Species delimitation of three species within the Russula subgenus Compacta in Korea: R. eccentrica,R. nigricans,and R. subnigricans

Distinguishing individual Russula species can be very difficult due to extensive phenotypic plasticity and obscure morphological and anatomical discontinuities. In this study, we use the internal transcribed spacer (ITS) and 28S nuclear ribosomal large subunit (LSU) markers to identify and study the genetic diversity of species in the Russula subgenus Compacta in Korea. We focus on two morphologically similar species that are often misidentified for each other: R. nigricans and R. subnigricans. Based on molecular phylogenetic analyses, we identify three subgroups of R. nigricans, with two from Asia and one from Europe/North America. Surprisingly, we find Korean R. subnigricans are more closely related to R. eccentrica from North America than the type specimen of R. subnigricans from Japan. These molecular data, along with habitat data, reveal that Korean R. subnigricans had previously been misclassified and should now be recognized as R. eccentrica. Both ITS and LSU exhibit high interspecific and low intraspecific variation for R. eccentrica, R. nigricans, and R. subnigricans. These markers provide enough resolutional power to differentiate these species and uncover phylogeographic structure, and will be powerful tools for future ecological studies of Russula.     

Nearline acquisition and processing of liquid chromatography-tandem mass spectrometry data

Liquid chromatography–mass spectrometry (LC–MS) is a commonly used analytical platform for non-targeted metabolite profiling experiments. Although data acquisition, processing and statistical analyses are almost routine in such experiments, further annotation and subsequent identification of chemical compounds are not. For identification, tandem mass spectra provide valuable information towards the structure of chemical compounds. These are typically acquired online, in data-dependent mode, or offline, using handcrafted acquisition methods and manually extracted from raw data. Here, we present several methods to fast-track and improve both the acquisition and processing of LC–MS/MS data. Our nearly online (nearline) data-dependent tandem MS strategy creates a minimal set of LC–MS/MS acquisition methods for relevant features revealed by a preceding non-targeted profiling experiment. Using different filtering criteria, such as intensity or ion type, the acquisition of irrelevant spectra is minimized. Afterwards, LC–MS/MS raw data are processed with feature detection and grouping algorithms. The extracted tandem mass spectra can be used for both library search and de-novo identification methods. The algorithms are implemented in the R package MetShot and support the export to Bruker, Agilent or Waters QTOF instruments and the vendor-independent TraML standard. We evaluate the performance of our workflow on a Bruker micrOTOF-Q by comparison of automatically acquired and extracted tandem mass spectra obtained from a mixture of natural product standards against manually extracted reference spectra. Using Arabidopsis thaliana wild-type and biosynthetic gene knockout plants, we characterize the metabolic products of a biosynthetic pathway and demonstrate the integration of our approach into a typical non-targeted metabolite profiling workflow.     

PedGenie: meta genetic association testing in mixed family and case-control designs

Background

With the increased availability of high throughput data, such as DNA microarray data, researchers are capable of producing large amounts of biological data. During the analysis of such data often there is the need to further explore the similarity of genes not only with respect to their expression, but also with respect to their functional annotation which can be obtained from Gene Ontology (GO).

Results

We present the freely available software package GOSim, which allows to calculate the functional similarity of genes based on various information theoretic similarity concepts for GO terms. GOSim extends existing tools by providing additional lately developed functional similarity measures for genes. These can e.g. be used to cluster genes according to their biological function. Vice versa, they can also be used to evaluate the homogeneity of a given grouping of genes with respect to their GO annotation. GOSim hence provides the researcher with a flexible and powerful tool to combine knowledge stored in GO with experimental data. It can be seen as complementary to other tools that, for instance, search for significantly overrepresented GO terms within a given group of genes.

