96 research outputs found

    Complex selection on 5' splice sites in intron-rich organisms

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    In contrast to the typically streamlined genomes of prokaryotes, many eukaryotic genomes are riddled with long intergenic regions, spliceosomal introns, and repetitive elements. What explains the persistence of these and other seemingly suboptimal structures? There are three general hypotheses: (1) the structures in question are not actually suboptimal but optimal, being favored by selection, for unknown reasons; (2) the structures are not suboptimal, but of (essentially) equal fitness to 'optimal' ones; or (3) the structures are truly suboptimal, but selection is too weak to systematically eliminate them. The 5' splice sites of introns offer a rare opportunity to directly test these hypotheses. Intron-poor species show a clear consensus splice site; most introns begin with the same six nucleotide sequence (typically GTAAGT or GTATGT), indicating efficient selection for this consensus sequence. In contrast, intron-rich species have much less pronounced boundary consensus sequences, and only small minorities of introns in intron-rich species share the same boundary sequence. We studied rates of evolutionary change of 5' splice sites in three groups of closely related intron-rich species--three primates, five Drosophila species, and four Cryptococcus fungi. Surprisingly, the results indicate that changes from consensus-to-variant nucleotides are generally disfavored by selection, but that changes from variant to consensus are neither favored nor disfavored. This evolutionary pattern is consistent with selective differences across introns, for instance, due to compensatory changes at other sites within the gene, which compensate for the otherwise suboptimal consensus-to-variant changes in splice boundaries

    Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires

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    Background The dieback epidemic decimating common ash (Fraxinus excelsior) in Europe is caused by the invasive fungus Hymenoscyphus fraxineus. In this study we analyzed the genomes of H. fraxineus and H. albidus, its native but, now essentially displaced, non-pathogenic sister species, and compared them with several other members of Helotiales. The focus of the analyses was to identify signals in the genome that may explain the rapid establishment of H. fraxineus and displacement of H. albidus. Results The genomes of H. fraxineus and H. albidus showed a high level of synteny and identity. The assembly of H. fraxineus is 13 Mb longer than that of H. albidus', most of this difference can be attributed to higher dispersed repeat content (i.e. transposable elements [TEs]) in H. fraxineus. In general, TE families in H. fraxineus showed more signals of repeat-induced point mutations (RIP) than in H. albidus, especially in Long-terminal repeat (LTR)/Copia and LTR/Gypsy elements. Comparing gene family expansions and 1:1 orthologs, relatively few genes show signs of positive selection between species. However, several of those did appeared to be associated with secondary metabolite genes families, including gene families containing two of the genes in the H. fraxineus-specific, hymenosetin biosynthetic gene cluster (BGC). Conclusion The genomes of H. fraxineus and H. albidus show a high degree of synteny, and are rich in both TEs and BGCs, but the genomic signatures also indicated that H. albidus may be less well equipped to adapt and maintain its ecological niche in a rapidly changing environment

    Distributed pattern mining and data publication in life sciences using big data technologies

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    Evolutionary genomics : statistical and computational methods

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    This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

    Algorithms for the analysis of molecular sequences

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    Comparative Genomic Characterization of the Multimammate Mouse Mastomys coucha.

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    Mastomys are the most widespread African rodent and carriers of various diseases such as the plague or Lassa virus. In addition, mastomys have rapidly gained a large number of mammary glands. Here, we generated a genome, variome, and transcriptomes for Mastomys coucha. As mastomys diverged at similar times from mouse and rat, we demonstrate their utility as a comparative genomic tool for these commonly used animal models. Furthermore, we identified over 500 mastomys accelerated regions, often residing near important mammary developmental genes or within their exons leading to protein sequence changes. Functional characterization of a noncoding mastomys accelerated region, located in the HoxD locus, showed enhancer activity in mouse developing mammary glands. Combined, our results provide genomic resources for mastomys and highlight their potential both as a comparative genomic tool and for the identification of mammary gland number determining factors

    FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes

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    FungiDB (fungidb.org) is a free online resource for data mining and functional genomics analysis for fungal and oomycete species. FungiDB is part of the Eukaryotic Pathogen Genomics Database Resource (EuPathDB, eupathdb.org) platform that integrates genomic, transcriptomic, proteomic, and phenotypic datasets, and other types of data for pathogenic and non-pathogenic, free-living and parasitic organisms. FungiDB is one of the largest EuPathDB databases containing nearly 100 genomes obtained from GenBank, AspGD, The Broad Institute, JGI, Ensembl, and other sources. FungiDB offers a user-friendly web interface with embedded bioinformatics tools that support custom in silico experiments that leverage FungiDB-integrated data. In addition, a Galaxy-based workspace enables users to generate custom pipelines for large scale data analysis (e.g. RNA-Seq, variant calling, etc.). This review provides an introduction to the FungiDB resources and focuses on available features, tools and queries and how they can be used to mine data across a diverse range of integrated FungiDB datasets and records
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