Searching journal content for articles similar to Mondragón-Palomino et al. 12 (9): 1305.

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Research: Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions
- Kyuha Choi,
- Xiaohui Zhao,
- Andrew J. Tock,
- Christophe Lambing,
- Charles J. Underwood,
- Thomas J. Hardcastle,
- Heïdi Serra,
- Juhyun Kim,
- Hyun Seob Cho,
- Jaeil Kim,
- Piotr A. Ziolkowski,
- Nataliya E. Yelina,
- Ildoo Hwang,
- Robert A. Martienssen,
- and Ian R. Henderson
Genome Res. April 2018 28: 532-546; Published in Advance March 12, 2018, doi:10.1101/gr.225599.117
...that recognize pathogens in animals and fungi (Jones et al. 2016). Plant NBS-LRR genes are among the most diverse gene class observed within and between plant species (Jacob et al. 2013; Jones et al. 2016). In A. thaliana, 73 of 197 NBS-LRR genes are within 500 bp of a SPO11-1-oligo active transposon...
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Research: Limited allele-specific gene expression in highly polyploid sugarcane
- Gabriel Rodrigues Alves Margarido,
- Fernando Henrique Correr,
- Agnelo Furtado,
- Frederik C. Botha,
- and Robert James Henry
Genome Res. February 2022 32: 297-308; Published in Advance December 23, 2021, doi:10.1101/gr.275904.121
...-specific expression (ASE) has been widely reported, but the proportion and nature of genes showing this characteristic have not been well defined. We now report an analysis of the frequency and patterns of ASE at the whole- level in the highly polyploid sugarcane . Very high depth whole- sequencing and RNA sequencing...
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Research: Human long intrinsically disordered protein regions are frequent targets of positive selection
- Arina Afanasyeva,
- Mathias Bockwoldt,
- Christopher R. Cooney,
- Ines Heiland,
- and Toni I. Gossmann
Genome Res. July 2018 28: 975-982; Published in Advance June 1, 2018, doi:10.1101/gr.232645.117
...in the complete NBS-LRR gene family of Arabidopsis thaliana. Genome Res 12: 1305–1315. ↵Mosca R, Pache RA, Aloy P. 2012. The role of structural disorder in the rewiring of protein interactions through evolution. Mol Cell Proteomics 11: M111.014969. ↵Nabholz B, Uwimana N, Lartillot N. 2013. Reconstructing...
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Resource: An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations
- Bernardo J. Clavijo,
- Luca Venturini,
- Christian Schudoma,
- Gonzalo Garcia Accinelli,
- Gemy Kaithakottil,
- Jonathan Wright,
- Philippa Borrill,
- George Kettleborough,
- Darren Heavens,
- Helen Chapman,
- James Lipscombe,
- Tom Barker,
- Fu-Hao Lu,
- Neil McKenzie,
- Dina Raats,
- Ricardo H. Ramirez-Gonzalez,
- Aurore Coince,
- Ned Peel,
- Lawrence Percival-Alwyn,
- Owen Duncan,
- Josua Trösch,
- Guotai Yu,
- Dan M. Bolser,
- Guy Namaati,
- Arnaud Kerhornou,
- Manuel Spannagl,
- Heidrun Gundlach,
- Georg Haberer,
- Robert P. Davey,
- Christine Fosker,
- Federica Di Palma,
- Andrew L. Phillips,
- A. Harvey Millar,
- Paul J. Kersey,
- Cristobal Uauy,
- Ksenia V. Krasileva,
- David Swarbreck,
- Michael W. Bevan,
- and Matthew D. Clark
Genome Res. May 2017 27: 885-896; Published in Advance April 18, 2017, doi:10.1101/gr.217117.116
.... Among these, 98% have complete transcripts compared with only 2% in the CSS assembly. We also used NLR-parser (Steuernagel et al. 2015) to predict the coiled-coil (CC-) NBS-LRR subclass of R-genes. We identified 859 complete CC-NBS-LRR genes supported by specific MEME motifs (Jupe et al. 2012) compared...