Conclusion

GOSim is implemented as a package for the statistical computing environment R and is distributed under GPL within the CRAN project.     

dendroTools: R package for studying linear and nonlinear responses between tree-rings and daily environmental data

We introduce in this paper the dendroTools R package for studying the statistical relationships between tree-ring parameters and daily environmental data. The core function of the package is daily_response(), which works by sliding a moving window through daily environmental data and calculating statistical metrics with one or more tree ring proxies. Possible metrics are correlation coefficient, coefficient of determination and adjusted coefficient of determination. In addition to linear regression, it is possible to use a nonlinear artificial neural network with the Bayesian regularization training algorithm (brnn). dendroTools provides the opportunity to use daily climate data and robust nonlinear functions for the analysis of climate-growth relationships. Models should thus be better adapted to the real (continuous) growth of trees and should gain in predictive capabilities. The dendroTools R package is freely available in the CRAN repository. The functionality of the package is demonstrated on two examples, one using a mean vessel area (MVA) chronology and one a traditional tree-ring width (TRW).     

A normalization strategy for comparing tag count data

Background

High-throughput sequencing, such as ribonucleic acid sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) analyses, enables various features of organisms to be compared through tag counts. Recent studies have demonstrated that the normalization step for RNA-seq data is critical for a more accurate subsequent analysis of differential gene expression. Development of a more robust normalization method is desirable for identifying the true difference in tag count data.

Results

We describe a strategy for normalizing tag count data, focusing on RNA-seq. The key concept is to remove data assigned as potential differentially expressed genes (DEGs) before calculating the normalization factor. Several R packages for identifying DEGs are currently available, and each package uses its own normalization method and gene ranking algorithm. We compared a total of eight package combinations: four R packages (edgeR, DESeq, baySeq, and NBPSeq) with their default normalization settings and with our normalization strategy. Many synthetic datasets under various scenarios were evaluated on the basis of the area under the curve (AUC) as a measure for both sensitivity and specificity. We found that packages using our strategy in the data normalization step overall performed well. This result was also observed for a real experimental dataset.

Conclusion

Our results showed that the elimination of potential DEGs is essential for more accurate normalization of RNA-seq data. The concept of this normalization strategy can widely be applied to other types of tag count data and to microarray data.     

Efficient Bayesian analysis of occupancy models with logit link functions

Occupancy models (Ecology, 2002; 83: 2248) were developed to infer the probability that a species under investigation occupies a site. Bayesian analysis of these models can be undertaken using statistical packages such as WinBUGS, OpenBUGS, JAGS, and more recently Stan, however, since these packages were not developed specifically to fit occupancy models, one often experiences long run times when undertaking an analysis. Bayesian spatial single‐season occupancy models can also be fit using the R package stocc. The approach assumes that the detection and occupancy regression effects are modeled using probit link functions. The use of the logistic link function, however, is algebraically more tractable and allows one to easily interpret the coefficient effects of an estimated model by using odds ratios, which is not easily done for a probit link function for models that do not include spatial random effects. We develop a Gibbs sampler to obtain posterior samples from the posterior distribution of the parameters of various occupancy models (nonspatial and spatial) when logit link functions are used to model the regression effects of the detection and occupancy processes. We apply our methods to data extracted from the 2nd Southern African Bird Atlas Project to produce a species distribution map of the Cape weaver (Ploceus capensis) and helmeted guineafowl (Numida meleagris) for South Africa. We found that the Gibbs sampling algorithm developed produces posterior samples that are identical to those obtained when using JAGS and Stan and that in certain cases the posterior chains mix much faster than those obtained when using JAGS, stocc, and Stan. Our algorithms are implemented in the R package, Rcppocc. The software is freely available and stored on GitHub ( https://github.com/AllanClark/Rcppocc ).     

i2dash: Creation of Flexible,Interactive, and Web-based Dashboards for Visualization of Omics Data

