromatin are likely to have important roles in modulating gene expression and variability within species.