Abstract
Rice (Oryza sativa L.) chromosome 3 is evolutionarily conserved across the cultivated cereals and shares large blocks of synteny with maize and sorghum, which diverged from rice more than 50 million years ago. To begin to completely understand this chromosome, we sequenced, finished, and annotated 36.1 Mb (∼97%) from O. sativa subsp. japonica cv Nipponbare. Annotation features of the chromosome include 5915 genes, of which 913 are related to transposable elements. A putative function could be assigned to 3064 genes, with another 757 genes annotated as expressed, leaving 2094 that encode hypothetical proteins. Similarity searches against the proteome of Arabidopsis thaliana revealed putative homologs for 67% of the chromosome 3 proteins. Further searches of a nonredundant amino acid database, the Pfam domain database, plant Expressed Sequence Tags, and genomic assemblies from sorghum and maize revealed only 853 nontransposable element related proteins from chromosome 3 that lacked similarity to other known sequences. Interestingly, 426 of these have a paralog within the rice genome. A comparative physical map of the wild progenitor species, Oryza nivara, with japonica chromosome 3 revealed a high degree of sequence identity and synteny between these two species, which diverged ∼10,000 years ago. Although no major rearrangements were detected, the deduced size of the O. nivara chromosome 3 was 21% smaller than that of japonica. Synteny between rice and other cereals using an integrated maize physical map and wheat genetic map was strikingly high, further supporting the use of rice and, in particular, chromosome 3, as a model for comparative studies among the cereals.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 1284-1291 |
| Number of pages | 8 |
| Journal | Genome Research |
| Volume | 15 |
| Issue number | 9 |
| DOIs | |
| State | Published - Sep 2005 |
Fingerprint
ASJC Scopus subject areas
- Genetics
Cite this
Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. The Rice Chromosome 3 Sequencing Consortium. / Buell, C. Robin; McCombie, W. Richard; Wing, Rod A; Yuan, Qiaoping; Ouyang, Shu; Liu, Jia; Zhu, Wei; Wang, Aihui; Maiti, Rama; Haas, Brian; Wortman, Jennifer; Pertea, Mihaela; Jones, Kristine M.; Kim, Mary; Overton, Larry; Tsitrin, Tamara; Fadrosh, Douglas; Bera, Jayati; Weaver, Jayati; Jin, Shaohua; Johri, Shivani; Reardon, Matt; Webb, Kristen; Hill, Jessica; Moffat, Kelly; 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; Yu, Yeisoo; Kim, HeyRan; Rambo, Teri; Currie, Jennifer; Collura, Kristi; Kernodle-Thompson, Shelly; Wei, Fusheng; Kudrna, David A; Ammiraju, Jetty Siva S; Luo, Meizhong; Goicoechea, Jos Luis; Wing, Rod A.; Henry, David; Oates, Ryan; Palmer, Michael; Pries, Gina; Saski, Christopher; Simmons, Jessica; Soderlund, Carol; Nelson, William; Soderlund, Carol; De La Bastide, Melissa; Spiegel, Lori; Nascimento, Lidia; Huang, Emily; Preston, Raymond; Zutavern, Theresa; Palmer, Lance; O'haughnessy, Andrew; Dike, Sujit; McCombie, W. Richard; Minx, Pat; Cordum, Holly; Wilson, Richard; Jin, Weiwei; Lee, Hye Ran; Jiang, Jiming; Jackson, Scott.
In: Genome Research, Vol. 15, No. 9, 09.2005, p. 1284-1291.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. The Rice Chromosome 3 Sequencing Consortium
AU - Buell, C. Robin
AU - McCombie, W. Richard
AU - Wing, Rod A
AU - Yuan, Qiaoping
AU - Ouyang, Shu
AU - Liu, Jia
AU - Zhu, Wei
AU - Wang, Aihui
AU - Maiti, Rama
AU - Haas, Brian
AU - Wortman, Jennifer
AU - Pertea, Mihaela
AU - Jones, Kristine M.
AU - Kim, Mary
AU - Overton, Larry
AU - Tsitrin, Tamara
AU - Fadrosh, Douglas
AU - Bera, Jayati
AU - Weaver, Jayati
AU - Jin, Shaohua
AU - Johri, Shivani
AU - Reardon, Matt
AU - Webb, Kristen
AU - Hill, Jessica
AU - Moffat, Kelly
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 - Yu, Yeisoo
AU - Kim, HeyRan
AU - Rambo, Teri
AU - Currie, Jennifer
AU - Collura, Kristi
AU - Kernodle-Thompson, Shelly
AU - Wei, Fusheng
AU - Kudrna, David A
AU - Ammiraju, Jetty Siva S
AU - Luo, Meizhong
AU - Goicoechea, Jos Luis
AU - Wing, Rod A.
