299 research outputs found

    Gene order data from a model amphibian (Ambystoma): new perspectives on vertebrate genome structure and evolution

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    BACKGROUND: Because amphibians arise from a branch of the vertebrate evolutionary tree that is juxtaposed between fishes and amniotes, they provide important comparative perspective for reconstructing character changes that have occurred during vertebrate evolution. Here, we report the first comparative study of vertebrate genome structure that includes a representative amphibian. We used 491 transcribed sequences from a salamander (Ambystoma) genetic map and whole genome assemblies for human, mouse, rat, dog, chicken, zebrafish, and the freshwater pufferfish Tetraodon nigroviridis to compare gene orders and rearrangement rates. RESULTS: Ambystoma has experienced a rate of genome rearrangement that is substantially lower than mammalian species but similar to that of chicken and fish. Overall, we found greater conservation of genome structure between Ambystoma and tetrapod vertebrates, nevertheless, 57% of Ambystoma-fish orthologs are found in conserved syntenies of four or more genes. Comparisons between Ambystoma and amniotes reveal extensive conservation of segmental homology for 57% of the presumptive Ambystoma-amniote orthologs. CONCLUSION: Our analyses suggest relatively constant interchromosomal rearrangement rates from the euteleost ancestor to the origin of mammals and illustrate the utility of amphibian mapping data in establishing ancestral amniote and tetrapod gene orders. Comparisons between Ambystoma and amniotes reveal some of the key events that have structured the human genome since diversification of the ancestral amniote lineage

    Evaluating synteny for improved comparative studies

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    Motivation: Comparative genomics aims to understand the structure and function of genomes by translating knowledge gained about some genomes to the object of study. Early approaches used pairwise comparisons, but today researchers are attempting to leverage the larger potential of multi-way comparisons. Comparative genomics relies on the structuring of genomes into syntenic blocks: blocks of sequence that exhibit conserved features across the genomes. Syntenic blocs are required for complex computations to scale to the billions of nucleotides present in many genomes; they enable comparisons across broad ranges of genomes because they filter out much of the individual variability; they highlight candidate regions for in-depth studies; and they facilitate whole-genome comparisons through visualization tools. However, the concept of syntenic block remains loosely defined. Tools for the identification of syntenic blocks yield quite different results, thereby preventing a systematic assessment of the next steps in an analysis. Current tools do not include measurable quality objectives and thus cannot be benchmarked against themselves. Comparisons among tools have also been neglected—what few results are given use superficial measures unrelated to quality or consistency. Results: We present a theoretical model as well as an experimental basis for comparing syntenic blocks and thus also for improving or designing tools for the identification of syntenic blocks. We illustrate the application of the model and the measures by applying them to syntenic blocks produced by three different contemporary tools (DRIMM-Synteny, i-ADHoRe and Cyntenator) on a dataset of eight yeast genomes. Our findings highlight the need for a well founded, systematic approach to the decomposition of genomes into syntenic blocks. Our experiments demonstrate widely divergent results among these tools, throwing into question the robustness of the basic approach in comparative genomics. We have taken the first step towards a formal approach to the construction of syntenic blocks by developing a simple quality criterion based on sound evolutionary principles. Contact: [email protected]

    CYNTENATOR: Progressive Gene Order Alignment of 17 Vertebrate Genomes

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    Whole genome gene order evolution in higher eukaryotes was initially considered as a random process. Gene order conservation or conserved synteny was seen as a feature of common descent and did not imply the existence of functional constraints. This view had to be revised in the light of results from sequencing dozens of vertebrate genomes

    \u3ci\u3eAMBYSTOMA\u3c/i\u3e: PERSPECTIVES ON ADAPTATION AND THE EVOLUTION OF VERTEBRATE GENOMES

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    Tiger salamanders, and especially the Mexican axolotl (Ambystoma mexicanum), are important model organisms in biological research. This dissertation describes new genomic resources and scientific results that greatly extend the utility of tiger salamanders. With respect to new resources, this dissertation describes the development of expressed sequence tags and assembled contigs, a comparative genome map, a web-portal that makes genomic information freely available to the scientific community, and a computer program that compares structure features of organism genomes. With respect to new scientific results, this dissertation describes a quantitative trait locus that is associated with ecologically and evolutionarily relevant variation in developmental timing, the evolutionary history of the tiger salamander genome in relation to other vertebrate genomes, the likely origin of amniote sex chromosomes, and the identification of the Mexican axolotl sex-determining locus. This dissertation is concluded with a brief outline of future research directions that can extend from the works that are presented here

