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  • Computational finishing of large sequence contigs reveals interspersed nested repeats and gene islands in the rf1-associated region of maize.

    Author(s) : Kronmiller, B. A.Wise, R. P.

    Author Affiliation : Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011-1020, USA.

    Author Email : rpwise@iastate.edu

    Journal article : Plant Physiology 2009 Vol.151 No.2 pp.483-495 ref.many

    Abstract : The architecture of grass genomesgenomesSubject Category: Miscellaneous
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    varies on multiple levels. Large long terminal repeat retrotransposon clusters occupy significant portions of the intergenic regions, and islands of protein-encoding genes are interspersed among the repeat clusters. Hence, advanced assembly techniques are required to obtain completely finished genomes as well as to investigate gene and transposable element distributions. To characterize the organization and distribution of repeat clusters and gene islands across large grass genomes, we present 961- and 594-kb contiguous sequence contigs associated with the rf1 (for restorer of fertility1) locus in the near-centromeric region of maizemaizeSubject Category: Commodities and Products
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    (Zea mayszea maysSubject Category: Organism Names
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    ) chromosome 3. We present two methods for computational finishing of highly repetitive bacterial artificial chromosome clones that have proved successful to close all sequence gaps caused by transposable element insertions. Sixteen repeat clusters were observed, ranging in length from 23 to 155 kb. These repeat clusters are almost exclusively long terminal repeat retrotransposons, of which the paleontology of insertion varies throughout the cluster. Gene islands contain from one to four predicted genes, resulting in a gene density of one gene per 16 kb in gene islands and one gene per 111 kb over the entire sequenced region. The two sequence contigs, when compared with the ricericeSubject Category: Commodities and Products
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    (Oryza sativaoryza sativaSubject Category: Organism Names
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    ) and sorghum (Sorghum bicolorsorghum bicolorSubject Category: Organism Names
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    ) genomes, retain gene colinearity of 50% and 71%, respectively, and 70% and 100%, respectively, for high-confidence gene models. Collinear genes on single gene islands show that while most expansion of the maize genome has occurred in the repeat clusters, gene islands are not immune and have experienced growth in both intragene and intergene locations.

    ISSN : 0032-0889

    DOI : 10.1104/pp.109.143370

    Record Number : 20103043927

    Publisher : American Society of Plant Biologists

    Location of publication : Rockville

    Country of publication : USA

    Language of text : English

    Indexing terms for this abstract:

    Organism descriptor(s) : OryzaoryzaSubject Category: Organism Names
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    , Oryza sativaoryza sativaSubject Category: Organism Names
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    , Sorghum bicolorsorghum bicolorSubject Category: Organism Names
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    , Zea mayszea maysSubject Category: Organism Names
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    Descriptor(s) : genetic analysisgenetic analysisSubject Category: Techniques, Methodologies and Equipment
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    , genomesgenomesSubject Category: Miscellaneous
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    , maizemaizeSubject Category: Commodities and Products
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    , nucleotide sequencesnucleotide sequencesSubject Category: Chemicals and Chemical Groups
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    , ricericeSubject Category: Commodities and Products
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    , sweet sorghumsweet sorghumSubject Category: Commodities and Products
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    , transposable elementstransposable elementsSubject Category: Miscellaneous
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    Identifier(s) : corn, DNA insertion elements, DNA sequences, insertion elements, insertion sequences, mobile genetic elements, mobile sequences, paddy, sugar sorghum, transposons

    Broader term(s) : PoaceaepoaceaeSubject Category: Organism Names
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    , PoalespoalesSubject Category: Organism Names
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    , commelinidscommelinidsSubject Category: Organism Names
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    , monocotyledonsmonocotyledonsSubject Category: Organism Names
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    , angiospermsangiospermsSubject Category: Organism Names
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    , SpermatophytaspermatophytaSubject Category: Organism Names
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    , plantsplantsSubject Category: Organism Names
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    , eukaryoteseukaryotesSubject Category: Organism Names
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    , OryzaoryzaSubject Category: Organism Names
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    , SorghumsorghumSubject Category: Organism Names
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    , ZeazeaSubject Category: Organism Names
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