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Research: Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza
- Chenbo Gong,
- Yicheng Huang,
- Mengmeng Liu,
- Yong Zhou,
- Yinwei Xu,
- Nahed Mohammed,
- Xintong Qiao,
- Andrea Zuccolo,
- Weibo Xie,
- Rod A. Wing,
- Jianwei Zhang,
- Fei Zhou,
- and Yongjun Lin
Genome Res. June 2025 35: 1349-1363; Published in Advance April 25, 2025, doi:10.1101/gr.279609.124
...and mechanism of transfer of organellar DNA sequences in higher plants. We observe abundant insertions of organelle DNA into the nuclear s of 22 assemblies across seven Oryza species and further categorize nuclear organelle DNA (NORG) into 3406 orthologous groups. Analysis of the whole- resequencing data from...
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Method: CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes
- Marzia Rossato,
- Luca Marcolungo,
- Luca De Antoni,
- Giulia Lopatriello,
- Elisa Bellucci,
- Gaia Cortinovis,
- Giulia Frascarelli,
- Laura Nanni,
- Elena Bitocchi,
- Valerio Di Vittori,
- Leonardo Vincenzi,
- Filippo Lucchini,
- Kirstin E. Bett,
- Larissa Ramsay,
- David James Konkin,
- Massimo Delledonne,
- and Roberto Papa
Genome Res. May 2023 33: 787-797; Published in Advance May 1, 2023, doi:10.1101/gr.277628.122
...results will facilitate the large-scale genomic analysis of lentil as well as other plant species with large and highly repetitive s.ResultsDepletion of L. culinaris repetitive DNA using CRISPR-Cas9We designed a custom set of gRNAs to deplete the repetitive DNA content of the L. culinaris CDC Redberry...
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Research: Genome-wide mapping of nuclear mitochondrial DNA sequences links DNA replication origins to chromosomal double-strand break formation in Schizosaccharomyces pombe
- Sandrine Lenglez,
- Damien Hermand,
- and Anabelle Decottignies
Genome Res. September 2010 20: 1250-1261; Published in Advance August 5, 2010, doi:10.1101/gr.104513.109
...Genome-wide mapping of nuclear mitochondrial DNA sequences links DNA replication origins to chromosomal double-strand break formation in Schizosaccharomyces pombe Sandrine Lenglez 1 , Damien Hermand 2 and Anabelle Decottignies 1 , 3 1 Catholic...
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Research: Localized hypermutation and associated gene losses in legume chloroplast genomes
- Alan M. Magee,
- Sue Aspinall,
- Danny W. Rice,
- Brian P. Cusack,
- Marie Sémon,
- Antoinette S. Perry,
- Saša Stefanović,
- Dan Milbourne,
- Susanne Barth,
- Jeffrey D. Palmer,
- John C. Gray,
- Tony A. Kavanagh,
- and Kenneth H. Wolfe
Genome Res. December 2010 20: 1700-1710; Published in Advance October 26, 2010, doi:10.1101/gr.111955.110
...to be homogeneous across all regions of a genome. However, we have found a region of chloroplast DNA in plants related to sweetpea ( Lathyrus ) whose local point mutation rate is at least 20 times higher than elsewhere in the same molecule. There are very few precedents for such heterogeneity in any genome, and we...
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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
.... ↵ Arumuganathan, K. and Earle, E.D. 1991 . Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9 : 208 -218. ↵ The Arabidopsis Genome Initiative. 2000 . Analysis of the sequence of the flowering plant Arabidopsis thaliana. Nature 408 : 796 -815. ↵ Banks, J.A. 1999 . Gametophyte development...
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ARTICLE: Pattern of Organization of Human Mitochondrial Pseudogenes in the Nuclear Genome
- Markus Woischnik and
- Carlos T. Moraes
Genome Res. June 1, 2002 12: 885-893; Published in Advance May 16, 2002, doi:10.1101/gr.227202
...in the human nuclear genome have been previously described, mostly as a source of artifacts during the analysis of the mitochondrial genome. With the availability of the complete human genome sequence, we performed a comprehensive analysis of mtDNA insertions into the nucleus. We found 612 independent...
