RNA-clique: a method for computing genetic distances from RNA-seq data.

Background: Although RNA-seq data are traditionally used for quantifying gene expression levels, the same data could be useful in an integrated approach to compute genetic distances as well. Challenges to using mRNA sequences for computing genetic distances include the relatively high conservation of coding sequences and the presence of paralogous and, in some species, homeologous genes.

Results: We developed a new computational method, RNA-clique, for calculating genetic distances using assembled RNA-seq data and assessed the efficacy of the method using biological and simulated data.

CURatio: Genome-wide phylogenomic analysis method using ratios of total branch lengths.

Evolutionary hypotheses provide important underpinnings of biological and medical sciences, and comprehensive, genome-wide understanding of evolutionary relationships among organisms are needed to test and refine such hypotheses. Theory and empirical evidence clearly indicate that phylogenies (trees) of different genes (loci) should not display precisely matching topologies. The main reason for such phylogenetic incongruence is reticulated evolutionary history of most species due to meiotic sexual recombination in eukaryotes, or horizontal transfers of genetic material in prokaryotes.

Swainsonine Biosynthesis Genes in Diverse Symbiotic and Pathogenic Fungi.

Swainsonine-a cytotoxic fungal alkaloid and a potential cancer therapy drug-is produced by the insect pathogen and plant symbiont , the clover pathogen , locoweed symbionts belonging to sect. , and a recently discovered morning glory symbiont belonging to order Chaetothyriales. Genome sequence analyses revealed that these fungi share orthologous gene clusters, designated "," which included a multifunctional gene comprising predicted adenylylation and acyltransferase domains with their associated thiolation domains, a β-ketoacyl synthase domain, and two reductase domains.

Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016 : Cadiz, KY, USA. 8-10 April 2016.

I1 Proceedings of the Fifteenth Annual UT- KBRIN Bioinformatics Summit 2016 Eric C. Rouchka, Julia H. Chariker, Benjamin J.

Host Tissue Environment Directs Activities of an Epichloë Endophyte, While It Induces Systemic Hormone and Defense Responses in Its Native Perennial Ryegrass Host.

Increased resilience of pasture grasses mediated by fungal Epichloë endophytes is crucial to pastoral industries. The underlying mechanisms are only partially understood and likely involve very different activities of the endophyte in different plant tissues and responses of the plant to these. We analyzed the transcriptomes of Epichloë festucae and its host, Lolium perenne, in host tissues of different function and developmental stages.

A Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction.

Background: Colletotrichum graminicola is a hemibiotrophic fungal pathogen that causes maize anthracnose disease. It progresses through three recognizable phases of pathogenic development in planta: melanized appressoria on the host surface prior to penetration; biotrophy, characterized by intracellular colonization of living host cells; and necrotrophy, characterized by host cell death and symptom development. A "Mixed Effects" Generalized Linear Model (GLM) was developed and applied to an existing Illumina transcriptome dataset, substantially increasing the statistical power of the analysis of C.

Genetics, genomics and evolution of ergot alkaloid diversity.

The ergot alkaloid biosynthesis system has become an excellent model to study evolutionary diversification of specialized (secondary) metabolites. This is a very diverse class of alkaloids with various neurotropic activities, produced by fungi in several orders of the phylum Ascomycota, including plant pathogens and protective plant symbionts in the family Clavicipitaceae. Results of comparative genomics and phylogenomic analyses reveal multiple examples of three evolutionary processes that have generated ergot-alkaloid diversity: gene gains, gene losses, and gene sequence changes that have led to altered substrates or product specificities of the enzymes that they encode (neofunctionalization).

Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci.

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some-including the infamous ergot alkaloids-have potent effects on mammals.

A linear-time algorithm for finding a maximum-length ORF in a splice graph.

We present a linear-time, deterministic algorithm for finding a longest Open Reading Frame (ORF) in an alternatively spliced gene represented by a splice graph. Finding protein-encoding regions is a fundamental problem in genomic and transcriptomic analysis, and in some circumstances long ORFs can provide good predictions of such regions. Splice graphs are a common way of compactly representing what may be exponentially many alternative splicings of a sequence.

Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses.

Colletotrichum species are fungal pathogens that devastate crop plants worldwide. Host infection involves the differentiation of specialized cell types that are associated with penetration, growth inside living host cells (biotrophy) and tissue destruction (necrotrophy). We report here genome and transcriptome analyses of Colletotrichum higginsianum infecting Arabidopsis thaliana and Colletotrichum graminicola infecting maize.

Statistical phylogenetic tree analysis using differences of means.

We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by two input alignments, instead of comparing point estimations of trees. This statistical approach can be applied to gene tree analysis for example, detecting unusual events in genome evolution such as horizontal gene transfer and reshuffling.

Simulation study of the coil-globule transition of a polymer in solvent.

Molecular dynamics simulations are used to study the coil-globule transition for a system composed of a bead-spring polymer immersed in an explicitly modeled solvent. Two different versions of the model are used, which are differentiated by the nature of monomer-solvent, solvent-solvent, and nonbonded monomer-monomer interactions. For each case, a model parameter lambda determines the degree of hydrophobicity of the monomers by controlling the degree of energy mismatch between the monomers and solvent particles.

Preconditioning attenuates the shortening of recovery during coronary occlusion in isolated rabbit hearts with D-sotalol-induced long QT intervals.

The effects of 20-min ligations of the anterior branch of the left coronary artery were studied in Langendorff-perfused rabbit hearts with 92 microM D-sotalol added to the perfusate to induce long QT intervals and triggered arrhythmias. Epicardial electrograms, a left ventricular endocardial monophasic action potential, and simulated X and Y lead electrocardiograms were used to characterize ventricular conduction and recovery. In contrast to previous work showing that global ischemia eliminated triggered activity, coronary occlusion did not alter its mean incidence.