Data visualization and interactive data exploration are important aspects of illustrating complex concepts and results from analyses of omics data. A suitable visualization has to be intuitive and accessible. Web-based dashboards have become popular tools for the arrangement, consolidation, and display of such visualizations. However, the combination of automated data processing pipelines handling omics data and dynamically generated, interactive dashboards is poorly solved. Here, we present i2dash, an R package intended to encapsulate functionality for the programmatic creation of customized dashboards. It supports interactive and responsive (linked) visualizations across a set of predefined graphical layouts. i2dash addresses the needs of data analysts/software developers for a tool that is compatible and attachable to any R-based analysis pipeline, thereby fostering the separation of data visualization on one hand and data analysis tasks on the other hand. In addition, the generic design of i2dash enables the development of modular extensions for specific needs. As a proof of principle, we provide an extension of i2dash optimized for single-cell RNA sequencing analysis, supporting the creation of dashboards for the visualization needs of such experiments. Equipped with these features, i2dash is suitable for extensive use in large-scale sequencing/bioinformatics facilities. Along this line, we provide i2dash as a containerized solution, enabling a straightforward large-scale deployment and sharing of dashboards using cloud services. i2dash is freely available via the R package archive CRAN (https://CRAN.R-project.org/package=i2dash).     

Identification of novel genes for bitter taste receptors in sheep (Ovis aries)

Genetic studies on taste sensitivity, and bitter taste receptors (T2R) in particular, are an essential tool to understand ingestive behavior and its relation to variations of nutritional status occurring in ruminants. In the present study, we conducted a data-mining search to identify T2R candidates in sheep by comparison with the described T2R in cattle and using recently available ovine genome. In sheep, we identified eight orthologs of cattle genes: T2R16, T2R10B, T2R12, T2R3, T2R4, T2R67, T2R13 and T2R5. The in silico predicted genes were then confirmed by PCR and DNA sequencing. The sequencing results showed a 99% to 100% similarity with the in silico predicted sequence. Moreover, we address the chromosomal distribution and compare, in homology and phylogenetic terms, the obtained genes with the known T2R in human, mouse, dog, cattle, horse and pig. The eight novel genes identified map either to ovine chromosome 3 or 4. The phylogenetic data suggest a clustering by receptor type rather than by species for some of the receptors. From the species analyzed, we observed a clear proximity between the two ruminant species, sheep and cattle, in contrast with lower similarities obtained for the comparison of sheep with other mammals. Although further studies are needed to identify the complete T2R repertoire in domestic sheep, our data represent a first step for genetic studies on this field.     

Production of wheat-rye substitution lines and identification of chromosome composition of karyotypes using C-banding, GISH, and SSR markers

Based on the cross (Triticum aestivum L. × Secale cereale L.) × T. aestivum L., wheat-rye substitution lines (2n = 42) were produced with karyotypes containing, instead of a pair of homologous wheat chromosomes, a homeologous pair of rye chromosomes. The chromosome composition of these lines was described by GISH and C-banding methods, and SSR analysis. The results of genomic in situ hybridization demonstrated that karyotype of these lines included one pair of rye chromosomes each and lacked wheat-rye translocations. C-banding and SSR markers were used to identify rye chromosomes and determine the wheat chromosomes at which the substitution occurred. The lines were designated 1R(1D), 2R(2D)₂, 2R(2D)₃, 3R(3B), 6R(6A)₂. The chromosome composition of lines 1R(1A), 2R(W)₁, 5R(W), 5R(5A), and 6R(W)₁, which were earlier obtained according to the same scheme for crossing, was characterized using methods of telocentric analysis, GISH, C-banding, and SSR analysis. These lines were identified as 1R(1A), 2R(2D)₁, 5R(5D), 5R(5A), and 6R(6A)₁, C-banding of chromosomes belonging to line 1R(1A) revealed the presence of two translocated chromosomes (3DS.3DL-del. and 4AL.W) during simultaneous amplification of SSR markers located on 3DL and 4AS arms. The “combined” long arm of the newly derived chromosome 4A is assumed to be formed from the long arm of chromosome 4AS itself and a deleted segment 3DL. All examined lines are cytologically stable, except for 3R(3B), which does not affect the stability of rye 3R chromosome transfer. Chromosome identification and classification of the lines will permit them to be models for genetic studies that can be used thereafter as promising “secondary gene pools” for the purpose of plant breeding.     

