Global characterization of the root transcriptome of a wild species of rice, Oryza longistaminata, by deep sequencing

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Yang, Haiyuan ^a   Hu, Liwei ^a   Hurek, Thomas ^a   Reinhold Hurek, Barbara ^a  

^a UNIVERSITY OF BREMEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; NITROGEN;

ARTICLE; CONTIG MAPPING; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE FUNCTION; NITROGEN AVAILABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; ORYZA LONGISTAMINATA; PLANT LEAF; PLANT ROOT; PLANT SEED; PROTEIN DATABASE; PYROSEQUENCING; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RICE; SEQUENCE HOMOLOGY; SOUTHERN BLOTTING; TRANSCRIPTOMICS; UNINDEXED SEQUENCE; WILD SPECIES; CHROMOSOME MAP; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HIGH THROUGHPUT NUCLEOTIDE SEQUENCING; METHODOLOGY; MOLECULAR GENETICS; PLANT GENOME; REPRODUCIBILITY; SPECIES DIFFERENCE;

ORYZA LONGISTAMINATA; ORYZA SATIVA; ZIZANIA;

CHROMOSOME MAPPING; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; PLANT ROOTS; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 78650038997     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-705     Document Type: Article

References (34)

1. Choudhury TMA, Khanif YM. Evaluation of effects of nitrogen and magnesium fertilization on rice yield and fertilizer nitrogen efficiency using 15N tracer technique. J Plant Nutr 2001, 24:855-871.
2. De Datta SK, Buresh RJ. Integrated nitrogen management in irrigated rice. Adv Soil Sci 1989, 10:143-169.
3. Ponnamperuma FN. The chemistry of submerged soils. Advan Agron 1972, 24:29-96.
4. Sturz AV, Christie BR, Nowak J. Bacterial endophytes: Potential role in developing sustainable systems of crop production. Crit Rev Plant Sci 2000, 19:1-30.
5. Choudhury ATMA, Kennedy IR. Prospects and potentials for systems of biological nitrogen fixation in sustainable rice production. Biol Fertil Soils 2004, 39:219-227.
6. Bi YM, Kant S, Clarke J, Gidda S, Ming F, Xu J, Rochon A, Shelp BJ, Hao L, Zhao R, Mullen RT, Zhu T, Rothstein SJ. Increased nitrogen-use efficiency in transgenic rice plants over-expressing a nitrogen-responsive early nodulin gene identified from rice expression profiling. Plant Cell Environ 2009, 32:1749-1760. 10.1111/j.1365-3040.2009.02032.x, 19682292.
7. Lian X, Wang S, Zhang J, Feng Q, Zhang L, Fan D, Li X, Yuan D, Han B, Zhang Q. Expression profiles of 10,422 genes at early stage of low nitrogen stress in rice assayed using a cDNA microarray. Plant Mol Biol 2006, 60:617-631. 10.1007/s11103-005-5441-7, 16649102.
8. Shrawat AK, Carroll RT, DePauw M, Taylor GJ, Good AG. Genetic engineering of improved nitrogen use efficiency in rice by the tissue-specific expression of alanine aminotransferase. Plant Biotechnol J 2008, 6:722-732. 10.1111/j.1467-7652.2008.00351.x, 18510577.
9. Ge S, Sang T, Lu BR, Hong DY. Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc Natl Acad Sci USA 1999, 96:14400-14405. 10.1073/pnas.96.25.14400, 24448, 10588717.
10. Li C-B, Zhang D-M, Lu B-R, Hong D-Y. Differentiation and inter-genomic relationships among C, E and D genomes in the Oryza officinalis complex (Poaceae) as revealed by multicolor genomic in situ hybridization. Theoret Appl Genet 2001, 103:197-203.
