Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing View Full Text


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Article Info

DATE

2015-11-10

AUTHORS

Melissa C. Keinath, Vladimir A. Timoshevskiy, Nataliya Y. Timoshevskaya, Panagiotis A. Tsonis, S. Randal Voss, Jeramiah J. Smith

ABSTRACT

Vertebrates exhibit substantial diversity in genome size and some of the largest genomes exist in species that uniquely inform diverse areas of basic and biomedical research. For example, the salamander Ambystoma mexicanum (the Mexican axolotl) is a model organism for studies of regeneration, development and genome evolution, yet its genome is ~10× larger than the human genome. As part of a hierarchical approach toward improving genome resources for the species, we generated 600 Gb of shotgun sequence data and developed methods for sequencing individual laser-captured chromosomes. Based on these data, we estimate that the A. mexicanum genome is ~32 Gb. Notably, as much as 19 Gb of the A. mexicanum genome can potentially be considered single copy, which presumably reflects the evolutionary diversification of mobile elements that accumulated during an ancient episode of genome expansion. Chromosome-targeted sequencing permitted the development of assemblies within the constraints of modern computational platforms, allowed us to place 2062 genes on the two smallest A. mexicanum chromosomes and resolves key events in the history of vertebrate genome evolution. Our analyses show that the capture and sequencing of individual chromosomes is likely to provide valuable information for the systematic sequencing, assembly and scaffolding of large genomes. More... »

PAGES

16413

References to SciGraph publications

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/srep16413

    DOI

    http://dx.doi.org/10.1038/srep16413

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1021432877

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/26553646


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    66 example
    67 expansion
    68 genes
    69 genome
    70 genome evolution
    71 genome expansion
    72 genome resources
    73 genome size
    74 hierarchical approach
    75 history
    76 human genome
    77 individual chromosomes
    78 information
    79 initial characterization
    80 key events
    81 large genomes
    82 method
    83 mexicanum
    84 mobile elements
    85 model organisms
    86 modern computational platforms
    87 organisms
    88 part
    89 platform
    90 regeneration
    91 research
    92 resources
    93 salamander Ambystoma mexicanum
    94 scaffolding
    95 sequence data
    96 sequencing
    97 shotgun
    98 shotgun sequence data
    99 single copy
    100 size
    101 species
    102 study
    103 study of regeneration
    104 substantial diversity
    105 systematic sequencing
    106 valuable information
    107 vertebrate genome evolution
    108 vertebrates
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