AU - Henry, David
AU - Oates, Ryan
AU - Palmer, Michael
AU - Pries, Gina
AU - Saski, Christopher
AU - Simmons, Jessica
AU - Soderlund, Carol
AU - Nelson, William
AU - Soderlund, Carol
AU - De La Bastide, Melissa
AU - Spiegel, Lori
AU - Nascimento, Lidia
AU - Huang, Emily
AU - Preston, Raymond
AU - Zutavern, Theresa
AU - Palmer, Lance
AU - O'haughnessy, Andrew
AU - Dike, Sujit
AU - McCombie, W. Richard
AU - Minx, Pat
AU - Cordum, Holly
AU - Wilson, Richard
AU - Jin, Weiwei
AU - Lee, Hye Ran
AU - Jiang, Jiming
AU - Jackson, Scott
PY - 2005/9
Y1 - 2005/9
N2 - Rice (Oryza sativa L.) chromosome 3 is evolutionarily conserved across the cultivated cereals and shares large blocks of synteny with maize and sorghum, which diverged from rice more than 50 million years ago. To begin to completely understand this chromosome, we sequenced, finished, and annotated 36.1 Mb (∼97%) from O. sativa subsp. japonica cv Nipponbare. Annotation features of the chromosome include 5915 genes, of which 913 are related to transposable elements. A putative function could be assigned to 3064 genes, with another 757 genes annotated as expressed, leaving 2094 that encode hypothetical proteins. Similarity searches against the proteome of Arabidopsis thaliana revealed putative homologs for 67% of the chromosome 3 proteins. Further searches of a nonredundant amino acid database, the Pfam domain database, plant Expressed Sequence Tags, and genomic assemblies from sorghum and maize revealed only 853 nontransposable element related proteins from chromosome 3 that lacked similarity to other known sequences. Interestingly, 426 of these have a paralog within the rice genome. A comparative physical map of the wild progenitor species, Oryza nivara, with japonica chromosome 3 revealed a high degree of sequence identity and synteny between these two species, which diverged ∼10,000 years ago. Although no major rearrangements were detected, the deduced size of the O. nivara chromosome 3 was 21% smaller than that of japonica. Synteny between rice and other cereals using an integrated maize physical map and wheat genetic map was strikingly high, further supporting the use of rice and, in particular, chromosome 3, as a model for comparative studies among the cereals.
AB - Rice (Oryza sativa L.) chromosome 3 is evolutionarily conserved across the cultivated cereals and shares large blocks of synteny with maize and sorghum, which diverged from rice more than 50 million years ago. To begin to completely understand this chromosome, we sequenced, finished, and annotated 36.1 Mb (∼97%) from O. sativa subsp. japonica cv Nipponbare. Annotation features of the chromosome include 5915 genes, of which 913 are related to transposable elements. A putative function could be assigned to 3064 genes, with another 757 genes annotated as expressed, leaving 2094 that encode hypothetical proteins. Similarity searches against the proteome of Arabidopsis thaliana revealed putative homologs for 67% of the chromosome 3 proteins. Further searches of a nonredundant amino acid database, the Pfam domain database, plant Expressed Sequence Tags, and genomic assemblies from sorghum and maize revealed only 853 nontransposable element related proteins from chromosome 3 that lacked similarity to other known sequences. Interestingly, 426 of these have a paralog within the rice genome. A comparative physical map of the wild progenitor species, Oryza nivara, with japonica chromosome 3 revealed a high degree of sequence identity and synteny between these two species, which diverged ∼10,000 years ago. Although no major rearrangements were detected, the deduced size of the O. nivara chromosome 3 was 21% smaller than that of japonica. Synteny between rice and other cereals using an integrated maize physical map and wheat genetic map was strikingly high, further supporting the use of rice and, in particular, chromosome 3, as a model for comparative studies among the cereals.
UR - http://www.scopus.com/inward/record.url?scp=24344490228&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=24344490228&partnerID=8YFLogxK
U2 - 10.1101/gr.3869505
DO - 10.1101/gr.3869505
M3 - Article
C2 - 16109971
AN - SCOPUS:24344490228
VL - 15
SP - 1284
EP - 1291
JO - PCR Methods and Applications
JF - PCR Methods and Applications
SN - 1088-9051
IS - 9
ER -