Rates of genomic divergence in humans,chimpanzees and their lice

The rate of DNA mutation and divergence is highly variable across the tree of life. However, the reasons underlying this variation are not well understood. Comparing the rates of genetic changes between hosts and parasite lineages that diverged at the same time is one way to begin to understand differences in genetic mutation and substitution rates. Such studies have indicated that the rate of genetic divergence in parasites is often faster than that of their hosts when comparing single genes. However, the variation in this relative rate of molecular evolution across different genes in the genome is unknown. We compared the rate of DNA sequence divergence between humans, chimpanzees and their ectoparasitic lice for 1534 protein-coding genes across their genomes. The rate of DNA substitution in these orthologous genes was on average 14 times faster for lice than for humans and chimpanzees. In addition, these rates were positively correlated across genes. Because this correlation only occurred for substitutions that changed the amino acid, this pattern is probably produced by similar functional constraints across the same genes in humans, chimpanzees and their ectoparasites.     

Systematic Phenotyping of a Large-Scale Candida glabrata Deletion Collection Reveals Novel Antifungal Tolerance Genes

The opportunistic fungal pathogen Candida glabrata is a frequent cause of candidiasis, causing infections ranging from superficial to life-threatening disseminated disease. The inherent tolerance of C. glabrata to azole drugs makes this pathogen a serious clinical threat. To identify novel genes implicated in antifungal drug tolerance, we have constructed a large-scale C. glabrata deletion library consisting of 619 unique, individually bar-coded mutant strains, each lacking one specific gene, all together representing almost 12% of the genome. Functional analysis of this library in a series of phenotypic and fitness assays identified numerous genes required for growth of C. glabrata under normal or specific stress conditions, as well as a number of novel genes involved in tolerance to clinically important antifungal drugs such as azoles and echinocandins. We identified 38 deletion strains displaying strongly increased susceptibility to caspofungin, 28 of which encoding proteins that have not previously been linked to echinocandin tolerance. Our results demonstrate the potential of the C. glabrata mutant collection as a valuable resource in functional genomics studies of this important fungal pathogen of humans, and to facilitate the identification of putative novel antifungal drug target and virulence genes.     

Invasive species and land bird diversity on remote South Atlantic islands

Invasive species pose significant threats to biodiversity, especially on islands. They cause extinctions and population declines, yet little is known about their consequences on the emergent, metacommunity-level patterns of native species in island assemblages. We investigated differences in species–area relationships, nestedness, and occupancy of 9 species of native land birds between island assemblages with and without invasive Norway rats (Rattus norvegicus) in the Falkland Archipelago. We found that species–area curves, nestedness, and individual species’ occurrences differed between island assemblages with and without rats. Rat-free islands had, on average, 2.1 more land bird species than rat-infested islands of similar size. Passerine bird communities on islands with and without rats were significantly nested, but nestedness was significantly higher on rat-free islands than on rat-infested islands. The presence of rats was associated with differences in the incidence of many, but not all bird species. On rat free islands the occurrence of all species increased with island area. The occurrence of most, albeit not all, bird species was lower on islands with than on islands without rats. Two species of conservation concern, Troglodytes aedon cobbi and Cinclodes antarcticus, were abundant on rat-free islands, but absent or found at very low frequencies on islands with rats. The occurrence of three species was not associated with the presence of rats. The patterns presented here can be used to evaluate the consequences of ongoing rat eradications for passerine diversity, distribution, and abundance.     

Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas

Background

Molecular mechanisms associated with frequent relapse of diffuse large B-cell lymphoma (DLBCL) are poorly defined. It is especially unclear how primary tumor clonal heterogeneity contributes to relapse. Here, we explore unique features of B-cell lymphomas - VDJ recombination and somatic hypermutation - to address this question.

Results

We performed high-throughput sequencing of rearranged VDJ junctions in 14 pairs of matched diagnosis-relapse tumors, among which 7 pairs were further characterized by exome sequencing. We identify two distinctive modes of clonal evolution of DLBCL relapse: an early-divergent mode in which clonally related diagnosis and relapse tumors diverged early and developed in parallel; and a late-divergent mode in which relapse tumors developed directly from diagnosis tumors with minor divergence. By examining mutation patterns in the context of phylogenetic information provided by VDJ junctions, we identified mutations in epigenetic modifiers such as KMT2D as potential early driving events in lymphomagenesis and immune escape alterations as relapse-associated events.

Conclusions

Altogether, our study for the first time provides important evidence that DLBCL relapse may result from multiple, distinct tumor evolutionary mechanisms, providing rationale for therapies for each mechanism. Moreover, this study highlights the urgent need to understand the driving roles of epigenetic modifier mutations in lymphomagenesis, and immune surveillance factor genetic lesions in relapse.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0432-0) contains supplementary material, which is available to authorized users.     

Growth,plant quality and leaf damage patterns in a dioecious tree species: is gender important?

Frequently, female plants allocate more resources to reproductive structures and defense-related secondary compounds in comparison with male plants that invest more resources to growth, reflecting trade-offs between reproduction, growth and defense. Therefore, differences in herbivory can be expected between genders. In this study, over two years, we analyzed the differences in plant chemical defense, nutritional quality, plant size and herbivory between genders in the dioecious tree, Spondias purpurea in a Mexican tropical dry forest. We estimated the total leaf area and the area consumed by folivory using a digital image of each leaf. The nutritional quality was estimated as water content, and the concentration of chlorophyll and total nonstructural carbohydrates. The secondary metabolites analyzed were total content of soluble phenolics, flavonoids, protein precipitation capacity of tannins, gallotannins, soluble proanthocyanidins, hydrolyzable tannins and ellagitannins. Our results differ from most of studies that analyze the differential herbivory patterns in dioecious plants. We found that female trees had higher levels of herbivory than male trees of S. purpurea. In the same way, female trees showed higher size and nutritional quality than males, while chemical defense was higher in male trees. The higher percentage of folivory in female trees of S. purpurea is associated with greater nutritional quality and lower chemical defenses. Our results show that male-biased herbivory might not be universal in dioecious species. Therefore, studies of fitness components affected by herbivory are necessary to understand the evolution of dioecy and the importance of herbivores as selective agents on breeding system features.     

Bioinformatics Pipelines for Targeted Resequencing and Whole-Exome Sequencing of Human and Mouse Genomes: A Virtual Appliance Approach for Instant Deployment

Targeted resequencing by massively parallel sequencing has become an effective and affordable way to survey small to large portions of the genome for genetic variation. Despite the rapid development in open source software for analysis of such data, the practical implementation of these tools through construction of sequencing analysis pipelines still remains a challenging and laborious activity, and a major hurdle for many small research and clinical laboratories. We developed TREVA (Targeted REsequencing Virtual Appliance), making pre-built pipelines immediately available as a virtual appliance. Based on virtual machine technologies, TREVA is a solution for rapid and efficient deployment of complex bioinformatics pipelines to laboratories of all sizes, enabling reproducible results. The analyses that are supported in TREVA include: somatic and germline single-nucleotide and insertion/deletion variant calling, copy number analysis, and cohort-based analyses such as pathway and significantly mutated genes analyses. TREVA is flexible and easy to use, and can be customised by Linux-based extensions if required. TREVA can also be deployed on the cloud (cloud computing), enabling instant access without investment overheads for additional hardware. TREVA is available at http://bioinformatics.petermac.org/treva/.