Isolation and characterization of conserved non-coding sequences among rice (Oryza sativa L.) paralogous regions

被引：5

作者：

Li, Xianran ^{[1
,2
,3
,4
]}

Tan, Lubin ^{[1
,2
,3
,4
]}

Wang, Liguo ^{[5
]}

Hu, Songnian ^{[5
]}

Sun, Chuanqing ^{[1
,2
,3
,4
]}

机构：

[1] China Agr Univ, Dept Genet & Plant Breeding, State Key Lab Plant Physiol & Biochem, Beijing 100193, Peoples R China

[2] Natl Ctr Evaluat Agr Wild Plants Rice, Beijing 100193, Peoples R China

[3] Minist Educ, Key Lab Crop Heterosis & Utilizat, Beijing 100193, Peoples R China

[4] Minist Agr, Key Lab Crop Genet Improvement & Genome, Beijing 100193, Peoples R China

[5] Chinese Acad Sci, Beijing Inst Gen, Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China

来源：

MOLECULAR GENETICS AND GENOMICS | 2009年 / 281卷 / 01期

关键词：

Oryza sativa L; Conserved non-coding sequence; Metabolic network; ELEMENTS; GENES; EVOLUTION; ENHANCER; GENOMES; TOOL;

D O I：

10.1007/s00438-008-0388-4

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Segmental duplication is particularly frequent within plant genomes and the ability of the original single-copy gene to gain a new function for the change of regulatory elements is one of the prominent consequences of duplication. Thus, it is important to study the pattern of conserved non-coding sequence (CNS) between paralogous genes. We report the result of a survey of CNSs among paralogous regions in rice (Oryza sativa L.), as well as the comparison of CNS dataset between rice and Arabidopsis thaliana. Some common properties, such as the change of A + T content near the CNS boundaries and CNS are enriched in regulatory genes, were observed. However, the content of CNSs differs between rice and Arabidopsis, and it is interesting that the rice metabolic network includes both CNS-poor and CNS-rich genes, which indicated a fine-tuned metabolic network presents in rice.

引用

页码：11 / 18

页数：8

共 29 条

[11] Utility and distribution of conserved noncoding sequences in the grasses [J].

Kaplinsky, NJ ;

Braun, DM ;

Penterman, J ;

Goff, SA ;

Freeling, M .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (09) :6147-6151

[12] Analysis of the genome sequence of the flowering plant Arabidopsis thaliana [J].

Kaul, S ;

Koo, HL ;

Jenkins, J ;

Rizzo, M ;

Rooney, T ;

Tallon, LJ ;

Feldblyum, T ;

Nierman, W ;

Benito, MI ;

Lin, XY ;

Town, CD ;

Venter, JC ;

Fraser, CM ;

Tabata, S ;

Nakamura, Y ;

Kaneko, T ;

Sato, S ;

Asamizu, E ;

Kato, T ;

Kotani, H ;

Sasamoto, S ;

Ecker, JR ;

Theologis, A ;

Federspiel, NA ;

Palm, CJ ;

Osborne, BI ;

Shinn, P ;

Conway, AB ;

Vysotskaia, VS ;

Dewar, K ;

Conn, L ;

Lenz, CA ;

Kim, CJ ;

Hansen, NF ;

Liu, SX ;

Buehler, E ;

Altafi, H ;

Sakano, H ;

Dunn, P ;

Lam, B ;

Pham, PK ;

Chao, Q ;

Nguyen, M ;

Yu, GX ;

Chen, HM ;

Southwick, A ;

Lee, JM ;

Miranda, M ;

Toriumi, MJ ;

Davis, RW .

NATURE, 2000, 408 (6814) :796-815

[13] Enrichment of regulatory signals in conserved non-coding genomic sequence [J].

Levy, S ;

Hannenhalli, S ;

Workman, C .

BIOINFORMATICS, 2001, 17 (10) :871-877

[14] Plant conserved non-coding sequences and paralogue evolution [J].

