DNA is structured as a linear 'jigsaw puzzle' in the genomes of Arabidopsis, rice, and budding yeast.

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  • Additional Information
    • Author-Supplied Keywords:
      Arabidopsis
      DNA structuring and organization
      génétique
      genetics
      levure
      rice
      riz
      structuration et organisation de l'ADN
      variation and evolution
      variation et évolution
      yeast
      Arabidopsis
      génétique
      levure
      riz
      structuration et organisation de l'ADN
      variation et évolution
      Language of Keywords: English; French
    • Abstract:
      Knowledge of how a genome is structured and organized from its constituent elements is crucial to understanding its biology and evolution. Here, we report the genome structuring and organization pattern as revealed by systems analysis of the sequences of three model species, Arabidopsis, rice and yeast, at the whole-genome and chromosome levels. We found that all fundamental function elements (FFE) constituting the genomes, including genes (GEN), DNA transposable elements (DTE), retrotransposable elements (RTE), simple sequence repeats (SSR), and (or) low complexity repeats (LCR), are structured in a nonrandom and correlative manner, thus leading to a hypothesis that the DNA of the species is structured as a linear 'jigsaw puzzle'. Furthermore, we showed that different FFE differ in their importance in the formation and evolution of the DNA jigsaw puzzle structure between species. DTE and RTE play more important roles than GEN, LCR, and SSR in Arabidopsis, whereas GEN and RTE play more important roles than LCR, SSR, and DTE in rice. The genes having multiple recognized functions play more important roles than those having single functions. These results provide useful knowledge necessary for better understanding genome biology and evolution of the species and for effective molecular breeding of rice. [ABSTRACT FROM AUTHOR]
    • Abstract:
      La connaissance de l'organisation et de la structure d'un génome à partir de ses éléments constituants est cruciale pour comprendre la biologie et l'évolution d'un génome. Dans ce travail, les auteurs décrivent les modes de structuration et d'organisation des génomes tels que révélés par une analyse systémique des séquences de trois espèces modèles ( Arabidopsis, le riz et la levure) à l'échelle du génome et des chromosomes. Les auteurs ont trouvé que tous les éléments fonctionnels fondamentaux (FFE) constituant les génomes, incluant les gènes (GEN), les éléments transposables à ADN (DTE), les rétro-éléments (RTE), les séquences simples répétées (SSR) et les séquences répétées à faible complexité (LCR) sont organisés de manière non-aléatoire et corrélée, ce qui les amène à formuler l'hypothèse que l'ADN des différentes espèces est structuré à la manière d'un « puzzle » linéaire. De plus, les auteurs montrent que différents FFE diffèrent quant à leur importance dans la formation et l'évolution de la structure du puzzle d'ADN entre espèces. Les DTE et RTE joueraient des rôles plus importants que les GEN, LCR et SSR chez Arabidopsis, tandis que les GEN et RTE joueraient des rôles plus importants que les LCR, SSR et DTE chez le riz. Les gènes ayant plusieurs fonctions reconnues joueraient un rôle plus important que ceux n'ayant qu'une seule fonction. Ces résultats fournissent un éclairage utile pour mieux comprendre la biologie et l'évolution des génomes des espèces et pour plus efficacement améliorer le riz. [Traduit par la Rédaction] [ABSTRACT FROM AUTHOR]
    • Abstract:
      Copyright of Genome is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
    • Author Affiliations:
      1Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843-2474, USA.
      2College of Life Science, Jilin Agricultural University, Changchun, Jilin 130118, China.
    • ISSN:
      0831-2796
    • Accession Number:
      10.1139/gen-2013-0099
    • Accession Number:
      94628226
  • Citations
    • ABNT:
      LIU, Y.-H. et al. DNA is structured as a linear “jigsaw puzzle” in the genomes of Arabidopsis, rice, and budding yeast. Genome, [s. l.], v. 57, n. 1, p. 9–19, 2014. DOI 10.1139/gen-2013-0099. Disponível em: http://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=asn&AN=94628226&custid=s8280428. Acesso em: 25 jan. 2020.
    • AMA:
      Liu Y-H, Zhang M, Wu C, Huang JJ, Zhang H-B, Gulick P. DNA is structured as a linear “jigsaw puzzle” in the genomes of Arabidopsis, rice, and budding yeast. Genome. 2014;57(1):9-19. doi:10.1139/gen-2013-0099.
    • APA:
      Liu, Y.-H., Zhang, M., Wu, C., Huang, J. J., Zhang, H.-B., & Gulick, P. (2014). DNA is structured as a linear “jigsaw puzzle” in the genomes of Arabidopsis, rice, and budding yeast. Genome, 57(1), 9–19. https://doi.org/10.1139/gen-2013-0099
    • Chicago/Turabian: Author-Date:
      Liu, Yun-Hua, Meiping Zhang, Chengcang Wu, James J. Huang, Hong-Bin Zhang, and P. Gulick. 2014. “DNA Is Structured as a Linear ‘Jigsaw Puzzle’ in the Genomes of Arabidopsis, Rice, and Budding Yeast.” Genome 57 (1): 9–19. doi:10.1139/gen-2013-0099.
    • Harvard:
      Liu, Y.-H. et al. (2014) ‘DNA is structured as a linear “jigsaw puzzle” in the genomes of Arabidopsis, rice, and budding yeast’, Genome, 57(1), pp. 9–19. doi: 10.1139/gen-2013-0099.
    • Harvard: Australian:
      Liu, Y-H, Zhang, M, Wu, C, Huang, JJ, Zhang, H-B & Gulick, P 2014, ‘DNA is structured as a linear “jigsaw puzzle” in the genomes of Arabidopsis, rice, and budding yeast’, Genome, vol. 57, no. 1, pp. 9–19, viewed 25 January 2020, .
    • MLA:
      Liu, Yun-Hua, et al. “DNA Is Structured as a Linear ‘Jigsaw Puzzle’ in the Genomes of Arabidopsis, Rice, and Budding Yeast.” Genome, vol. 57, no. 1, Jan. 2014, pp. 9–19. EBSCOhost, doi:10.1139/gen-2013-0099.
    • Chicago/Turabian: Humanities:
      Liu, Yun-Hua, Meiping Zhang, Chengcang Wu, James J. Huang, Hong-Bin Zhang, and P. Gulick. “DNA Is Structured as a Linear ‘Jigsaw Puzzle’ in the Genomes of Arabidopsis, Rice, and Budding Yeast.” Genome 57, no. 1 (January 2014): 9–19. doi:10.1139/gen-2013-0099.
    • Vancouver/ICMJE:
      Liu Y-H, Zhang M, Wu C, Huang JJ, Zhang H-B, Gulick P. DNA is structured as a linear “jigsaw puzzle” in the genomes of Arabidopsis, rice, and budding yeast. Genome [Internet]. 2014 Jan [cited 2020 Jan 25];57(1):9–19. Available from: http://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=asn&AN=94628226&custid=s8280428