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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
..., and sorghum chromosomes. Results AGK reconstruction Grass genomic synteny, exemplified by rice, sorghum, maize, and Brachypodium, representing three separate subfamilies of species and 8.53-fold genomic expansions, was analyzed using alignment parameters and statistical tests (see Methods) to identify...
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LETTER: Improvement of whole-genome annotation of cereals through comparative analyses
- Wei Zhu and
- C. Robin Buell
Genome Res. March 2007 17: 299-310; Published in Advance February 6, 2007, doi:10.1101/gr.5881807
...is the first finished cereal , the rice annotation will be used extensively in the annotation of genes in other cereals and grass species. As with other eukaryotic species, annotation of the rice was initiated using gene predictions from ab initio gene finders and further improved by using cDNA and expressed...
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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
...rice, have permitted the alignment of genes derived from common ancestral grass chromosomes ( Swigonova et al. 2004 ). It appears that the two progenitors of maize and the progenitor of sorghum were n = 5 species that diverged about 11.9 million years ago (Mya). The two maize progenitors are believed...
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LETTER: Analyses of LTR-Retrotransposon Structures Reveal Recent and Rapid Genomic DNA Loss in Rice
- Jianxin Ma,
- Katrien M. Devos,
- and Jeffrey L. Bennetzen
Genome Res. May 2004 14: 860-869; Published in Advance April 12, 2004, doi:10.1101/gr.1466204
...-Copy-Number Families in Rice Preliminary annotations of the rice suggest that LTR retrotransposons comprise ∼7.4% of rice chromosome 4 ( Feng et al. 2002 ). As numerous retroelements have not been identified yet, or have been inappropriately annotated, the fraction of LTR retrotransposons in the rice is likely...
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LETTER: Rice Transposable Elements: A Survey of 73,000 Sequence-Tagged-Connectors
- Long Mao,
- Todd C. Wood,
- Yeisoo Yu,
- Muhammad A. Budiman,
- Jeff Tomkins,
- Sung-sick Woo,
- Maciek Sasinowski,
- Gernot Presting,
- David Frisch,
- Steve Goff,
- Ralph A. Dean,
- and Rod A. Wing
Genome Res. July 1, 2000 10: 982-990; doi:10.1101/gr.10.7.982
...and is of great economic importance. Among the cereal grasses, rice has the smallest size (430 Mb) and, as revealed by comparative mapping, has substantial conservation of synteny with other cereal crops such as maize, sorghum, and wheat ( Gale and Devos 1998 ). Consequently, rice is an ideal representative...
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LETTER: Characterization of the Maize Endosperm Transcriptome and Its Comparison to the Rice Genome
- Jinsheng Lai,
- Nrisingha Dey,
- Cheol-Soo Kim,
- Arvind K. Bharti,
- Stephen Rudd,
- Klaus F.X. Mayer,
- Brian A. Larkins,
- Philip Becraft,
- and Joachim Messing
Genome Res. October 2004 14: 1932-1937; doi:10.1101/gr.2780504
...with the close evolutionary distance between them (50 million years ago, Mya), and, at the same time, with the evidence of rapid divergence within the grass family ( Song et al. 2002 ). Furthermore, because the homoeologous genes in rice were spread over the entire length of all 12 chromosomes (Supplemental Fig...
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LETTER: Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice
- Guangming He,
- Xiaojin Luo,
- Feng Tian,
- Kegui Li,
- Zuofeng Zhu,
- Wei Su,
- Xiaoyin Qian,
- Yongcai Fu,
- Xiangkun Wang,
- Chuanqing Sun,
- and Jinshui Yang
Genome Res. May 2006 16: 618-626; Published in Advance April 10, 2006, doi:10.1101/gr.4814006
..., China. 6 ↵ 6 These authors contributed equally to this work. Abstract By constructing nearly isogenic lines (NILs) that differ only at a single quantitative trait locus (QTL), we fine-mapped the yield-improving QTL qGY2–1 to a 102.9-kb region on rice chromosome 2. Comparison...
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LETTER: Comparative Genomics Between Rice and Arabidopsis Shows Scant Collinearity in Gene Order
- Hong Liu,
- Ravi Sachidanandam,
- and Lincoln Stein
Genome Res. December 1, 2001 11: 2020-2026; doi:10.1101/gr.194501
...( Oryza sativa ), a model system for grasses, has also shown collinearity with other monocots. In a 1.9-cM region of rice, five genes show interrupted collinearity with maize Chromosome 4 ( Tarchini et al. 2000 ). Moreover, three genes in the ∼20-kb Sh2–A1 region show complete collinearity with sorghum...
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RESOURCE: Analysis and Functional Annotation of an Expressed Sequence Tag Collection for Tropical Crop Sugarcane
- André L. Vettore,
- Felipe R. da Silva,
- Edson L. Kemper,
- Glaucia M. Souza,
- Aline M. da Silva,
- Maria Inês T. Ferro,
- Flavio Henrique-Silva,
- Éder A. Giglioti,
- Manoel V.F. Lemos,
- Luiz L. Coutinho,
- Marina P. Nobrega,
- Helaine Carrer,
- Suzelei C. França,
- Maurício Bacci, Jr.,
- Maria Helena S. Goldman,
- Suely L. Gomes,
- Luiz R. Nunes,
- Luis E.A. Camargo,
- Walter J. Siqueira,
- Marie-Anne Van Sluys,
- Otavio H. Thiemann,
- Eiko E. Kuramae,
- Roberto V. Santelli,
- Celso L. Marino,
- Maria L.P.N. Targon,
- Jesus A. Ferro,
- Henrique C.S. Silveira,
- Danyelle C. Marini,
- Eliana G.M. Lemos,
- Claudia B. Monteiro-Vitorello,
- José H.M. Tambor,
- Dirce M. Carraro,
- Patrícia G. Roberto,
- Vanderlei G. Martins,
- Gustavo H. Goldman,
- Regina C. de Oliveira,
- Daniela Truffi,
- Carlos A. Colombo,
- Magdalena Rossi,
- Paula G. de Araujo,
- Susana A. Sculaccio,
- Aline Angella,
- Marleide M.A. Lima,
- Vicente E. de Rosa, Jr,
- Fábio Siviero,
- Virginia E. Coscrato,
- Marcos A. Machado,
- Laurent Grivet,
- Sonia M.Z. Di Mauro,
- Francisco G. Nobrega,
- Carlos F.M. Menck,
- Marilia D.V. Braga,
- Guilherme P. Telles,
- Frank A.A. Cara,
- Guilherme Pedrosa,
- João Meidanis,
- and Paulo Arruda
Genome Res. December 2003 13: 2725-2735; Published in Advance January 1, 2003, doi:10.1101/gr.1532103
...to have been covered ( Dufour et al. 1997 ). Synteny with other grasses has been described based on genetic map comparisons done with common marker sets. Such comparisons have shown that collinearity between sugarcane and sorghum chromosomes is high ( Ming et al. 1998 ). A bacterial artificial chromosome...
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METHODS: The Automatic Detection of Homologous Regions (ADHoRe) and Its Application to Microcolinearity Between Arabidopsis and Rice
- Klaas Vandepoele,
- Yvan Saeys,
- Cedric Simillion,
- Jeroen Raes,
- and Yves Van de Peer
Genome Res. November 1, 2002 12: 1792-1801; doi:10.1101/gr.400202
...gene pairs. We predict the number of homologous regions and the extent of microcolinearity to increase significantly once better annotations of the rice become available. Comparative analysis has demonstrated that across different plant species, which diverged from a common ancestor but currently tend...

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