Skip to main content

Advertisement

SpringerLink
Log in

A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies

  • Published:
Plant Molecular Biology Aims and scope Submit manuscript

Abstract

Relatively few indica rice full-length cDNAs were available to aid in the annotation of rice genes. The data presented here described the sequencing and analysis of 10,096 full-length cDNAs from Oryza sativa subspecies indica Guangluai 4. Of them, 9,029 matched rice genomic sequences in publicly-available databases, and 1,200 were identified as new rice genes. Comparison with the knowledge-based Oryza Molecular Biological Encyclopedia japonica cDNA collection indicated that 3,316 (41.6%) of the 7,965 indica-japonica cDNA pairs showed no distinct variations at protein level (2,117 indica-japonica cDNA pairs showed fully identical and 1,199 indica-japonica cDNA pairs showed no frame shift). Moreover, 3,645 (45.8%) of the indica-japonica pairs showed substantial differences at the protein level due to single nucleotide polymorphisms (SNPs), insertions or deletions, and sequence-segment variations between indica and japonica subspecies. Further experimental verifications using PCR screening and quantitative reverse transcriptional PCR revealed unique transcripts for indica subspecies. Comparative analysis also showed that most of rice genes were evolved under purifying selection. These variations might distinguish the phenotypic changes of the two cultivated rice subspecies indica and japonica. Analysis of these cDNAs extends known rice genes and identifies new ones in rice.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P,Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res 29:37–41

    Article  PubMed  CAS  Google Scholar 

  • Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL (2004) The Pfam protein familiesdatabase. Nucleic Acids Res 32:D138–D141

    Article  PubMed  CAS  Google Scholar 

  • Bennetzen J (2002) Opening the door to comparative plant biology. Science 296:60–63

    Article  PubMed  Google Scholar 

  • Brent MR (2005) Genome annotation past, present and future: how to define an ORFat each locus. Genome Res 15:1777–1786

    Article  PubMed  CAS  Google Scholar 

  • Campbell MA, Haas BJ, Hamilton JP, Mount SM, Buell CR (2006) Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 7:327 doi: 10.1186/1471-2164-7-327

    Google Scholar 

  • Carninci P, Shibata Y, Hayatsu N, Sugahara Y, Shibata K, Itoh M, Konno H, Okazaki Y, Muramatsu M, Hayashizaki Y (2000) Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Res 10:1617–1630

    Article  PubMed  CAS  Google Scholar 

  • Carninci P, Waki K, Shiraki T, Konno H, Shibata K, Itoh M, Aizawa K, Arakawa T, Ishii Y, Sasaki D, Bono H, Kondo S, Sugahara Y, Saito R, Osato N, Fukuda S, Sato K, Watahiki A, Hirozane-Kishikawa T, Nakamura M, Shibata Y, Yasunishi A, Kikuchi N, Yoshiki A, Kusakabe M, Gustincich S, Beisel K, Pavan W, Aidinis V, Nakagawara A, Held WA, Iwata H, Kono T, Nakauchi H, Lyons P, Wells C, Hume DA, Fagiolini M, Hensch TK, Brinkmeier M, Camper S, Hirota J, Mombaerts P, Muramatsu M, Okazaki Y, Kawai J, Hayashizaki Y (2003) Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Genome Res 13:1273–1289

    Article  PubMed  Google Scholar 

  • Castelli V, Aury JM, Jaillon O, Wincker P, Clepet C, Menard M, Cruaud C, Quetier F, Scarpelli C, Schachter V, Temple G, Caboche M, Weissenbach J, Salanoubat M (2004) Whole genome sequence comparisons and “full-length” cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation. Genome Res 14:406–413

    Article  PubMed  Google Scholar 

  • Chou HH, Holmes MH (2001) DNA sequence quality trimming and vector removal. Bioinformatics 17:1093–1104

    Article  PubMed  CAS  Google Scholar 

  • Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194

    PubMed  CAS  Google Scholar 

  • Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Zhang Q (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice,encodes a putative transmembrane protein. Theor Appl Genet 112:1164–1171

    Article  PubMed  CAS  Google Scholar 

  • Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y, Hu X, Jia P, Zhang Y, Zhao Q, Ying K, Yu S, Tang Y, Weng Q, Zhang L, Lu Y, Mu J, Lu Y, 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, Zhang Y, 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

    Article  PubMed  CAS  Google Scholar 

  • Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631–1638

    Article  PubMed  CAS  Google Scholar 

  • Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence the rice genome Oryza sativa L. ssp. japonica. Science 296:92–100

    Article  PubMed  CAS  Google Scholar 

  • Guigo R, Dermitzakis ET, Agarwal P, Ponting CP, Parra G, Reymond A, Abril JF, Keibler E, Lyle R, Ucla C, Antonarakis SE, Brent MR (2003) Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. Proc Natl Acad Sci USA 100:1140–1145

    Article  PubMed  CAS  Google Scholar 

  • Han B, Xue Y (2003) Genome-wide intraspecific DNA-sequence variations in rice. Curr. Opin Plant Biol 6:134–138

    Article  PubMed  CAS  Google Scholar 

  • Huang X, Madan A (1999) A DNA sequence assembly program. Genome Res9:868–877

    Google Scholar 

  • International Rice Genome Sequencing Project (IRGSP) (2005) The map-based sequence of the rice genome. Nature 436:793–800

