Transposable elements, gene creation and genome rearrangement in flowering plants.

Plant genome structure is largely derived from the differing specificities, abundances and activities of transposable elements. Recent studies indicate that both the amplification and the removal of transposons are rapid processes in plants, accounting for the general lack of intergenic homology between species that last shared a common ancestor more than 10 million years ago. Two newly discovered transposon varieties, Helitrons and Pack-MULEs, acquire and fuse fragments of plant genes, creating the raw material for the evolution of new genes and new genetic functions. Many of these recently assembled, chimeric gene-candidates are expressed, suggesting that some might escape epigenetic silencing and mutational decay, but a proven case of gene creation by any transposable element activity in plants remains to be demonstrated.

[1]  J. Bennetzen,et al.  Genetic mapping and characterization of sorghum and related crops by means of maize DNA probes. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[2]  J. Bennetzen,et al.  Nested Retrotransposons in the Intergenic Regions of the Maize Genome , 1996, Science.

[3]  S. Henikoff,et al.  Poised for contagion: evolutionary origins of the infectious abilities of invertebrate retroviruses. , 2000, Genome research.

[4]  L. Comai,et al.  The effect of stress on genome regulation and structure. , 2004, Annals of botany.

[5]  Jianxin Ma,et al.  Rapid recent growth and divergence of rice nuclear genomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Andrea Gallavotti,et al.  A novel class of Helitron- related transposable elements in maize contain portions of multiple pseudogenes , 2004, Plant Molecular Biology.

[7]  B. Mcclintock,et al.  The significance of responses of the genome to challenge. , 1984, Science.

[8]  Jianxin Ma,et al.  Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. , 2004, Genome research.

[9]  S. Wessler,et al.  Transduction of a cellular gene by a plant retroelement , 1994, Cell.

[10]  J. Bennetzen,et al.  Mechanisms and rates of genome expansion and contraction in flowering plants , 2002, Genetica.

[11]  Jianxin Ma,et al.  Consistent over-estimation of gene number in complex plant genomes. , 2004, Current opinion in plant biology.

[12]  Yujun Zhang,et al.  Sequence and analysis of rice chromosome 4 , 2002, Nature.

[13]  J. Bennetzen,et al.  Colinearity and its exceptions in orthologous adh regions of maize and sorghum. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[14]  J. Jurka,et al.  Rolling-circle transposons in eukaryotes , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Jonathan F Wendel,et al.  Polyploidy and Genome Evolution in Plants This Review Comes from a Themed Issue on Genome Studies and Molecular Genetics Edited , 2022 .

[16]  William H. Majoros,et al.  A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome , 2002, Science.

[17]  B. Han,et al.  Genome-wide intraspecific DNA-sequence variations in rice. , 2003, Current opinion in plant biology.

[18]  Phillip SanMiguel,et al.  The paleontology of intergene retrotransposons of maize , 1998, Nature Genetics.

[19]  K. Boivin,et al.  The Arabidopsis Genome Sequence as a Tool for Genome Analysis in Brassicaceae. A Comparison of the Arabidopsis and Capsella rubella Genomes1[w] , 2004, Plant Physiology.

[20]  T. Wicker,et al.  Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution. , 2001, The Plant journal : for cell and molecular biology.

[21]  C. Aquadro,et al.  The evolutionary analysis of "orphans" from the Drosophila genome identifies rapidly diverging and incorrectly annotated genes. , 2001, Genetics.

[22]  Sean R. Eddy,et al.  Pack-MULE transposable elements mediate gene evolution in plants , 2004, Nature.

[23]  J. Bennetzen,et al.  Integration and nonrandom mutation of a plasma membrane proton ATPase gene fragment within the Bs1 retroelement of maize. , 1994, The Plant cell.

[24]  T. Wicker,et al.  Rapid Genome Divergence at Orthologous Low Molecular Weight Glutenin Loci of the A and A m Genomes of Wheat , 2003 .

[25]  H. Puchta,et al.  Species‐specific double‐strand break repair and genome evolution in plants , 2000, The EMBO journal.

[26]  Joachim Messing,et al.  Gene expression of a gene family in maize based on noncollinear haplotypes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[27]  S. Wright,et al.  Mutator-like elements in Arabidopsis thaliana. Structure, diversity and evolution. , 2000, Genetics.

[28]  Nuclear DNA amounts in angiosperms , 1982, Proceedings of the Royal Society of London. Series B. Biological Sciences.

[29]  M. Feldman,et al.  Sequence Elimination and Cytosine Methylation Are Rapid and Reproducible Responses of the Genome to Wide Hybridization and Allopolyploidy in Wheat , 2001, The Plant Cell Online.

[30]  G. Moore,et al.  Cereal Genome Evolution: Grasses, line up and form a circle , 1995, Current Biology.

[31]  J. Bennetzen,et al.  Structural Analysis of the Maize Rp1 Complex Reveals Numerous Sites and Unexpected Mechanisms of Local Rearrangement Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.006338. , 2002, The Plant Cell Online.

[32]  V. Chandler,et al.  Characterization of a highly conserved sequence related to mutator transposable elements in maize. , 1988, Molecular biology and evolution.

[33]  P. Schulze-Lefert,et al.  A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. , 2000, Genome research.

[34]  Giorgio Pea,et al.  Origins, genetic organization and transcription of a family of non-autonomous helitron elements in maize. , 2005, The Plant journal : for cell and molecular biology.

[35]  James K. M. Brown,et al.  Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. , 2002, Genome research.

[36]  M. Yano,et al.  Conservation of Duplicated Segments between Rice Chromosome 11 and 12 , 1995 .

[37]  B. Birren,et al.  Sequencing and comparison of yeast species to identify genes and regulatory elements , 2003, Nature.

[38]  J. Bennetzen,et al.  Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes. , 2002, Genetics.

[39]  J. Bennetzen,et al.  Gene loss and movement in the maize genome. , 2004, Genome research.

[40]  Michele Morgante,et al.  Evolution of DNA Sequence Nonhomologies among Maize Inbredsw⃞ , 2005, The Plant Cell Online.

[41]  J. Bennetzen,et al.  A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[42]  H. Fu,et al.  Intraspecific violation of genetic colinearity and its implications in maize , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[43]  J. Bennetzen,et al.  Mechanisms of recent genome size variation in flowering plants. , 2005, Annals of botany.

[44]  M. Morgante,et al.  Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize , 2005, Nature Genetics.

[45]  J. Bennetzen,et al.  The generation of Mutator transposable element subfamilies in maize , 2004, Theoretical and Applied Genetics.

[46]  J. Jurka,et al.  Molecular paleontology of transposable elements in the Drosophila melanogaster genome , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[47]  R. Poulter,et al.  Vertebrate helentrons and other novel Helitrons. , 2003, Gene.

[48]  Joachim Messing,et al.  Gene movement by Helitron transposons contributes to the haplotype variability of maize. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[49]  Volker Brendel,et al.  The Maize Genome Contains a Helitron Insertion Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.008375. , 2003, The Plant Cell Online.

[50]  M. Chandler,et al.  Insertion Sequences , 1998, Microbiology and Molecular Biology Reviews.

[51]  S. Tanksley,et al.  RFLP Maps Based on a Common Set of Clones Reveal Modes of Chromosomal Evolution in Potato and Tomato. , 1988, Genetics.

[52]  J. Bennetzen,et al.  Grasses as a single genetic system: genome composition, collinearity and compatibility. , 1993, Trends in genetics : TIG.

[53]  W. Gilbert.  Why genes in pieces? , 1978, Nature.