Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. The Rice Chromosome 3 Sequencing Consortium

C. Robin Buell, W. Richard McCombie, Rod A Wing, Qiaoping Yuan, Shu Ouyang, Jia Liu, Wei Zhu, Aihui Wang, Rama Maiti, Brian Haas, Jennifer Wortman, Mihaela Pertea, Kristine M. Jones, Mary Kim, Larry Overton, Tamara Tsitrin, Douglas Fadrosh, Jayati Bera, Jayati Weaver, Shaohua JinShivani Johri, Matt Reardon, Kristen Webb, Jessica Hill, Kelly Moffat, Luke Tallon, Susan Van Aken, Matthew Lewis, Teresa Utterback, Tamara Feldblyum, Victoria Zismann, Stacey Iobst, Joseph Hsiao, Aymeric R. De Vazeille, Steven L. Salzberg, Owen White, Claire Fraser, Yeisoo Yu, HeyRan Kim, Teri Rambo, Jennifer Currie, Kristi Collura, Shelly Kernodle-Thompson, Fusheng Wei, David A Kudrna, Jetty Siva S Ammiraju, Meizhong Luo, Jos Luis Goicoechea, Rod A. Wing, David Henry, Ryan Oates, Michael Palmer, Gina Pries, Christopher Saski, Jessica Simmons, Carol Soderlund, William Nelson, Carol Soderlund, Melissa De La Bastide, Lori Spiegel, Lidia Nascimento, Emily Huang, Raymond Preston, Theresa Zutavern, Lance Palmer, Andrew O'haughnessy, Sujit Dike, W. Richard McCombie, Pat Minx, Holly Cordum, Richard Wilson, Weiwei Jin, Hye Ran Lee, Jiming Jiang, Scott Jackson

Research output: Contribution to journalArticle

51 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)1284-1291
Number of pages8
JournalGenome Research
Volume15
Issue number9
DOIs
StatePublished - Sep 2005

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Synteny
Chromosomes, Human, Pair 3
Poaceae
Sequence Analysis
Zea mays
Sorghum
Chromosomes
Databases
Genes
Proteins
DNA Transposable Elements
Oryza
Expressed Sequence Tags
Proteome
Arabidopsis
Triticum
Genome
Amino Acids

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 journalArticle

Buell, CR, McCombie, WR, Wing, RA, Yuan, Q, Ouyang, S, Liu, J, Zhu, W, Wang, A, Maiti, R, Haas, B, Wortman, J, Pertea, M, Jones, KM, Kim, M, Overton, L, Tsitrin, T, Fadrosh, D, Bera, J, Weaver, J, Jin, S, Johri, S, Reardon, M, Webb, K, Hill, J, Moffat, K, Tallon, L, Van Aken, S, Lewis, M, Utterback, T, Feldblyum, T, Zismann, V, Iobst, S, Hsiao, J, De Vazeille, AR, Salzberg, SL, White, O, Fraser, C, Yu, Y, Kim, H, Rambo, T, Currie, J, Collura, K, Kernodle-Thompson, S, Wei, F, Kudrna, DA, Ammiraju, JSS, Luo, M, Goicoechea, JL, Wing, RA, Henry, D, Oates, R, Palmer, M, Pries, G, Saski, C, Simmons, J, Soderlund, C, Nelson, W, Soderlund, C, De La Bastide, M, Spiegel, L, Nascimento, L, Huang, E, Preston, R, Zutavern, T, Palmer, L, O'haughnessy, A, Dike, S, McCombie, WR, Minx, P, Cordum, H, Wilson, R, Jin, W, Lee, HR, Jiang, J & Jackson, S 2005, 'Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. The Rice Chromosome 3 Sequencing Consortium', Genome Research, vol. 15, no. 9, pp. 1284-1291. https://doi.org/10.1101/gr.3869505
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. / Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. The Rice Chromosome 3 Sequencing Consortium. In: Genome Research. 2005 ; Vol. 15, No. 9. pp. 1284-1291.
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title = "Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. The Rice Chromosome 3 Sequencing Consortium",
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.",
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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.

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