Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress

Rotational-invariant model of the states with K? = 1+ and their contribution to the scissors mode

Within the Random-Phase Approximation the method of self-consistent determination of the isoscalar and isovector effective separable interactions restoring a broken symmetry of the deformed mean-field is given. The method allows to treat more rigorously without free parameters the properties of the scissors mode and is used to develop the rotational invariant microscopic model of the states with K? = 1+. The spurious state separates out and has zero energy. An important consequence of this separation is the fragmentation of the scissors mode and the collectivization of the low-lying 1+ states. In addition to the isoscalar restoring interactions the consideration of the isovector restoring forces in calculations causes the splitting of the states with large B(M1) strength at low energy. The model contains a single parameter of isovector spin-spin interactions and it allows one to describe satisfactorily the fragmentation of the scissors mode and the dependence of the summed B(M1) strength on ?2 and A in deformed nuclei

Capturing Long-Term Dependencies for Protein Secondary Structure Prediction

Abstract. Bidirectional recurrent neural network(BRNN) is a noncausal system that captures both upstream and downstream information for protein secondary structure prediction. Due to the problem of vanishing gradients, the BRNN can not learn remote information efficiently. To limit this problem, we propose segmented memory recurrent neural network(SMRNN) and use SMRNNs to replace the standard RNNs in BRNN. The resulting architecture is called bidirectional segmented-memory recurrent neural network(BSMRNN). Our experiment with BSMRNN for protein secondary structure prediction on the RS126 set indicates improvement in the prediction accuracy.

Gene and repetitive sequence annotation in the Triticeae

The Triticeae tribe contains some of the world’s most important agricultural crops (wheat, barley and rye) and is perhaps, one of the most challenging for genome annotation because Triticeae genomes are primarily composed of repetitive sequences. Further complicating the challenge is the polyploidy found in wheat and particularly in the hexaploid bread wheat genome. Genomic sequence data are available for the Triticeae in the form of large collections of Expressed Sequence Tags (>1.5 million) and an increasing number of bacterial artificial chromosome clone sequences. Given that high repetitive sequence content in the Triticeae confounds annotation of protein-coding genes, repetitive sequences have been identified, annotated, and collated into public databases. Protein coding genes in the Triticeae are structurally annotated using a combination of ab initio gene finders and experimental evidence. Functional annotation of protein coding genes involves assessment of sequence similarity to known proteins, expression evidence, and the presence of domain and motifs. Annotation methods and tools for Triticeae genomic sequences have been adapted from existing plant genome annotation projects and were designed to allow for flexibility of single sequence annotation while allowing a whole community annotation effort to be developed. With the availability of an increasing number of annotated grass genomes, comparative genomics can be exploited to accelerate and enhance the quality of Triticeae sequences annotation. This chapter provides a brief overview of the Triticeae genomes features that are challenging for genome annotation and describes the resources and methods available for sequence annotation with a particular emphasis on problems caused by the repetitive fraction of these genomes