Morphological descriptions of the eggcases of skates (Rajidae) from the central-western Mediterranean,with notes on their distribution

Eggcases of eight rajiform skates (Dipturus nidarosiensis, D. oxyrinchus, Leucoraja melitensis, Raja asterias, R. brachyura, R. clavata, R. miraletus and R. polystigma) present in the central-western Mediterranean are described, based on specimens obtained from fishery surveys. Eggcase features such as dimensions, horns and apron lengths, and presence/absence of lateral keels were crucial to discriminate the eggcases of the various species. Morphological and morphometric data, confirmed by the multivariate analysis, indicated that the eggcase of R. miraletus and L. melitensis were distinct from those of the other species for being unkeeled. Within the species having keeled eggcases, those of the genus Dipturus and R. brachyura were discriminated from the remaining group by having the largest dimensions and aprons. Sandy bottoms (<100–150 m depth) were identified as egg-laying sites (i.e. sites with females bearing eggcases in uteri) for many species belonging to genus Raja Raja asterias, R. brachyura, R. miraletus and R. polystigma). The finding of R. asterias and R. miraletus carrying eggcases yearly on the same sites, seems to confirm the theory that many rajid species demonstrate site fidelity, returning to the same depositional area on an annual basis. Some remarks on reproductive biology of these skates are also provided. The eggcase identification key reported here represents the first for the Mediterranean and may be useful, in the future, to identify egg-laying grounds of skates with a nonlethal method.     

Natural hybridization and introgression among sympatrically distributed Rhododendron species in Guizhou,China

Natural hybridizations occur among Rhododendron delavayi, R. decorum and R. irroratum, however, there was little study that had addressed the interbreeding behaviors when the three species grew in the same geographic areas. In this study, 37 accessions, containing the three species and the putative hybrids, were obtained from Baili Rhododendron Nature Reserve, Guizhou, China. Examinations of hybridization patterns with AFLP markers have led to a total of 107 diagnostic DNA fragments, which were analyzed with Principal Co-ordinate, Structure and NewHybirds analyses. The data confirmed that the existence of hybrids originated from the interbreeding between R. delavayi and R. irroratum in Baili Rhododendron Nature Reserve. R. decorum did not appear to be involved in the hybridization. Furthermore, most hybrids detected were a result of backcrossing, indicating that this hybrid differed from F1 dominant hybrids between R. delavayi and R. irroratum found in previous studies.     

pRRophetic: An R Package for Prediction of Clinical Chemotherapeutic Response from Tumor Gene Expression Levels

We recently described a methodology that reliably predicted chemotherapeutic response in multiple independent clinical trials. The method worked by building statistical models from gene expression and drug sensitivity data in a very large panel of cancer cell lines, then applying these models to gene expression data from primary tumor biopsies. Here, to facilitate the development and adoption of this methodology we have created an R package called pRRophetic. This also extends the previously described pipeline, allowing prediction of clinical drug response for many cancer drugs in a user-friendly R environment. We have developed several other important use cases; as an example, we have shown that prediction of bortezomib sensitivity in multiple myeloma may be improved by training models on a large set of neoplastic hematological cell lines. We have also shown that the package facilitates model development and prediction using several different classes of data.     

New features in the dendroTools R package: Bootstrapped and partial correlation coefficients for monthly and daily climate data

Climate-growth relationships are usually analysed using monthly climate data. The dendroTools R package also provides methodological approaches that enable climate-growth analysis for daily climate data. Such analysis reveals more complete climate signal patterns. In this article, new functions of the dendroTools R package are presented. Partial correlation coefficients are now implemented and can be used to calculate the strength of a linear relationship between two variables, while controlling for a third variable. Bootstrapped correlations can then be used to provide insights into the confidence intervals of statistical estimates. The calculation of partial and bootstrapped correlations is available for daily and monthly data. Finally, data transformation, S3 generic plotting and summary functions are also presented here.     