11. Brar DS, Khush GS. Alien introgression in rice. Plant Mol Biol 1997, 35:35-47. 10.1023/A:1005825519998, 9291958.
12. Tanksley SD, McCouch SR. Seed banks and molecular maps: unlocking genetic potential from the wild. Science 1997, 277:1063-1066. 10.1126/science.277.5329.1063, 9262467.
13. Xiao J, Li J, Grandillo S, Ahn SN, Yuan L, Tanksley SD, McCouch SR. Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon. Genetics 1998, 150:899-909. 1460369, 9755218.
14. Xiao J, Grandillo S, Ahn SN, McCouch SR, Tanksley SD, Li J, Yuan L. Genes from wild rice improve yield. Nature 1996, 384:223-224.
15. Hu FY, Tao DY, Sacks E, Fu BY, Xu P, Li J, Yang Y, McNally K, Khush GS, Paterson AH, Li ZK. Convergent evolution of perenniality in rice and sorghum. Proc Natl Acad Sci USA 2003, 100:4050-4054. 10.1073/pnas.0630531100, 153046, 12642667.
16. Sacks EJ, Roxas JP, Sta Cruz MT. Developing perennial upland rice II: Filed performance of S1 families from an intermated Oryza sativa/O. longistaminata population. Crop Sci 2003, 43:129-134.
17. Song WY, Wang GL, Chen LL, Kim HS, Pi LY, Holsten T, Gardner J, Wang B, Zhai WX, Zhu LH, Fauquet C, Ronald P. A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 1995, 270:1804-1806. 10.1126/science.270.5243.1804, 8525370.
18. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Li J, Liu Z, Qi Q, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Zhao W, Li P, Chen W, Zhang Y, Hu J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Tao M, Zhu L, Yuan L, Yang H. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 2002, 296:79-92. 10.1126/science.1068037, 11935017.
19. Matsumoto T, Wu J, Kanamori H, Katayose Y, Fujisawa M, Namiki N, Mizuno H, Yamamoto K, Antonio B, 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, Naito S, Nakashima M, Nakama Y, Nakamichi Y, Nakamura M, Meguro A, Negishi M, Ohta I, Ohta T, Okamoto M, Ono N, Saji S, Sakaguchi M, Sakai K, Shibata M, Shimokawa T, Song J, Takazaki Y, Terasawa K, Tsugane M, Tsuji K, Ueda S, Waki K, Yamagata H, Yamamoto M, Yamamoto S, Yamane H, Yoshiki S, Yoshihara R, Yukawa K, Zhong H, Yano M, Sasaki T, Yuan Q, Shu O, Liu J, Jones K, Gansberger K, Moffat K, Hill J, Bera J, Fadrosh D, Jin S, Johri S, Kim M, Overton L, Reardon M, Tsitrin T, Vuong H, Weaver B, Ciecko A, Tallon L, Jackson J, Pai G, Van Aken S, Utterback T, Reidmuller S, Feldblyum T, Hsiao J, Zismann V, Iobst S, de Vazeille A, Buell C, Ying K, Li Y, Lu T, Huang Y, Zhao Q, Feng Q, Zhang L, Zhu J, Weng Q, Mu J, Lu Y, Fan D, Liu Y, Guan J, Zhang Y, Yu S, Liu X, Zhang Y, Hong G, Han B, Choisne N, Demange N, Orjeda G, Samain S, Cattolico L, Pelletier E, Couloux A, Segurens B, Wincker P, D'Hont A, Scarpelli C, Weissenbach J, Salanoubat M, Quetier F, Yu Y, Kim H, Rambo T, Currie J, Collura K, Luo M, Yang T, Ammiraju J, Engler F, Soderlund C, Wing R, Palmer L, de la Bastide M, Spiegel L, Nascimento L, Zutavern T, O'Shaughnessy A, Dike S, Dedhia N, Preston R, Balija V, McCombie W, Chow T, Chen H, Chung M, Chen C, Shaw J, Wu H, Hsiao K, Chao Y, Chu M, Cheng C, Hour A, Lee P, Lin S, Lin Y, Liou J, Liu S, Hsing Y, Raghuvanshi S, Mohanty A, Bharti A, Gaur A, Gupta V, Kumar D, Ravi V, Vij S, Kapur A, Khurana P, Khurana J, Tyagi A, Gaikwad K, Singh A, Dalal V, Srivastava S, Dixit A, Pal A, Ghazi I, Yadav M, Pandit A, Bhargava A, Sureshbabu K, Batra