Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs

DNA-DNA hybridization (DDH) is a widely applied wet-lab technique to obtain an estimate of the overall similarity between the genomes of two organisms. To base the species concept for prokaryotes ultimately on DDH was chosen by microbiologists as a pragmatic approach for deciding about the recognition of novel species, but also allowed a relatively high degree of standardization compared to other areas of taxonomy. However, DDH is tedious and error-prone and first and foremost cannot be used to incrementally establish a comparative database. Recent studies have shown that in-silico methods for the comparison of genome sequences can be used to replace DDH. Considering the ongoing rapid technological progress of sequencing methods, genome-based prokaryote taxonomy is coming into reach. However, calculating distances between genomes is dependent on multiple choices for software and program settings. We here provide an overview over the modifications that can be applied to distance methods based in high-scoring segment pairs (HSPs) or maximally unique matches (MUMs) and that need to be documented. General recommendations on determining HSPs using BLAST or other algorithms are also provided. As a reference implementation, we introduce the GGDC web server (http://ggdc.gbdp.org).     

Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison

The pragmatic species concept for Bacteria and Archaea is ultimately based on DNA-DNA hybridization (DDH). While enabling the taxonomist, in principle, to obtain an estimate of the overall similarity between the genomes of two strains, this technique is tedious and error-prone and cannot be used to incrementally build up a comparative database. Recent technological progress in the area of genome sequencing calls for bioinformatics methods to replace the wet-lab DDH by in-silico genome-to-genome comparison. Here we investigate state-of-the-art methods for inferring whole-genome distances in their ability to mimic DDH. Algorithms to efficiently determine high-scoring segment pairs or maximally unique matches perform well as a basis of inferring intergenomic distances. The examined distance functions, which are able to cope with heavily reduced genomes and repetitive sequence regions, outperform previously described ones regarding the correlation with and error ratios in emulating DDH. Simulation of incompletely sequenced genomes indicates that some distance formulas are very robust against missing fractions of genomic information. Digitally derived genome-to-genome distances show a better correlation with 16S rRNA gene sequence distances than DDH values. The future perspectives of genome-informed taxonomy are discussed, and the investigated methods are made available as a web service for genome-based species delineation.     

Flexibility in crosstalk between H2B ubiquitination and H3 methylation in vivo

Histone H2B ubiquitination is a dynamic modification that promotes methylation of histone H3K79 and H3K4. This crosstalk is important for the DNA damage response and has been implicated in cancer. Here, we show that in engineered yeast strains, ubiquitins tethered to every nucleosome promote H3K79 and H3K4 methylation from a proximal as well as a more distal site, but only if in a correct orientation. This plasticity indicates that the exact location of the attachment site, the native ubiquitin-lysine linkage and ubiquitination cycles are not critical for trans-histone crosstalk in vivo. The flexibility in crosstalk also indicates that other ubiquitination events may promote H3 methylation.     

Dissolved and particulate nutrient flux from three adjacent agricultural watersheds: A five-year study

Fluxes of dissolved and particulate nitrogen (N) and phosphorus(P) from three adjacent watersheds were quantified with ahigh-resolution sampling program over a five-year period. The watershedsvary by an order of magnitude in area (12,875, 7968 and 1206 ha), and inall three watersheds intensive agriculture comprises > 90% ofland. Annual fluxes of dissolved N and P per unit watershed area (exportcoefficients) varied 2X among watersheds, and patterns were notdirectly related to watershed size. Over the five-year period, meanannual flux of soluble reactive P (SRP) was 0.583 kg P ·ha^–1 · yr^–1 from the smallestwatershed and 0.295 kg P · ha^–1 ·yr^–1 from the intermediate-sized watershed, which hadthe lowest SRP flux. Mean annual flux of nitrate was 20.53 kg N ·ha^–1 · yr^–1 in the smallestwatershed and 44.77 kg N · ha^–1 ·yr^–1 in the intermediate-sized watershed, which had thehighest nitrate flux. As a consequence, the export ratio of dissolvedinorganic N to SRP varied from 80 (molar) in the smallest watershed to335 in the intermediate-sized watershed. Because most N was exported asnitrate, differences among watersheds in total N flux were similar tothose for nitrate. Hence, the total N:P export ratio was 42(molar) for the smallest watershed and 109 for the intermediate-sizedwatershed. In contrast, there were no clear differences among watershedsin the export coefficients of particulate N, P, or carbon, even though> 50% of total P was exported as particulate P in allwatersheds. All nutrient fractions were exported at higher rates in wetyears than in dry years, but precipitation-driven variability in exportcoefficients was greater for particulate fractions than for dissolvedfractions.Examination of hydrological regimes showed that, for all nutrientfractions, most export occurred during stormflow. However, theproportion of nitrate flux exported as baseflow was much greater thanthe proportion of SRP flux exported as baseflow, for all threewatersheds (25–37% of nitrate exported as baseflow vs.3–13% of SRP exported as baseflow). In addition, baseflowcomprised a greater proportion of total discharge in theintermediate-sized watershed (43.7% of total discharge) than theother two watersheds (29.3 and 30.1%). Thus, higher nitrateexport coefficients in the intermediate-sized watershed may haveresulted from the greater contribution of baseflow in this watershed.Other factors potentially contributing to higher nitrate exportcoefficients in this watershed may be a thicker layer of loess soils anda lower proportion of riparian forest than the other watersheds. Theamong-watershed variability in SRP concentrations and exportcoefficients remains largely unexplained, and might represent theminimum expected variation among similar agriculturalwatersheds.     

What is the ultimate fate of superoxide anion in vivo?

For three decades, oxidative stress and the role of reactive oxygen species in biology have been extensively studied. Recently, a new interest in these areas has emerged with the discovery of superoxide reductases, a family of familiar bacterial metalloenzymes whose heretofore unknown function has now been apparently revealed. In a series of experiments utilizing genetic, molecular biological, and biochemical methods, these enzymes have been shown to be physiologically competent at removing superoxide. The role of these enzymes and their biological relationship to the well-known superoxide dismutases is discussed.     

Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

Background

Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog.

Results

Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal.

Conclusions

Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.