The effectiveness of molecular markers for the identification of Lr28, Lr35, and Lr47 genes in common wheat

The effectiveness of molecular markers for the identification of leaf rust resistance genes Lr28, Lr35 and Lr47 transferred to common wheat from Ae. speltoides was assessed using samples of Triticum spp. and Aegilops spp. The markers Sr39F2/R3, BCD260F1/35R2 of the gene Lr35 and PS10 of the Lr47 gene were characterized by high efficiency and were revealed in the lines of common wheat containing these genes, and samples of Ae. speltoides species, the donor of these genes. The marker SCS421 of the Lr28 gene and the markers Sr39#22r, Sr39#50s, BE500705 of the Lr35/Sr39 genes turned out to be less specific. The marker SCS421 was amplified in the samples of the T. timopheevii species, line KS90WRC010 (Lr41), the cultivar of common wheat Pamyati Maystrenko, obtained using synthetic hexaploid T. timopheevii × Ae. tauschii and introgressive lines obtained using Ae. speltoides. The marker BE500705, which indicates the absence of the Lr35/Sr39 genes, was not revealed in the lines TcLr35 and MqSr39, in Ae. speltoides, Ae. tauschii and T. boeoticum (kk-61034, 61038). Analysis of the nucleotide sequences of amplification products obtained with the markers SCS421 and Sr39#22r indicated their low homology with TcLr28 and TcLr35. Using molecular markers, a different distribution of the Lr28 (77%), Lr35 (100%) and Lr47 (15%) genes in 13 studied samples of Ae. speltoides was shown. In introgressive lines derived from Ae. speltoides, contemporary Russian cultivars of common wheat and triticale the Lr28, Lr35, Lr47 genes were not revealed.     

BactMAP: An R package for integrating,analyzing and visualizing bacterial microscopy data

High-throughput analyses of single-cell microscopy data are a critical tool within the field of bacterial cell biology. Several programs have been developed to specifically segment bacterial cells from phase-contrast images. Together with spot and object detection algorithms, these programs offer powerful approaches to quantify observations from microscopy data, ranging from cell-to-cell genealogy to localization and movement of proteins. Most segmentation programs contain specific post-processing and plotting options, but these options vary between programs and possibilities to optimize or alter the outputs are often limited. Therefore, we developed BactMAP (Bacterial toolbox for Microscopy Analysis & Plotting), a command-line based R package that allows researchers to transform cell segmentation and spot detection data generated by different programs into various plots. Furthermore, BactMAP makes it possible to perform custom analyses and change the layout of the output. Because BactMAP works independently of segmentation and detection programs, inputs from different sources can be compared within the same analysis pipeline. BactMAP complies with standard practice in R which enables the use of advanced statistical analysis tools, and its graphic output is compatible with ggplot2, enabling adjustable plot graphics in every operating system. User feedback will be used to create a fully automated Graphical User Interface version of BactMAP in the future. Using BactMAP, we visualize key cell cycle parameters in Bacillus subtilis and Staphylococcus aureus, and demonstrate that the DNA replication forks in Streptococcus pneumoniae dissociate and associate before splitting of the cell, after the Z-ring is formed at the new quarter positions. BactMAP is available from https://veeninglab.com/bactmap .     

Genetic diversity of rhizobia nodulating common bean (Phaseolus vulgaris L.) in the Central Black Sea Region of Turkey

We have analyzed 30 rhizobial isolates obtained from common bean (Phaseolus vulgaris L.) root nodules grown in the Middle Blacksea Region of Turkey, using ARDRA and nucleotide sequence data. ARDRA analysis with enzymes CfoI, HinfI, NdeII, MspI and PstI revealed three patterns. Based on sequence data from 16S rDNA, the patterns were identified as, Rhizobium leguminosarum bv. phaseoli (n = 16), R. etli bv. phaseoli (n = 8) and R. phaseoli (n = 6). On the other hand, nucleotide sequence phylogenies of housekeeping genes (recA, atpD and glnII) selected to confirm the 16S rDNA phylogeny revealed different evolutionary relationships. These results suggested the possibility of lateral transfers of these genes amongst different rhizobial species (including R. leguminosarum, R. etli and R. phaseoli) sharing the same ecological niche (nodulating P. vulgaris) which also indicates that there may be no true genetic barier among these species. Phylogenetic analysis based on DNA sequence data from the nodA and nifH genes showed that all rhizobial species obtained in this study were carrying nodA and nifH haplotypes which were the same or similar to those of CFN42 (R. etli type strain), suggesting a further support for the lateral transfer of CFN42 Sym plasmid, p42, amongst Turkish common bean nodulating rhizobial isolates.