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LETTER: Widespread genome duplications throughout the history of flowering plants
- Liying Cui,
- P. Kerr Wall,
- James H. Leebens-Mack,
- Bruce G. Lindsay,
- Douglas E. Soltis,
- Jeff J. Doyle,
- Pamela S. Soltis,
- John E. Carlson,
- Kathiravetpilla Arumuganathan,
- Abdelali Barakat,
- Victor A. Albert,
- Hong Ma,
- and Claude W. dePamphilis
Genome Res. June 2006 16: 738-749; Published in Advance May 15, 2006, doi:10.1101/gr.4825606
...previously reported for core eudicots and members of Poaceae. These lower substitution rates permit inference of older duplication events. We hypothesize that evidence of an ancient duplication observed in the Nuphar data may represent a genome duplication in the common ancestor of all or most extant...
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PERSPECTIVE: The Arabidopsis genome: A foundation for plant research
- Michael Bevan and
- Sean Walsh
Genome Res. December 2005 15: 1632-1642; doi:10.1101/gr.3723405
...Centre, Norwich NR4 7UJ, United Kingdom Abstract The sequence of the first plant genome was completed and published at the end of 2000. This spawned a series of large-scale projects aimed at discovering the functions of the 25,000+ genes identified in Arabidopsis thaliana ( Arabidopsis...
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LETTER: Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes
- Brian C. Thomas,
- Brent Pedersen,
- and Michael Freeling
Genome Res. July 2006 16: 934-946; Published in Advance June 7, 2006, doi:10.1101/gr.4708406
...the best single explanation for the retention of gene pairs following large-scale genomic duplications ( Freeling and Thomas 2006 ). Mechanisms explaining clusters of retained genes Biased fractionation generates clusters on the overfractionated homeolog. However clusters of over-retention occur (albeit...
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Research: Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes
- Konstantinos Kritsas,
- Samuel E. Wuest,
- Daniel Hupalo,
- Andrew D. Kern,
- Thomas Wicker,
- and Ueli Grossniklaus
Genome Res. December 2012 22: 2455-2466; Published in Advance September 17, 2012, doi:10.1101/gr.129346.111
...). We searched whether ULEs are depleted from segmental duplications (SDs). During evolution, Arabidopsis has undergone multiple whole- and large-scale duplication events. We took into account SDs identified in Arabidopsis by Blanc et al. (2003), i.e., chromosome regions that share similar genes...
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LETTER: Dynamic evolution at pericentromeres
- Anne E. Hall,
- Gregory C. Kettler,
- and Daphne Preuss
Genome Res. March 2006 16: 355-364; Published in Advance February 6, 2006, doi:10.1101/gr.4399206
...., Hokamp, K., and Wolfe, K.H. 2003 . A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis . Genome Res. 13 : 137 –144. ↵ Boivin, K., Acarkan, A., Mbulu, R.S., Clarenz, O., and Schmidt, R. 2004 . The Arabidopsis sequence as a tool for analysis in Brassicaceae. A comparison...
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Methods: Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps
- Haibao Tang,
- Xiyin Wang,
- John E. Bowers,
- Ray Ming,
- Maqsudul Alam,
- and Andrew H. Paterson
Genome Res. December 2008 18: 1944-1954; Published in Advance October 2, 2008, doi:10.1101/gr.080978.108
...Biology, University of Illinois at Urbana–Champaign, Champaign, Illinois 61801, USA; 5 Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii 96822, USA Abstract Large-scale (segmental or whole) genome duplication has been recurring...
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LETTER: Differential methylation of genes and repeats in land plants
- Pablo D. Rabinowicz,
- Robert Citek,
- Muhammad A. Budiman,
- Andrew Nunberg,
- Joseph A. Bedell,
- Nathan Lakey,
- Andrew L. O'Shaughnessy,
- Lidia U. Nascimento,
- W. Richard McCombie,
- and Robert A. Martienssen
Genome Res. October 2005 15: 1431-1440; doi:10.1101/gr.4100405
.... ↵ ———. 2002 . DNA methylation patterns and epigenetic memory. Genes &amp; Dev. 16 : 6 -21. ↵ Blanc, G., Hokamp, K., and Wolfe, K.H. 2003 . A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis . Genome Res. 13 : 137 -144. ↵ Chandler, V.L. and Walbot, V. 1986 . DNA modification...
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Research: Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor
- Ruth A. Swanson-Wagner,
- Steven R. Eichten,
- Sunita Kumari,
- Peter Tiffin,
- Joshua C. Stein,
- Doreen Ware,
- and Nathan M. Springer
Genome Res. December 2010 20: 1689-1699; Published in Advance October 29, 2010, doi:10.1101/gr.109165.110
..., B73, affords the opportunity to assess structural variation and complexitywithin this species (Schnable et al. 2009). Detailed analyses of specific loci as well as genomic approaches have identified numerous duplications within the maize , many of which are located in colinear regions (Schnable et...
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LETTER: Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: A somatic view of the germline
- Laurent Duret,
- Jean Cohen,
- Claire Jubin,
- Philippe Dessen,
- Jean-François Goût,
- Sylvain Mousset,
- Jean-Marc Aury,
- Olivier Jaillon,
- Benjamin Noël,
- Olivier Arnaiz,
- Mireille Bétermier,
- Patrick Wincker,
- Eric Meyer,
- and Linda Sperling
Genome Res. April 2008 18: 585-596; Published in Advance February 6, 2008, doi:10.1101/gr.074534.107
...is a complete MAC chromosome as indicated by correctly oriented telomere repeats at either end. Four additional clusters also consist of a pair of scaffolds, but at least one of the four scaffold ends is not marked by telomere repeats. The Paramecium appears to have undergone remarkably few large-scale...

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