OMAP Publications

Jacquemin J, C. Chaparro, M. Laudie, A. Berger, F. Gavory, J.L. Goicoechea, R.A. Wing, R. Cooke. 2011.
Long-range and targeted ectopic recombination between the two homeologous chromosomes 11 and 12 in Oryza species
Mol. Biol. Evo.

Tian, Z., Y. Yu, L. Feng, Y. Yu, P. SanMiguel, R.A. Wing, S.R. McCouch, J. Ma, and S.A. Jackson. 2011.
Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis
BMC Genomics 12:142.

Ammiraju, J.S.S, X. Song, M. Luo, N. Sisneros, A. Angelova, D. Kudrna, H.R. Kim, Y. Yu, J.L. Goicoechea, M. Lorieux, N. Kurata, D. Brar, D. Ware, S. Jackson, and R.A. Wing. 2010.
The Oryza BAC Resource: A genus-wide and genome scale tool for exploring rice genome evolution and leveraging useful genetic diversity from wild relatives
Breeding Science 60:536-543.

Chen, M., F. Lu, S.A. Jackson, and R.A. Wing. 2010.
Dynamic Genome Evolution of Oryza - A Genus-Wide Comparative Analysis.
In: Darwin's Heritage Today: Proceedings of the Darwin 200 Beijing International Conference. M. Long, H. Gu, Z. Zhou eds, High Education Press, Beijing, Pp. 76-83.

Gill, N., P. SanMiguel, B.D. Dhillon, B. Aberhnathy, N. Jiang, HR Kim, L. Stein, D. Ware, R.A. Wing and S.A. Jackson. 2010.
Dynamic Oryza genomes: Repetitive DNA sequences as genome modeling agents
RICE 3:251-269.

Goicoechea, J.L, J.S.S. Ammiraju, P.R. Marri, M. Chen, S. Jackson, Y. Yu, S. Rounsley, and R.A. Wing. 2010.
The Future of Rice Genomics: Sequencing the Collective Oryza Genome
RICE 3:89-97.

Hurwitz, B. D. Kudrna, Y. Yu, A. Sebastian, A. Zuccolo, S.A. Jackson, D. Ware, R.A. Wing*, L. Stein*. 2010.
Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza
Plant Journal 63:990-1003. (*co-corresponding authors).

Ammiraju, J.S.S., C. Fan, Y. Yu, X. Song, K.A. Cranston, A.C. Pontaroli, F.L., A. Sanyal, N. Jiang, T. Rambo, J. Currie, K. Collura, J. Talag, J.L. Bennetzen, M. Chen, S. Jackson and R.A. Wing. 2010.
Spatio-temporal patterns of genome evolution in homeologous Adh1 - Adh2 regions from four allotetraploid species of the genus Oryza
Plant Journal 63:430-442.

Gill, N., B.D. Dhillon, B. Abernathy, R.A. Wing and S.A. Jackson. 2010.
Use of fragmentary sequence data to identify Conserved Non-coding Sequences: an example from the genus Oryza
Mol Biol Evol.

Geraldes, A., T. Rambo, R.A. Wing, N. Ferrand, and M.W. Nachman. 2010.
Extensive gene conversion drives the concerted evolution of paralogous copies of the SRY gene in European rabbits
Mol Biol Evol. 27:2437-2440.

Zuccolo, A., A. Sebastian, Y. Yu, S. Jackson, S. Rounsley, D. Billheimer, R.A. Wing. 2010.
Assessing the extent of substitution rate variation of Retrotransposon Long Terminal Repeat sequences in Oryza sativa and Oryza glaberrima
RICE 3:242-250.

Dai, J. Wu, X. Li, X. Wang, C. Jantasuriyarat, D. Kudrna, R.A. Wing, B. Zhou, G.-L. Wang. 2010.
Genomic structure and evolution of the Pi2/9 Locus in wild rice species
Theor Appl Genet. 121:295-309.

Sanyal, A., A. Jetty, F. Lu, Y. Yu, T Rambo, J. Currie, K. Kollura, HR. Kim, J. Ma, P.S. Miguel, M. Chen*, R.A. Wing* and S.A. Jackson*. 2010.
Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and disruptions to microsynteny in sorghum
Mol Biol Evol 27:2487-2506. (*co-corresponding authors).

Cranston, K., B. Hurwitz, M.J. Sanderson, D. Ware, R.A. Wing, L. Stein. 2010.
Phylogenomic analysis of BAC-end sequences in Oryza (Poaceae)
Systematic Botany. 35:512-523.

Cranston, K., B. Hurwitz, D. Ware, L. Stein, R.A. Wing. 2009.
Species trees from highly incongruent gene trees in rice
Systematic Biology 58:489-500.

Gao, D., N. Gill, H.R. Kim, J.G. Walling, W. Zhang, C. Fan, Y. Yu, J. Ma, P. SanMiguel, N. Jiang, Z. Cheng, R.A. Wing, J. Jiang, S.A. Jackson. 2009.
A lineage-specific centromere retrotransposon in Oryza brachyantha
Plant Journal 60:820-831.

Rounsley, S., P.R. Marri, Y. Yu, R. He, N. Sisneros, J.L. Goicoechea, S.J. Lee, A. Angelova, D. Kudrna, M. Luo, J. Affourtit, B. Desany, J. Knight, F. Niazi, M. Egholm, R.A. Wing. 2009.
De novo next generation sequencing of plant genomes
RICE 2:35-43

Lu*, F., J.S.S. Ammiraju*, A. Sanyal*, S. Zhang*, R. Song*, J. Chen, G. Li, Y. Sui, X. Song, Z. Cheng, A.C. deOliveira, J.L. Bennetzen#, S.A. Jackson#, R.A. Wing#, M. Chen# (*Co-first authors, #Co-corresponding authors). 2009.
Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes
Proc Natl Acad Sci USA 106:2071-2076.

