Insights into the bamboo genome: Syntenic relationships to rice and sorghum

Journal of Integrative Plant Biology

Volumn 52, Issue 11, 2010, Pages 1008-1015

  Gui, Yi Jie ^a   Zhou, Yan ^b,d   Wang, Yu ^a   Wang, Sheng ^c   Wang, Sheng Yue ^d   Hu, Yan ^e   Bo, Shi Ping ^a   Chen, Huan ^a   Zhou, Chang Ping ^f   Ma, Nai Xun ^g   Zhang, Tian Zhen ^e   Fan, Long Jiang ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b FUDAN UNIVERSITY   (China)

^c HANGZHOU DIANZI UNIVERSITY   (China)

^d CHINESE NATIONAL HUMAN GENOME CENTER AT SHANGHAI   (China)

^e NANJING AGRICULTURAL UNIVERSITY   (China)

^f Zhejiang Anji Bamboo Exposition Garden   (China)

^g RESEARCH INSTITUTE OF FORESTRY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BAMBOO; CHROMOSOME; GENOME; PHYLOGENETICS; RICE;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; BAMBUSA; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; MAIZE; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; PLANT GENE; PLANT GENOME; RICE; SORGHUM; SYNTENY;

BAMBUSA; BASE SEQUENCE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CLONING, MOLECULAR; GENES, PLANT; GENOME, PLANT; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; SORGHUM; SYNTENY; ZEA MAYS;

BACTERIA (MICROORGANISMS); BAMBUSOIDEAE; PHYLLOSTACHYS PUBESCENS; POACEAE;

EID: 77958542585     PISSN: 16729072     EISSN: 17447909     Source Type: Journal    
DOI: 10.1111/j.1744-7909.2010.00965.x     Document Type: Article

References (23)

1. Chaparro C, Guyot R, Zuccolo A, Piegu B, Panaud O (2007) RetrOryza: a database of the rice LTR-retrotransposons. Nucleic Acids Res. 35, D66-D70.
2. Clark LG (1996) Diversity, biogeography and evolution of Chusquea. In: Chapman GP, ed. International Symposium on Bamboos. Academic Press Ltd, London
3. Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y, Hu X, Jia P, Zhao Q, Ying K, Yu S, Tang Y, Weng Q, Zhang L, Lu Y, Mu J, Zhang LS, Yu Z, Fan D, Liu X, Lu T, Li C, Wu Y, Sun T, Lei H, Li T, Hu H, Guan J, Wu M, Zhang R, Zhou B, Chen Z, Chen L, Jin Z, Wang R, Yin H, Cai Z, Ren S, Lv G, Gu W, Zhu G, Tu Y, Jia J, Chen J, Kang H, Chen X, Shao C, Sun Y, Hu Q, Zhang X, Zhang W, Wang L, Ding C, Sheng H, Gu J, Chen S, Ni L, Zhu F, Chen W, Lan L, Lai Y, Cheng Z, Gu M, Jiang J, Li J, Hong G, Xue Y, Han B (2002) Sequence and analysis of rice chromosome 4. Nature 420, 316-320.
4. Gaut BS (2002) Evolutionary dynamics of grass genomes. New Phytol. 154, 15-28.
5. Gaut BS, Morton BR, McCaig BC, Clegg MT (1996) Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc. Natl. Acad. Sci. USA 93, 10274-10279.
6. Gielis J, Valente P, Bridts C, Verbelen JP (1996) Estimation of DNA content of bamboos using flow cytometry and confocal laser scanning microscopy. In: Chapman GP, ed. International Symposium on Bamboos. Academic Press Ltd, London
7. Gui Y, Wang S, Quan L, Zhou C, Long S, Zheng H, Jin L, Zhang X, Ma N, Fan L (2007) Genome size and sequence composition of moso bamboo: a comparative study. Sci. China Ser. C 50, 700-705.
8. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436, 793-800.
9. Jiang ZH (2002) Bamboo and Rattan in the World. Liaoning Science and Technology Publishing House, Shenyang
10. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462-467.
11. Klinkenborg V (2001) Bamboo for Gardens. Times Book Rev, New York
12. Kellogg EA (1998) Relationships of cereal crops and other grasses. Proc. Natl. Acad. Sci. USA 95, 2005-2010.
13. Koressaar T, Remm M (2007) Enhancements and modifications of primer design program Primer3. Bioinformatics 23, 1289-1291.
14. Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5, 150-163.
15. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380.
16. Ouyang S, Buell CR (2004) The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res. 32, D360-D363.
17. Paterson AH, Freeling M, Sasaki T (2005) Grains of knowledge: genomics of model cereals. Genome Res. 15, 1643-1650.
18. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob ur R, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS (2009) The sorghum bicolor genome and the diversification of grasses. Nature 457, 551-556.
19. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat. Genet. 20, 43-45.
20. Tettelin H, Radune D, Kasif S, Khouri H, Salzberg SL (1999) Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project. Genomics 62, 500-507.
21. Tu Z (2001) Eight novel families of miniature inverted repeat transposable elements in the African malaria mosquito, Anopheles gambiae. Proc. Natl. Acad. Sci. USA 98, 1699-1704.
22. Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, Zhang J, Zhang Y, Li R, Xu Z, Li X, Zheng H, Cong L, Lin L, Yin J, Geng J, Li G, Shi J, Liu J, Lv H, Li J, Deng Y, Ran L, Shi X, Wang X, Wu Q, Li C, Ren X, Li D, Liu D, Zhang X, Ji Z, Zhao W, Sun Y, Zhang Z, Bao J, Han Y, Dong L, Ji J, Chen P, Wu S, Xiao Y, Bu D, Tan J, Yang L, Ye C, Xu J, Zhou Y, Yu Y, Zhang B, Zhuang S, Wei H, Liu B, Lei M, Yu H, Li Y, Xu H, Wei S, He X, Fang L, Huang X, Su Z, Tong W, Tong Z, Ye J, Wang L, Lei T, Chen C, Chen H, Huang H, Zhang F, Li N, Zhao C, Huang Y, Li L, Xi Y, Qi Q, Li W, Hu W, Tian X, Jiao Y, Liang X, Jin J, Gao L, Zheng W, Hao B, Liu S, Wang W, Yuan L, Cao M, McDermott J, Samudrala R, Wong GK, Yang H (2005) The genome of Oryza sativa: a history of duplications. PLoS Biol. 3, e38.
23. Zhang H (2000). Construction and Manipulation of Large-insert Bacterial Clone Libraries-Manual. Texas A&M University, Texas