Lockton, S ;

Gaut, BS .

TRENDS IN GENETICS, 2005, 21 (01) :60-65

[15] The map-based sequence of the rice genome [J].

Matsumoto, T ;

Wu, JZ ;

Kanamori, H ;

Katayose, Y ;

Fujisawa, M ;

Namiki, N ;

Mizuno, H ;

Yamamoto, K ;

Antonio, BA ;

Baba, T ;

Sakata, K ;

Nagamura, Y ;

Aoki, H ;

Arikawa, K ;

Arita, K ;

Bito, T ;

Chiden, Y ;

Fujitsuka, N ;

Fukunaka, R ;

Hamada, M ;

Harada, C ;

Hayashi, A ;

Hijishita, S ;

Honda, M ;

Hosokawa, S ;

Ichikawa, Y ;

Idonuma, A ;

Iijima, M ;

Ikeda, M ;

Ikeno, M ;

Ito, K ;

Ito, S ;

Ito, T ;

Ito, Y ;

Iwabuchi, A ;

Kamiya, K ;

Karasawa, W ;

Kurita, K ;

Katagiri, S ;

Kikuta, A ;

Kobayashi, H ;

Kobayashi, N ;

Machita, K ;

Maehara, T ;

Masukawa, M ;

Mizubayashi, T ;

Mukai, Y ;

Nagasaki, H ;

Nagata, Y .

NATURE, 2005, 436 (7052) :793-800

[16] Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis [J].

McEwen, GK ;

Woolfe, A ;

Goode, D ;

Vavouri, T ;

Callaway, H ;

Elgar, G .

GENOME RESEARCH, 2006, 16 (04) :451-465

[17] The TIGR Rice Genome Annotation Resource: Improvements and new features [J].

Ouyang, Shu ;

Zhu, Wei ;

Hamilton, John ;

Lin, Haining ;

Campbell, Matthew ;

Childs, Kevin ;

Thibaud-Nissen, Francoise ;

Malek, Renae L. ;

Lee, Yuandan ;

Zheng, Li ;

Orvis, Joshua ;

Haas, Brian ;

Wortman, Jennifer ;

Buell, C. Robin .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D883-D887

[18] In vivo enhancer analysis of human conserved non-coding sequences [J].

Pennacchio, Len A. ;

Ahituv, Nadav ;

Moses, Alan M. ;

Prabhakar, Shyam ;

Nobrega, Marcelo A. ;

Shoukry, Malak ;

Minovitsky, Simon ;

Dubchak, Inna ;

Holt, Amy ;

Lewis, Keith D. ;

Plajzer-Frick, Ingrid ;

Akiyama, Jennifer ;

De Val, Sarah ;

Afzal, Veena ;

Black, Brian L. ;

Couronne, Olivier ;

Eisen, Michael B. ;

Visel, Axel ;

Rubin, Edward M. .

NATURE, 2006, 444 (7118) :499-502

[19] Accelerated evolution of conserved noncoding sequences in humans [J].

Prabhakar, Shyam ;

Noonan, James P. ;

Paeaebo, Svante ;

Rubin, Edward M. .

SCIENCE, 2006, 314 (5800) :786-786

[20] Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus m maize [J].

Salvi, Silvio ;

Sponza, Giorgio ;

Morgante, Michele ;

Tomes, Dwight ;

Niu, Xiaomu ;

Fengler, Kevin A. ;

Meeley, Robert ;

Ananiev, Evgueni V. ;

Svitashev, Sergei ;

Bruggemann, Edward ;

Li, Bailin ;

Hainey, Christine F. ;

Radovic, Slobodanka ;

Zaina, Giusi ;

Rafalski, J.-Antoni ;

Tingey, Scott V. ;

Miao, Guo-Hua ;

Phillips, Ronald L. ;

Tuberosa, Roberto .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (27) :11376-11381

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