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RESOURCE: Sequencing of natural strains of Arabidopsis thaliana with short reads
- Stephan Ossowski,
- Korbinian Schneeberger,
- Richard M. Clark,
- Christa Lanz,
- Norman Warthmann,
- and Detlef Weigel
Genome Res. December 2008 18: 2024-2033; Published in Advance September 25, 2008, doi:10.1101/gr.080200.108
...for biology ( The Arabidopsis Genome Initiative 2000 ). Apart from accelerating functional analyses and providing insights into gene content and evolution, the 119-Mb euchromatic reference sequence of the Columbia (Col-0) accession propelled A. thaliana to the forefront of efforts to understand...
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Methods: Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays
- Georg Zeller,
- Richard M. Clark,
- Korbinian Schneeberger,
- Anja Bohlen,
- Detlef Weigel,
- and Gunnar Rätsch
Genome Res. June 2008 18: 918-929; Published in Advance March 6, 2008, doi:10.1101/gr.070169.107
...data ( Clark et al. 2007 ), as well as from studies of a select set of NB-LRR genes in A. thaliana ( Grant et al. 1998 ; Bakker et al. 2006 ; Shen et al. 2006 ). Nevertheless, polymorphism levels for individual NB-LRR genes varied greatly; some genes were almost entirely included in PRs, while others...
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Research: Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus
- Eli Rodgers-Melnick,
- Shrinivasrao P. Mane,
- Palitha Dharmawardhana,
- Gancho T. Slavov,
- Oswald R. Crasta,
- Steven H. Strauss,
- Amy M. Brunner,
- and Stephen P. DiFazio
Genome Res. January 2012 22: 95-105; Published in Advance October 5, 2011, doi:10.1101/gr.125146.111
...and Petrov 2005; Maere et al. 2005). Meanwhile, the converse is true for other genes, such as those containing NBS-LRR motifs (Meyers et al. 2003, 2005; Leister 2004; Zhang et al. 2010). The availability of whole sequence and transcriptome data allows us to test the extent to which natural patterns...
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LETTER: Many or most genes in Arabidopsis transposed after the origin of the order Brassicales
- Michael Freeling,
- Eric Lyons,
- Brent Pedersen,
- Maqsudul Alam,
- Ray Ming,
- and Damon Lisch
Genome Res. December 2008 18: 1924-1937; Published in Advance October 3, 2008, doi:10.1101/gr.081026.108
...changing. If positive selection is strong but acts only periodically, the result could be a constantly shifting population of genes within a family whose positions would vary over time. Clear examples of this are the NB-LRR genes (91% transposed). As new or altered pathogens are encountered, old copies...
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LETTER: MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant
- Cheng Lu,
- Karthik Kulkarni,
- Frédéric F. Souret,
- Ramesh MuthuValliappan,
- Shivakundan Singh Tej,
- R. Scott Poethig,
- Ian R. Henderson,
- Steven E. Jacobsen,
- Wenzhong Wang,
- Pamela J. Green,
- and Blake C. Meyers
Genome Res. October 2006 16: 1276-1288; Published in Advance September 5, 2006, doi:10.1101/gr.5530106
...of low molecular weight RNA isolated from inflorescence tissues. Canonical miRNAs generally require DCL1 (not DCL2 , 3 or 4 ), but not RDR2 or RDR6 , while 21-nt siRNAs from ta-siRNA loci require DCL1 , DCL4 , and RDR6 but not RDR2 . Arabidopsis mutants with defects in Dicer and RdRp genes, therefore...
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LETTER: Pathogen corruption and site-directed recombination at a plant disease resistance gene cluster
- Ervin D. Nagy and
- Jeffrey L. Bennetzen
Genome Res. December 2008 18: 1918-1923; Published in Advance August 21, 2008, doi:10.1101/gr.078766.108
..., a gene controlling the reaction to a fungal pathogen and its host-selective toxin . Theor. Appl. Genet. 114 : 961 – 970 . ↵ Palomino, M.M. , Meyers, B.C. , Michelmore, R.W. , Gaut, B.S. ( 2002 ) Patterns of positive selection in the complete NBS–LRR gene family of Arabidopsis thaliana . Genome Res. 12...

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