Transposable element distribution, abundance and role in genome size variation in the genus Oryza

[1]  L. Stein,et al.  The Oryza Map Alignment Project , 2008 .

[2]  E. D. Earle,et al.  Nuclear DNA content of some important plant species , 1991, Plant Molecular Biology Reporter.

[3]  J. Bennetzen,et al.  Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution , 2006, Proceedings of the National Academy of Sciences.

[4]  S. Jackson,et al.  Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. , 2006, Genome research.

[5]  Rod A Wing,et al.  Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. , 2006, Genome research.

[6]  J. Macas,et al.  Significant Expansion of Vicia pannonica Genome Size Mediated by Amplification of a Single Type of Giant Retroelement , 2006, Genetics.

[7]  J. Jurka,et al.  Self-synthesizing DNA transposons in eukaryotes. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[8]  S. Jackson,et al.  The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. , 2005, Genome research.

[9]  Ya-long Guo,et al.  Molecular Phylogeny of Oryzeae (poaceae) Based on Dna Sequences from Chloroplast, Mitochondrial, and Nuclear Genomes Ya-long Guo 2 and Song Ge , 2022 .

[10]  Takuji Sasaki,et al.  The map-based sequence of the rice genome , 2005, Nature.

[11]  李佩芳.  International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. , 2005 .

[12]  J. Jurka,et al.  Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.

[13]  O. Panaud,et al.  LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model , 2005, Cytogenetic and Genome Research.

[14]  David M. A. Martin,et al.  Retrotransposon populations of Vicia species with varying genome size , 2005, Molecular Genetics and Genomics.

[15]  J. Stewart,et al.  Estimation of the nuclear DNA content of gossypium species. , 2005, Annals of botany.

[16]  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 .

[17]  W. Rooney,et al.  Genome evolution in the genus Sorghum (Poaceae). , 2005, Annals of botany.

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

[19]  C. Soderlund,et al.  The Oryza Map Alignment Project: The Golden Path to Unlocking the Genetic Potential of Wild Rice Species , 2005, Plant Molecular Biology.

[20]  Sudhir Kumar,et al.  MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment , 2004, Briefings Bioinform..

[21]  M. Savontaus,et al.  Abstracts of Papers Presented at the Sixteenth Meeting of the Scandinavian Association of Geneticists June 15–18, 1996, Turku, Finland , 2004 .

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

[23]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[24]  T. Schmidt.  LINEs, SINEs and repetitive DNA: non-LTR retrotransposons in plant genomes , 1999, Plant Molecular Biology.

[25]  G. Khush.  Origin, dispersal, cultivation and variation of rice , 1997, Plant Molecular Biology.

[26]  D. Smyth,et al.  An abundant LINE-like element amplified in the genome of Lilium speciosum , 1993, Molecular and General Genetics MGG.

[27]  O. Panaud,et al.  Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L. , 2003, Molecular biology and evolution.

[28]  K. Kadowaki,et al.  Diversity in the Oryza genus. , 2003, Current opinion in plant biology.

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

[30]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) , 2002, Science.

[31]  J. Bennetzen.  Opening the Door to Comparative Plant Biology , 2002, Science.

[32]  J. Bennetzen.  The rice genome. Opening the door to comparative plant biology. , 2002, Science.

[33]  A. Oliphant,et al.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). , 2002, Science.

[34]  J. McDonald,et al.  Long terminal repeat retrotransposons of Oryza sativa , 2002, Genome Biology.

[35]  Hui-Hsien Chou,et al.  DNA sequence quality trimming and vector removal , 2001, Bioinform..

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

[37]  K. Wolfe.  The rice genome , 2000, Nature reviews genetics.

[38]  M A Budiman,et al.  Rice transposable elements: a survey of 73,000 sequence-tagged-connectors. , 2000, Genome research.

[39]  P. Rabinowicz.  Are obese plant genomes on a diet? , 2000, Genome research.

[40]  T. Sang,et al.  Phylogeny of rice genomes with emphasis on origins of allotetraploid species. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[41]  Eviatar Nevo,et al.  Retrotransposon BARE-1 and Its Role in Genome Evolution in the Genus Hordeum , 1999, Plant Cell.

[42]  A. Flavell,et al.  Phylogeny and transpositional activity of Ty1-copia group retrotransposons in cereal genomes , 1999, Molecular and General Genetics MGG.

[43]  S. Goff,et al.  Rice as a model for cereal genomics. , 1999, Current opinion in plant biology.

[44]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[45]  K. Tsunewaki,et al.  Presence of wheat retrotransposons in Gramineae species and the origin of wheat retrotransposon families. , 1997, Genes & genetic systems.

[46]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[47]  P. Capy.  Evolution and Impact of Transposable Elements , 1997, Contemporary Issues in Genetics and Evolution.

[48]  Claude Bazin,et al.  Dynamics and evolution of trans-posable elements , 1996 .

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

[50]  D. Voytas,et al.  Multiple non-LTR retrotransposons in the genome of Arabidopsis thaliana. , 1996, Genetics.

[51]  H. Ahokas,et al.  Flow-cytometric determination of polyploidy level in spontaneous clones of strawberries , 1996 .

[52]  A. Flavell.  Retroelements, reverse transcriptase and evolution. , 1995, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology.

[53]  E. Earle,et al.  Nuclear DNA content of ten rice species as determined by flow cytometry , 1994 .

[54]  T. Eickbush,et al.  Origin and evolution of retroelements based upon their reverse transcriptase sequences. , 1990, The EMBO journal.

[55]  E. Pahlich,et al.  A rapid DNA isolation procedure for small quantities of fresh leaf tissue , 1980 .

[56]  C. A. Thomas.  The genetic organization of chromosomes. , 1971, Annual review of genetics.