    Evaluating synteny for improved comparative studies

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    Motivation: Comparative genomics aims to understand the structure and function of genomes by translating knowledge gained about some genomes to the object of study. Early approaches used pairwise comparisons, but today researchers are attempting to leverage the larger potential of multi-way comparisons. Comparative genomics relies on the structuring of genomes into syntenic blocks: blocks of sequence that exhibit conserved features across the genomes. Syntenic blocs are required for complex computations to scale to the billions of nucleotides present in many genomes; they enable comparisons across broad ranges of genomes because they filter out much of the individual variability; they highlight candidate regions for in-depth studies; and they facilitate whole-genome comparisons through visualization tools. However, the concept of syntenic block remains loosely defined. Tools for the identification of syntenic blocks yield quite different results, thereby preventing a systematic assessment of the next steps in an analysis. Current tools do not include measurable quality objectives and thus cannot be benchmarked against themselves. Comparisons among tools have also been neglected-what few results are given use superficial measures unrelated to quality or consistency. Results: We present a theoretical model as well as an experimental basis for comparing syntenic blocks and thus also for improving or designing tools for the identification of syntenic blocks. We illustrate the application of the model and the measures by applying them to syntenic blocks produced by three different contemporary tools (DRIMM-Synteny, i-ADHoRe and Cyntenator) on a dataset of eight yeast genomes. Our findings highlight the need for a well founded, systematic approach to the decomposition of genomes into syntenic blocks. Our experiments demonstrate widely divergent results among these tools, throwing into question the robustness of the basic approach in comparative genomics. We have taken the first step towards a formal approach to the construction of syntenic blocks by developing a simple quality criterion based on sound evolutionary principles

    Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice

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    BACKGROUND: The identification of chromosomal homology will shed light on such mysteries of genome evolution as DNA duplication, rearrangement and loss. Several approaches have been developed to detect chromosomal homology based on gene synteny or colinearity. However, the previously reported implementations lack statistical inferences which are essential to reveal actual homologies. RESULTS: In this study, we present a statistical approach to detect homologous chromosomal segments based on gene colinearity. We implement this approach in a software package ColinearScan to detect putative colinear regions using a dynamic programming algorithm. Statistical models are proposed to estimate proper parameter values and evaluate the significance of putative homologous regions. Statistical inference, high computational efficiency and flexibility of input data type are three key features of our approach. CONCLUSION: We apply ColinearScan to the Arabidopsis and rice genomes to detect duplicated regions within each species and homologous fragments between these two species. We find many more homologous chromosomal segments in the rice genome than previously reported. We also find many small colinear segments between rice and Arabidopsis genomes

    MicroSyn: A user friendly tool for detection of microsynteny in a gene family

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    <p>Abstract</p> <p>Background</p> <p>The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootstrap values are frequently encountered in some nodes, suggesting low confidence or likely inappropriateness of placement of those members in those nodes.</p> <p>Results</p> <p>We introduce MicroSyn software as a means of detecting microsynteny in adjacent genomic regions surrounding genes in gene families. MicroSyn searches for conserved, flanking colinear homologous gene pairs between two genomic fragments to determine the relationship between two members in a gene family. The colinearity of homologous pairs is controlled by a statistical distance function. As a result, gene duplication history can be inferred from the output independent of gene sequences. MicroSyn was designed for both experienced and non-expert users with a user-friendly graphical-user interface. MicroSyn is available from: <url>http://fcsb.njau.edu.cn/microsyn/</url>.</p> <p>Conclusions</p> <p>Case studies of the microRNA167 genes in plants and Xyloglucan ndotransglycosylase/Hydrolase family in <it>Populus trichocarpa </it>were presented to show the utility of the software. The easy using of MicroSyn in these examples suggests that the software is an additional valuable means to address the problem intrinsic in the computational methods and sequence qualities themselves in gene family analysis.</p

    CHSMiner: a GUI tool to identify chromosomal homologous segments

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    <p>Abstract</p> <p>Background</p> <p>The identification of chromosomal homologous segments (CHS) within and between genomes is essential for comparative genomics. Various processes including insertion/deletion and inversion could cause the degeneration of CHSs.</p> <p>Results</p> <p>Here we present a Java software CHSMiner that detects CHSs based on shared gene content alone. It implements fast greedy search algorithm and rigorous statistical validation, and its friendly graphical interface allows interactive visualization of the results. We tested the software on both simulated and biological realistic data and compared its performance with similar existing software and data source.</p> <p>Conclusion</p> <p>CHSMiner is characterized by its integrated workflow, fast speed and convenient usage. It will be useful for both experimentalists and bioinformaticians interested in the structure and evolution of genomes.</p

    VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity

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