Abstract
Background: Rice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on the evolution of cereals and other grasses. Therefore, decoding its entire genome will be a prerequisite for applied and basic research on this species and all other cereals. Results: We have determined and analyzed the complete sequences of two of its chromosomes, 11 and 12, which total 55.9 Mb (14.3% of the entire genome length), based on a set of overlapping clones. A total of 5,993 non-transposable element related genes are present on these chromosomes. Among them are 289 disease resistance-like and 28 defense-response genes, a higher proportion of these categories than on any other rice chromosome. A three-Mb segment on both chromosomes resulted from a duplication 7.7 million years ago (mya), the most recent large-scale duplication in the rice genome. Paralogous gene copies within this segmental duplication can be aligned with genomic assemblies from sorghum and maize. Although these gene copies are preserved on both chromosomes, their expression patterns have diverged. When the gene order of rice chromosomes 11 and 12 was compared to wheat gene loci, significant synteny between these orthologous regions was detected, illustrating the presence of conserved genes alternating with recently evolved genes. Conclusion: Because the resistance and defense response genes, enriched on these chromosomes relative to the whole genome, also occur in clusters, they provide a preferred target for breeding durable disease resistance in rice and the isolation of their allelic variants. The recent duplication of a large chromosomal segment coupled with the high density of disease resistance gene clusters makes this the most recently envolved part of the rice genome. Based on syntenic alignments of these chromosomes, rice chromosome 11 and 12 do not appear to have resulted from a single whole-genome duplication event as peviously suggested.
| Original language | English (US) |
|---|---|
| Article number | 20 |
| Journal | BMC Biology |
| Volume | 3 |
| DOIs | |
| State | Published - Sep 27 2005 |
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ASJC Scopus subject areas
- Biotechnology
- Structural Biology
- Developmental Biology
- Physiology
- Plant Science
- Cell Biology
- Ecology, Evolution, Behavior and Systematics
Cite this
The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. / Choisne, Nathalie; Demange, Nadia; Orjeda, Gisela; Samain, Sylvie; D'Hont, Angélique; Cattolico, Laurence; Pelletier, Eric; Couloux, Arnaud; Segurens, Béatrice; Wincker, Patrick; Scarpelli, Claude; Weissenbach, Jean; Salanoubat, Marcel; Singh, Nagendra K.; Mohapatra, Trilochan; Sharma, Tilak R.; Gaikwad, Kishor; Singh, Archana; Dalal, Vivek; Srivastava, Subodh K.; Dixit, Anupam; Pal, Ajit K.; Ghazi, Irfan A.; Yadav, Mahavir; Pandit, Awadhesh; Bhargava, Ashutosh; Sureshbabu, K.; Dixit, Rekha; Singh, Harvinder; Swain, Suresh C.; Pal, Sumita; Ragiba, M.; Singh, Pradeep K.; Singhal, Vibha; Mendiratta, Sangeeta D.; Batra, Kamlesh; Raghuvanshi, Saurabh; Mohanty, Amitabh; Bharti, Arvind K.; Gaur, Anupama; Gupta, Vikrant; Kumar, Dibyendu; Vydianathan, Ravi; Vij, Shuba; Kapur, Anita; Khurana, Parul; Sharma, Sulabha; Khurana, Paramjit; Khurana, Jitendra P.; Tyagi, Akhilesh K.; Yuan, Qiaoping; Ouyang, Shu; Liu, Jia; Zhu, Wei; Wang, Aihui; Lin, Haining; Hamilton, John; Haas, Brian; Wortman, Jennifer; Jones, Kristine M.; Kim, Mary; Overton, Larry; Tsitrin, Tamara; Fadrosh, Douglas; Bera, Jayati; Weaver, Bruce; Jin, Shaohua; Johri, Shivani; Reardon, Matt; Vuong, Hue; Tallon, Luke; Van Aken, Susan; Lewis, Matthew; Utterback, Teresa; Feldblyum, Tamara; Zismann, Victoria; Iobst, Stacey; Hsiao, Joseph; de Vazeille, Aymeric R.; Salzberg, Steven L.; White, Owen; Fraser, Claire; Buell, C. Robin; Yu, Yeisoo; Rambo, Teri; Currie, Jennifer; Collura, Kristi; Kim, Hye Ran; Stum, Diana; Wang, Wenming; Kudrna, David A; Mueller, Christopher; Wing, Rod A; Kramer, Melissa; Spiegel, Lori; Nascimento, Lidia; Preston, Raymond; Zutavern, Theresa; Messing, Joachim.
In: BMC Biology, Vol. 3, 20, 27.09.2005.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications
AU - Choisne, Nathalie
AU - Demange, Nadia
AU - Orjeda, Gisela
AU - Samain, Sylvie
AU - D'Hont, Angélique
AU - Cattolico, Laurence
AU - Pelletier, Eric
AU - Couloux, Arnaud
AU - Segurens, Béatrice
AU - Wincker, Patrick
AU - Scarpelli, Claude
AU - Weissenbach, Jean
AU - Salanoubat, Marcel
AU - Singh, Nagendra K.
AU - Mohapatra, Trilochan
AU - Sharma, Tilak R.
AU - Gaikwad, Kishor
AU - Singh, Archana
AU - Dalal, Vivek
AU - Srivastava, Subodh K.
AU - Dixit, Anupam
AU - Pal, Ajit K.
AU - Ghazi, Irfan A.
AU - Yadav, Mahavir
AU - Pandit, Awadhesh
AU - Bhargava, Ashutosh
AU - Sureshbabu, K.
AU - Dixit, Rekha
AU - Singh, Harvinder
AU - Swain, Suresh C.
AU - Pal, Sumita
AU - Ragiba, M.
