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LETTER: Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana
- Manpreet S. Katari,
- Vivekanand Balija,
- Richard K. Wilson,
- Robert A. Martienssen,
- and W. Richard McCombie
Genome Res. April 2005 15: 496-504; doi:10.1101/gr.3239105
...Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana Manpreet S. Katari 1 , 2 , Vivekanand Balija 1 , Richard K. Wilson 3...
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LETTER: Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa
- Ryan D. Morin,
- Gozde Aksay,
- Elena Dolgosheina,
- H. Alexander Ebhardt,
- Vincent Magrini,
- Elaine R. Mardis,
- S. Cenk Sahinalp,
- and Peter J. Unrau
Genome Res. April 2008 18: 571-584; Published in Advance March 6, 2008, doi:10.1101/gr.6897308
...of Computing Science, Simon Fraser University, Burnaby V5A 1S6, Canada Abstract The diversity of microRNAs and small-interfering RNAs has been extensively explored within angiosperms by focusing on a few key organisms such as Oryza sativa and Arabidopsis thaliana . A deeper division of the plants...
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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
...species (Arabidopsis thaliana, Oryza sativa ssp. Japonica), and two non-grass monocots (Musa acuminata, Zostera marina). Boxes indicate Wolffia-specific, Wolffia-missing, and duckweed-specific genes. (B) Significant (FDR < 0.05) GO terms derived from Wolffia-specific OGs (A) were plotted in two...
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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
...genetics in the grasses . Proc. Natl. Acad. Sci. 95 : 1971 – 1974 . ↵ Goff, S.A. , Ricke, D. , Lan, T.H. , Presting, G. , Wang, R. , Dunn, M. , Glazebrook, J. , Sessions, A. , Oeller, P. , Varma, H. , et al. ( 2002 ) A draft sequence of the rice ( Oryza sativa L. ssp. japonica ) Science 296 : 92 – 100...
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RESOURCE: An SNP Resource for Rice Genetics and Breeding Based on Subspecies Indica and Japonica Genome Alignments
- F. Alex Feltus,
- Jun Wan,
- Stefan R. Schulze,
- James C. Estill,
- Ning Jiang,
- and Andrew H. Paterson
Genome Res. September 2004 14: 1812-1819; doi:10.1101/gr.2479404
...for applications such as DNA marker-assisted breeding. The recent sequencing of representatives from two diverse “subspecies” of rice provides an early glimpse into the genomic structure of variation in a monocot plant. After Arabidopsis (a dicot), the rice ( Oryza sativa ) is the most completely sequenced plant...
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LETTER: Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species Genome Res. September 2005 15: 1284-1291; Published in Advance August 18, 2005, doi:10.1101/gr.3869505

...., Varma, H., et al. 2002 . A draft sequence of the rice ( Oryza sativa L. ssp. japonica ). Science 296 : 92 -100. ↵ Greco, R., Ouwerkerk, P.B., Taal, A.J., Favalli, C., Beguiristain, T., Puigdomenech, P., Colombo, L., Hoge, J.H., and Pereira, A. 2001 . Early and multiple Ac transpositions in rice suitable...
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Resource: Evidence-based gene predictions in plant genomes
- Chengzhi Liang,
- Long Mao,
- Doreen Ware,
- and Lincoln Stein
Genome Res. October 2009 19: 1912-1923; Published in Advance June 18, 2009, doi:10.1101/gr.088997.108
...pipeline uses the Ensembl computing infrastructure with a novel data processing scheme. Using the previously annotated plant genomes, the dicot Arabidopsis thaliana and the monocot Oryza sativa , we show that the cross-species ESTs from within monocot or dicot class are a valuable source of evidence...
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LETTER: The evolutionary fate of MULE-mediated duplications of host gene fragments in rice
- Nikoleta Juretic,
- Douglas R. Hoen,
- Michael L. Huynh,
- Paul M. Harrison,
- and Thomas E. Bureau
Genome Res. September 2005 15: 1292-1297; doi:10.1101/gr.4064205
...( Eddy 1998 ) and RepeatMasker ( http://www.repeatmasker.org ) to identify sequences of the rice [ Oryza sativa , ssp. japonica ; International Rice Genome Sequencing Project 2005 (IRGSP) Build 2.0 pseudomolecules; http://rgp.dna.affrc.go.jp/IRGSP/Build2/build2.html ; DDBJ accessions AP006867-AP006877...
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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
...on information from only one species. New angiosperm sequences ( Table 1 ) promise to qualitatively improve our deductions about the evolution of angiosperm gene repertoire and arrangement. Arabidopsis ( Arabidopsis Genome Initiative 2000 ), rice ( Oryza sativa ) ( International Rice Genome Sequencing Project...
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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
...of the sequence of the two major subspecies of cultivated rice, Oryza sativa ssp. japonica and ssp. indica . The sequence of the japonica cultivar Nipponbare was recently completed by a consortium of 10 countries, which comprised the International Rice Genome Sequencing Project (IRGSP), and represents a map...

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