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LETTER: Evidence That Plant-Like Genes in Chlamydia Species Reflect an Ancestral Relationship between Chlamydiaceae, Cyanobacteria, and the Chloroplast
- Fiona S.L. Brinkman,
- Jeffrey L. Blanchard,
- Artem Cherkasov,
- Yossef Av-Gay,
- Robert C. Brunham,
- Rachel C. Fernandez,
- B. Brett Finlay,
- Sarah P. Otto,
- B.F. Francis Ouellette,
- Patrick J. Keeling,
- Ann M. Rose,
- Robert E.W. Hancock,
- and Steven J.M. Jones
Genome Res. August 1, 2002 12: 1159-1167; Published in Advance July 19, 2002, doi:10.1101/gr.341802
..., which are obligate intracellular bacterial pathogens of animals, are not likely exchanging DNA with their hosts. [Supplementary Material is available online at http://www.genome.org and at http://www.pathogenomics.bc.ca/BAE-watch.html .] Footnotes ↵ 12 Corresponding author...
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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
...and rates of expansion and contraction in flowering plants. Genetica 115 : 29 –36. ↵ Bennetzen, J.L. and Kellogg, E.A. 1997 . Do plants have a one-way ticket to genomic obesity? Plant Cell 9 : 1509 –1514. ↵ Bensasson, D., Petrov, D.A., Zhang, D.X., Hartl, D.L., and Hewitt, G.M. 2001 . Genomic gigantism: DNA...
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Article: Comparative genomics of protoploid Saccharomycetaceae
- The Génolevures Consortium,
- Jean-Luc Souciet,
- Bernard Dujon,
- Claude Gaillardin,
- Mark Johnston,
- Philippe V. Baret,
- Paul Cliften,
- David J. Sherman,
- Jean Weissenbach,
- Eric Westhof,
- Patrick Wincker,
- Claire Jubin,
- Julie Poulain,
- Valérie Barbe,
- Béatrice Ségurens,
- François Artiguenave,
- Véronique Anthouard,
- Benoit Vacherie,
- Marie-Eve Val,
- Robert S. Fulton,
- Patrick Minx,
- Richard Wilson,
- Pascal Durrens,
- Géraldine Jean,
- Christian Marck,
- Tiphaine Martin,
- Macha Nikolski,
- Thomas Rolland,
- Marie-Line Seret,
- Serge Casarégola,
- Laurence Despons,
- Cécile Fairhead,
- Gilles Fischer,
- Ingrid Lafontaine,
- Véronique Leh,
- Marc Lemaire,
- Jacky de Montigny,
- Cécile Neuvéglise,
- Agnès Thierry,
- Isabelle Blanc-Lenfle,
- Claudine Bleykasten,
- Julie Diffels,
- Emilie Fritsch,
- Lionel Frangeul,
- Adrien Goëffon,
- Nicolas Jauniaux,
- Rym Kachouri-Lafond,
- Célia Payen,
- Serge Potier,
- Lenka Pribylova,
- Christophe Ozanne,
- Guy-Franck Richard,
- Christine Sacerdot,
- Marie-Laure Straub,
- and Emmanuel Talla
Genome Res. October 2009 19: 1696-1709; Published in Advance June 12, 2009, doi:10.1101/gr.091546.109
...copies of rDNA repeat units, flanked by a series of Ns to constitute a total of 17 kb, weremanually inserted into the final assembly of these chromosomes. Assembled contigs correspond to entire chromosome sequences with the exception of the telomeric repeats. Sequences of Z. rouxii and K. thermotolerans...
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PERSPECTIVE: Grains of knowledge: Genomics of model cereals
- Andrew H. Paterson,
- Michael Freeling,
- and Takuji Sasaki
Genome Res. December 2005 15: 1643-1650; doi:10.1101/gr.3725905
...genetics methods include insertion mutant lines generated using Tos17 , T-DNA, and Ac / Ds elements, as well as populations of deletion mutants. The map-based sequence has proven especially useful for the identification of genes underlying diverse agronomic traits such as flowering time, plant architecture...

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