title: DNA is structured as a linear "jigsaw puzzle" in the genomes of Arabidopsis, rice, and budding yeast.
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.
authors.affiliation: a Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843-2474, USA.
authors.forename: Yun-Hua
authors.initials: YH
authors.lastname: Liu
authors.forename: Meiping
authors.initials: M
authors.lastname: Zhang
authors.forename: Chengcang
authors.initials: C
authors.lastname: Wu
authors.forename: James J
authors.initials: JJ
authors.lastname: Huang
authors.forename: Hong-Bin
authors.initials: HB
authors.lastname: Zhang
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D042622:DNA Repeat Expansion; D004271:DNA, Fungal / Q000737:chemistry*; D018744:DNA, Plant / Q000737:chemistry*; D019143:Evolution, Molecular; D016681:Genome, Fungal; D018745:Genome, Plant; D018895:Microsatellite Repeats; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018626:Retroelements; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D004271:DNA, Fungal; D018744:DNA, Plant; D010940:Plant Proteins; D018626:Retroelements; D029701:Saccharomyces cerevisiae Proteins