Ammiraju, JSS, F. Lu, A. Sanyal, Y. Yu, X. Song, N. Jiang, A.C. Pontaroli, T. Rambo, J. Currie, K. Collura, J. Talag, C. Fan, J.L. Goicoechea, A. Zuccolo, J. Chen, J.L. Bennetzen, M. Chen, S. Jackson, and R.A. Wing. 2008.
Dynamic evolution of Oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set
Plant Cell 20:3191-3209

Fan, C., Y. Zhang, Y. Yu, S. Rounsley, M. Long, R.A. Wing. 2008.
The subtelomere of Oryza sativa chromosome 3 short arm as a hot bed of new gene origination in rice
Molecular Plant 1:839-850.

Zuccolo, A., J.S.S. Ammiraju, H. Kim, A. Sanhyal, S.A. Jackson, R.A. Wing. 2008.
Rapid and differential proliferation of the Ty3-Gypsy LTR-retrotransposon Atlantys in the genus Oryza
RICE 1:85-99.

Kim, H., B. Hurwitz, Y. Yu, K. Collura, N. Gill, P. SanMiguel, J.C. Mullikin, C. Maher, W. Nelson, M. Wissotski, M. Braidotti, D. Kudrna, J.L. Goicoechea, L. Stein, D. Ware, S.A. Jackson, C. Soderlund, R.A. Wing. 2008.
Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza
Genome Biol 9: Article R45.

Roulin, A., B. Piegu, R.A. Wing, O. Panaud. 2008.
Evidence of multiple horizontal transfers of the long terminal repeat retrotransposon RIRE1 within the genus Oryza
Plant J 53:950-959.

Ammiraju, J.S., A. Zuccolo, Y. Yu, X. Song, B. Piegu, F. Chevalier, J.G. Walling, J. Ma, J. Talag, D.S. Brar, P.J. SanMiguel, N. Jiang, S.A. Jackson, O. Panaud, R.A. Wing. 2007.
Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza
Plant J 52:342-351.

Ma, J., R.A. Wing, J.L. Bennetzen, S.A. Jackson. 2007.
Evolutionary history and positional shift of a rice centromere
Genetics 177:1217-1220.

Zuccolo, A., A. Sebastian, J. Talag, Y. Yu, H. Kim, K. Collura, D. Kudrna, R.A. Wing. 2007.
Transposable element distribution, abundance and role in genome size variation in the genus Oryza
BMC Evol Biol 7: 152.

Kim, H., P. San Miguel, W. Nelson, K. Collura, M. Wissotski, J.G. Walling, J.P. Kim, S.A. Jackson, C. Soderlund, R.A. Wing. 2007.
Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type)
Genetics 176:379-390.

R.A. Wing, H.R. Kim, J.L. Goicoechea, Y. Yu, D. Kudrna, A. Zuccolo, S.S.A. Jetty, M. Luo, W. Nelson, J. Ma, P. SanMiguel, B. Hurwitz, D. Ware, D. Brar, D. Mackill, C. Soderlund, L. Stein, S. Jackson. 2007.
The Oryza Map Alignment Project (OMAP): A New Resource for Comparative Genome Studies within Oryza.
In: "Rice Functional Genomics- Challenges, Progress and Prospects". Editor: N. M. Upadhyaya. Springer (pages: 394-409).

Ma, J., R.A. Wing, J.L. Bennetzen, S.A. Jackson. 2007.
Plant centromere organization: a dynamic structure with conserved functions
Trends Genet 23:134-139.

Piegu, B., R. Guyot, N. Picault, A. Roulin, A. Saniyal, H. Kim, K. Collura, D.S. Brar, S. Jackson, R.A. Wing, O. Panaud. 2006.
Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice
Genome Res 16:1262-1269.

Hass-Jacobus, B.L., M. Futrell-Griggs, B. Abernathy, R. Westerman, J.L. Goicoechea, J. Stein, P. Klein, B. Hurwitz, B. Zhou, F. Rakhshan, A. Sanyal, N. Gill, J.Y. Lin, J.G. Walling, M.Z. Luo, J.S. Ammiraju, D. Kudrna, H.R. Kim, D. Ware, R.A. Wing, P. San Miguel, S.A. Jackson. 2006.
Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum
BMC Genomics 7: 199.

Ammiraju, J.S.S., M. Luo, J.L. Goicoechea, W. Wang, D. Kudrna, C. Mueller, J. Talag, H.R. Kim, N.B. Sisneros, B. Blackmon, E. Fang, J.B. Tomkins, D. Brar, D. MacKill, S. McCouch, N. Kurata, G. Lambert, D.W. Galbraith, K. Arumuganathan, K. Rao, J.G. Walling, N. Gill , Y. Yu, P. SanMiguel, C. Soderlund, S. Jackson, R.A. Wing. (2006).
The Oryza bacterial artificial chromosome library resource: Construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza
Genome Res 16:140-147.

The Rice Chromosome 3 Sequencing Consortium (R. Buell, W.R. McCombie & R.A. Wing ?C Corresponding Authors). 2005.
Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species
Genome Res 15:1-10.

Wing, R.A., J.S.S. Ammiraju, M. Luo, H.R. Kim, Y. Yu, D. Kudrna, J.L. Goicoechea, W. Wang, W. Nelson, K. Rao, C. Soderlund, D. Brar, D.J. Mackill, B. Han, L. Stein, P. SanMiguel, S. Jackson. 2005.
The Oryza Map Alignment Project: The golden path to unlocking the genetic potential of wild rice species
Plant Mol Biol 59:53-62.