AU - Singh, Pradeep K.
AU - Singhal, Vibha
AU - Mendiratta, Sangeeta D.
AU - Batra, Kamlesh
AU - Raghuvanshi, Saurabh
AU - Mohanty, Amitabh
AU - Bharti, Arvind K.
AU - Gaur, Anupama
AU - Gupta, Vikrant
AU - Kumar, Dibyendu
AU - Vydianathan, Ravi
AU - Vij, Shuba
AU - Kapur, Anita
AU - Khurana, Parul
AU - Sharma, Sulabha
AU - Khurana, Paramjit
AU - Khurana, Jitendra P.
AU - Tyagi, Akhilesh K.
AU - Yuan, Qiaoping
AU - Ouyang, Shu
AU - Liu, Jia
AU - Zhu, Wei
AU - Wang, Aihui
AU - Lin, Haining
AU - Hamilton, John
AU - Haas, Brian
AU - Wortman, Jennifer
AU - Jones, Kristine M.
AU - Kim, Mary
AU - Overton, Larry
AU - Tsitrin, Tamara
AU - Fadrosh, Douglas
AU - Bera, Jayati
AU - Weaver, Bruce
AU - Jin, Shaohua
AU - Johri, Shivani
AU - Reardon, Matt
AU - Vuong, Hue
AU - Tallon, Luke
AU - Van Aken, Susan
AU - Lewis, Matthew
AU - Utterback, Teresa
AU - Feldblyum, Tamara
AU - Zismann, Victoria
AU - Iobst, Stacey
AU - Hsiao, Joseph
AU - de Vazeille, Aymeric R.
AU - Salzberg, Steven L.
AU - White, Owen
AU - Fraser, Claire
AU - Buell, C. Robin
AU - Yu, Yeisoo
AU - Rambo, Teri
AU - Currie, Jennifer
AU - Collura, Kristi
AU - Kim, Hye Ran
AU - Stum, Diana
AU - Wang, Wenming
AU - Kudrna, David A
AU - Mueller, Christopher
AU - Wing, Rod A
AU - Kramer, Melissa
AU - Spiegel, Lori
AU - Nascimento, Lidia
AU - Preston, Raymond
AU - Zutavern, Theresa
AU - Messing, Joachim
PY - 2005/9/27
Y1 - 2005/9/27
N2 - Background: Rice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on the evolution of cereals and other grasses. Therefore, decoding its entire genome will be a prerequisite for applied and basic research on this species and all other cereals. Results: We have determined and analyzed the complete sequences of two of its chromosomes, 11 and 12, which total 55.9 Mb (14.3% of the entire genome length), based on a set of overlapping clones. A total of 5,993 non-transposable element related genes are present on these chromosomes. Among them are 289 disease resistance-like and 28 defense-response genes, a higher proportion of these categories than on any other rice chromosome. A three-Mb segment on both chromosomes resulted from a duplication 7.7 million years ago (mya), the most recent large-scale duplication in the rice genome. Paralogous gene copies within this segmental duplication can be aligned with genomic assemblies from sorghum and maize. Although these gene copies are preserved on both chromosomes, their expression patterns have diverged. When the gene order of rice chromosomes 11 and 12 was compared to wheat gene loci, significant synteny between these orthologous regions was detected, illustrating the presence of conserved genes alternating with recently evolved genes. Conclusion: Because the resistance and defense response genes, enriched on these chromosomes relative to the whole genome, also occur in clusters, they provide a preferred target for breeding durable disease resistance in rice and the isolation of their allelic variants. The recent duplication of a large chromosomal segment coupled with the high density of disease resistance gene clusters makes this the most recently envolved part of the rice genome. Based on syntenic alignments of these chromosomes, rice chromosome 11 and 12 do not appear to have resulted from a single whole-genome duplication event as peviously suggested.
AB - Background: Rice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on the evolution of cereals and other grasses. Therefore, decoding its entire genome will be a prerequisite for applied and basic research on this species and all other cereals. Results: We have determined and analyzed the complete sequences of two of its chromosomes, 11 and 12, which total 55.9 Mb (14.3% of the entire genome length), based on a set of overlapping clones. A total of 5,993 non-transposable element related genes are present on these chromosomes. Among them are 289 disease resistance-like and 28 defense-response genes, a higher proportion of these categories than on any other rice chromosome. A three-Mb segment on both chromosomes resulted from a duplication 7.7 million years ago (mya), the most recent large-scale duplication in the rice genome. Paralogous gene copies within this segmental duplication can be aligned with genomic assemblies from sorghum and maize. Although these gene copies are preserved on both chromosomes, their expression patterns have diverged. When the gene order of rice chromosomes 11 and 12 was compared to wheat gene loci, significant synteny between these orthologous regions was detected, illustrating the presence of conserved genes alternating with recently evolved genes. Conclusion: Because the resistance and defense response genes, enriched on these chromosomes relative to the whole genome, also occur in clusters, they provide a preferred target for breeding durable disease resistance in rice and the isolation of their allelic variants. The recent duplication of a large chromosomal segment coupled with the high density of disease resistance gene clusters makes this the most recently envolved part of the rice genome. Based on syntenic alignments of these chromosomes, rice chromosome 11 and 12 do not appear to have resulted from a single whole-genome duplication event as peviously suggested.
UR - http://www.scopus.com/inward/record.url?scp=27544478621&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=27544478621&partnerID=8YFLogxK
U2 - 10.1186/1741-7007-3-20
DO - 10.1186/1741-7007-3-20
M3 - Article
C2 - 16188032
AN - SCOPUS:27544478621
VL - 3
JO - BMC Biology
JF - BMC Biology
SN - 1741-7007
M1 - 20
ER -