K, Sharma T, Mohapatra T, Singh N, Messing J, Nelson A, Fuks G, Kavchok S, Keizer G, Llaca E, Song R, Tanyolac B, Young S, Il K, Hahn J, Sangsakoo G, Vanavichit A, de Mattos L, Zimmer P, Malone G, Dellagostin O, de Oliveira A, Bevan M, Bancroft I, Minx P, Cordum H, Wilson R, Cheng Z, Jin W, Jiang J, Leong S, Iwama H, Gojobori T, Itoh T, Niimura Y, Fujii Y, Habara T, Sakai H, Sato Y, Wilson G, Kumar K, McCouch S, Juretic N, Hoen D, Wright S, Bruskiewich R, Bureau T, Miyao A, Hirochika H, Nishikawa T, Kadowaki K, Sugiura M. The map-based sequence of the rice genome. Nature 2005, 436:793-800. 10.1038/nature03895, 16100779.
20. Cho SK, Ok SH, Jeung JU, Shim KS, Jung KW, You MK, Kang KH, Chung YS, Choi HC, Moon HP, Shin JS. Comparative analysis of 5,211 leaf ESTs of wild rice (Oryza minuta). Plant Cell Rep 2004, 22:839-847. 10.1007/s00299-004-0764-4, 14968263.
21. Lu T, Yu S, Fan D, Mu J, Shangguan Y, Wang Z, Minobe Y, Lin Z, Han B. Collection and comparative analysis of 1888 full-length cDNAs from wild rice Oryza rufipogon Griff. W1943. DNA Res 2008, 15:285-295. 10.1093/dnares/dsn018, 2575888, 18687674.
22. 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. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380. 1464427, 16056220.
23. Wicker T, Schlagenhauf E, Graner A, Close TJ, Keller B, Stein N. 454 sequencing put to the test using the complex genome of barley. BMC Genomics 2006, 7:275-286. 10.1186/1471-2164-7-275, 1633745, 17067373.
24. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008, 26:1135-1145. 10.1038/nbt1486, 18846087.
25. Knauth S, Hurek T, Brar D, Reinhold-Hurek B. Influence of different Oryza cultivars on expression of nifH gene pools in roots of rice. Environ Microbiol 2005, 7:1725-1733. 10.1111/j.1462-2920.2005.00841.x, 16232287.
26. Vega-Arreguin JC, Ibarra-Laclette E, Jimenez-Moraila B, Martinez O, Vielle-Calzada JP, Herrera-Estrella L, Herrera-Estrella A. Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencing. BMC Genomics 2009, 10:299-309. 10.1186/1471-2164-10-299, 2714558, 19580677.
27. Wang W, Wang Y, Zhang Q, Qi Y, Guo D. Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing. BMC Genomics 2009, 10:465-475. 10.1186/1471-2164-10-465, 2763888, 19818120.
28. Hurek T, Reinhold-Hurek B, Van Montagu M, Kellenberger E. Root colonization and systemic spreading of Azoarcus sp. strain BH72 in grasses. J Bacteriol 1994, 176:1913-1923. 205294, 8144457.
29. Egener T, Hurek T, Reinhold-Hurek B. Endophytic expression of nif genes of Azoarcus sp. strain BH72 in rice roots. Mol Plant-Microbe Interact 1999, 12:813-819.
30. Chang S, Puryear J, Cairney J. A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Reporter 1993, 11:113-116.
31. Allen GC, Flores-Vergara MA, Krasynanski S, Kumar S, Thompson WF. A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Nature Protocols 2006, 1:2320-2325. 10.1038/nprot.2006.384, 17406474.
32. Huang X, Madan A. CAP3: A DNA sequence assembly program. Genome Res 1999, 9:868-877. 10.1101/gr.9.9.868, 310812, 10508846.
33. Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000, 132:365-386.
34. Neuhaus-Url G, Neuhaus G. The use of nonradioactive digoxigenin chemiluminescent technology for plant genomic Southern blot hybridization: a comparison with radioactivity. Transgenic Res 1993, 2:115-120.