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Research: Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control
- Todd P. Michael,
- Evan Ernst,
- Nolan Hartwick,
- Philomena Chu,
- Douglas Bryant,
- Sarah Gilbert,
- Stefan Ortleb,
- Erin L. Baggs,
- K. Sowjanya Sree,
- Klaus J. Appenroth,
- Joerg Fuchs,
- Florian Jupe,
- Justin P. Sandoval,
- Ksenia V. Krasileva,
- Ljudmylla Borisjuk,
- Todd C. Mockler,
- Joseph R. Ecker,
- Robert A. Martienssen,
- and Eric Lam
Genome Res. February 2021 31: 225-238; Published in Advance December 23, 2020, doi:10.1101/gr.266429.120
...that the ratio between intact LTR-RTs and solo LTRs (solo:intact), which are left over after illegitimate recombination, is a proxy for how actively the is purging proliferating LTR-RTs (Devos et al. 2002). Although Spirodela has a high solo:intact ratio of 8 (Michael et al. 2017), Wolffia has an even higher...
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LETTER: Effects of Recombination Rate and Gene Density on Transposable Element Distributions in Arabidopsis thaliana
- Stephen I. Wright,
- Newton Agrawal,
- and Thomas E. Bureau
Genome Res. August 2003 13: 1897-1903; doi:10.1101/gr.1281503
..., S., Tijet, N., Perry, T., Heckel, D., Batterham, P., et al. 2002 . A single p450 allele associated with insecticide resistance in Drosophila. Science 297 : 2253 -2256. ↵ Devos, K.M., Brown, J.K., and Bennetzen, J.L. 2002 . Genome size reduction through illegitimate recombination counteracts...
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LETTER: Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families
- Thomas Wicker and
- Beat Keller
Genome Res. July 2007 17: 1072-1081; Published in Advance June 7, 2007, doi:10.1101/gr.6214107
...Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families Thomas Wicker 1 and Beat Keller Institute of Plant Biology...
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Letter: Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?
- Zhixi Tian,
- Carene Rizzon,
- Jianchang Du,
- Liucun Zhu,
- Jeffrey L. Bennetzen,
- Scott A. Jackson,
- Brandon S. Gaut,
- and Jianxin Ma
Genome Res. December 2009 19: 2221-2230; Published in Advance September 29, 2009, doi:10.1101/gr.083899.108
...↵ 5 These authors contributed equally to this work. Abstract In flowering plants, the accumulation of small deletions through unequal homologous recombination (UR) and illegitimate recombination (IR) is proposed to be the major process counteracting genome expansion, which is caused...
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Research: Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution
- Florent Murat,
- Jian-Hong Xu,
- Eric Tannier,
- Michael Abrouk,
- Nicolas Guilhot,
- Caroline Pont,
- Joachim Messing,
- and Jérôme Salse
Genome Res. November 2010 20: 1545-1557; Published in Advance September 28, 2010, doi:10.1101/gr.109744.110
...), triggered in part by polyploidization, could be considered a signal for chromosome-wide double-strand break repair (DSBR) processes. Illegitimate recombination mediated DSBR between sister chromatids has been suggested as a major evolutionary force of plant s in counteracting expansion through TE insertion...
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LETTER: The mode and tempo of genome size evolution in eukaryotes
- Matthew J. Oliver,
- Dmitri Petrov,
- David Ackerly,
- Paul Falkowski,
- and Oscar M. Schofield
Genome Res. May 2007 17: 594-601; Published in Advance April 9, 2007, doi:10.1101/gr.6096207
...resolved tree of life . Science 311 : 1283 – 1287 . ↵ Devos, K.M. , Brown, J.K.M. , Bennetzen, J.L. ( 2002 ) Genome size reduction through illegitimate recombination counteracts expansion in Arabidopsis . Genome Res. 12 : 1075 – 1079 . ↵ Diaz-Uriarte, R. , Garland, T.J. ( 1998 ) Effects of branch length...
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LETTER: Uneven chromosome contraction and expansion in the maize genome
- Rémy Bruggmann,
- Arvind K. Bharti,
- Heidrun Gundlach,
- Jinsheng Lai,
- Sarah Young,
- Ana C. Pontaroli,
- Fusheng Wei,
- Georg Haberer,
- Galina Fuks,
- Chunguang Du,
- Christina Raymond,
- Matt C. Estep,
- Renyi Liu,
- Jeffrey L. Bennetzen,
- Agnes P. Chan,
- Pablo D. Rabinowicz,
- John Quackenbush,
- W. Brad Barbazuk,
- Rod A. Wing,
- Bruce Birren,
- Chad Nusbaum,
- Steve Rounsley,
- Klaus F.X. Mayer,
- and Joachim Messing
Genome Res. October 2006 16: 1241-1251; Published in Advance August 10, 2006, doi:10.1101/gr.5338906
...regions but B1 or B2, or by a higher frequency of the small deletions (most caused by illegitimate recombination) that have been found to be responsible for shrinkage in rice and Arabidopsis ( Devos et al. 2002 ; Ma and Bennetzen 2004 ; Ma et al. 2004 ), or by a combination of the two. Another marked...
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LETTER: Incongruent Patterns of Local and Global Genome Size Evolution in Cotton
- Corrinne E. Grover,
- HyeRan Kim,
- Rod A. Wing,
- Andrew H. Paterson,
- and Jonathan F. Wendel
Genome Res. August 2004 14: 1474-1482; Published in Advance July 15, 2004, doi:10.1101/gr.2673204
.... Am. J. Botany 89 : 707 –725. ↵ Deutsch, M. and Long, M. 1999 . Intron–exon structure of eukaryotic model organisms. Nucleic Acids Res. 27 : 3219 –3228. ↵ Devos, K.M., Brown, J.K.M., and Bennetzen, J.L. 2002 . Genome size reduction through illegitimate recombination counteracts expansion...
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LETTER: Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome
- Regina S. Baucom,
- James C. Estill,
- Jim Leebens-Mack,
- and Jeffrey L. Bennetzen
Genome Res. February 2009 19: 243-254; Published in Advance November 24, 2008, doi:10.1101/gr.083360.108
.... , Batzer, M.A. , Feschotte, C. ( 2006 ) Birth of a chimeric primate gene by capture of the transposase gene from a mobile element . Proc. Natl. Acad. Sci. 103 : 8101 – 8106 . ↵ Devos, K.M. , Brown, J.K.M. , Bennetzen, J.L. ( 2002 ) Genome size reduction through illegitimate recombination counteracts...
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LETTER: Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium
- Jennifer S. Hawkins,
- HyeRan Kim,
- John D. Nason,
- Rod A. Wing,
- and Jonathan F. Wendel
Genome Res. October 2006 16: 1252-1261; Published in Advance September 5, 2006, doi:10.1101/gr.5282906
...and chloroplast genes. Am. J. Bot. 89 : 707 – 725 . ↵ Deutsch, M. , Long, M. ( 1999 ) Intron–exon structure of eukaryotic model organisms . Nucleic Acids Res. 27 : 3219 – 3228 . ↵ Devos, K.M. , Brown, J.K.M. , Bennetzen, J.L. ( 2002 ) Genome size reduction through illegitimate recombination counteracts expansion...

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