    Article  Google Scholar 

  • Jiao Y, Jia P, Wang X, Su N, Yu S, Zhang D, Ma L, Feng Q, Jin Z, Li L, Xue Y, Cheng Z, Zhao H, Han B, Deng XW (2005) A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription. Plant Cell 17:1641–1657

    Article  PubMed  CAS  Google Scholar 

  • Katari MS, Balija V, Wilson RK, Martienssen RA, McCombie WR (2005) Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana. Genome Res 15:496–504

    Article  PubMed  CAS  Google Scholar 

  • Khush GS (1997) Origin, dispersal, cultivation and variation of rice. Plant Mol. Biol 35:25–34

    Article  PubMed  CAS  Google Scholar 

  • Konno H, Fukunishi Y, Shibata K, Itoh M, Carninci P, Sugahara Y, Hayashizaki Y (2001) Computer-based methods for the mouse full-length cDNA encyclopedia: real-time sequence clustering for construction of a non redundant cDNA library. Genome Res 11:281–289

    Article  PubMed  Google Scholar 

  • Kristiansen TZ, Pandey A (2002) Resources for full-length cDNAs. Trends Biochem Sci 27:266–267

    Article  PubMed  CAS  Google Scholar 

  • Kuhl JC, Cheung F, Yuan Q, Martin W, Zewdie Y, McCallum J, Catanach A, Rutherford P, Sink KC, Jenderek M, Prince JP, Town CD, Havey MJ (2004) Aunique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders and Asparagales and Poales. Plant Cell 16:114–125

    Article  PubMed  Google Scholar 

  • Lewin B (2000) Genes VII. Oxford University Press, Oxford

    Google Scholar 

  • Li L, Wang X, Stolc V, Li X, Zhang D, Su N, Tongprasit W, Li S, Cheng Z, Wang J, Deng XW (2006) Genome-wide transcription analyses in rice using tiling microarrays. Nat Genetics 38:124–129

    Article  CAS  Google Scholar 

  • Lin SC, Min SK (1991) Rice varieties and their genealogy in China. Shanghai Scientific and Technical Publishers, Shanghai

    Google Scholar 

  • Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nucleargenomes. Proc Natl Acad Sci USA 101:12404–12410

    Article  PubMed  CAS  Google Scholar 

  • Nishiyama T, Fujita T, Shin-I T, Seki M, Nishide H, Uchiyama I, Kamiya A, Carninci P, Hayashizaki Y, Shinozaki K, Kohara Y, Hasebe M (2003) Comparativegenomics of Physcomiyrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution. Proc Natl Acad Sci USA 100:8007–8012

    Article  PubMed  CAS  Google Scholar 

  • Odenwald WF, Rasband W, Kuzin A, Brody T (2005) EVOPRINTER, a multigenomic comparative tool for rapid identification of functionally important DNA. Proc Natl Acad Sci USA 102:14700–14705

    Article  PubMed  CAS  Google Scholar 

  • Osato N, Itoh M, Konno H, Kondo S, Shibata K, Carninci P, Shiraki T, Shinagawa A, Arakawa T, Kikuchi S, Sato K, Kawai J, Hayashizaki Y (2002) A computer-based method of selecting clones for a full-length cDNA project: simultaneouscollection of negligibly redundant and variant cDNAs. Genome Res 12:1127–1134

    Article  CAS  Google Scholar 

  • Osato N, Yamada H, Satoh K, Ooka H, Yamamoto M, Suzuki K, Kawai J, Carninci P, Ohtomo Y, Murakami K, Matsubara K, Kikuchi S, Hayashizaki Y (2003) Antisense transcripts with rice full-length cDNAs. Genome Biol 5:R5

    Article  PubMed  Google Scholar 

  • Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, Wakamatsu A, Hayashi K, Sato H, Nagai K, Kimura K, Makita H, Sekine M, Obayashi M, Nishi T, Shibahara T, Tanaka T, Ishii S, Yamamoto J, Saito K, Kawai Y, Isono Y,Nakamura Y, Nagahari K, Murakami K, Yasuda T, Iwayanagi T, Wagatsuma M,Shiratori A, Sudo H, Hosoiri T, Kaku Y, Kodaira H, Kondo H, Sugawara M, Takahashi M, Kanda K, Yokoi T, Furuya T, Kikkawa E, Omura Y, Abe K, Kamihara K, Katsuta N, Sato K, Tanikawa M, Yamazaki M, Ninomiya K, Ishibashi T, Yamashita H, Murakawa K, Fujimori K, Tanai H, Kimata M, Watanabe M, Hiraoka S, Chiba Y, Ishida S, Ono Y, Takiguchi S, Watanabe S, Yosida M, Hotuta T, Kusano J, Kanehori K, Takahashi-Fujii A, Hara H, Tanase TO, Nomura Y, Togiya S, Komai F, Hara R, Takeuchi K, Arita M, Imose N, Musashino K, Yuuki H, Oshima A, Sasaki N, Aotsuka S, Yoshikawa Y, Matsunawa H, Ichihara T, Shiohata N, Sano S, Moriya S, Momiyama H, Satoh N, Takami S, Terashima Y, Suzuki O, Nakagawa S, Senoh A, Mizoguchi H, Goto Y, Shimizu F, Wakebe H, Hishigaki H, Watanabe T, Sugiyama A, Takemoto M, Kawakami B, Yamazaki M, Watanabe K, Kumagai A, Itakura S, Fukuzumi Y, Fujimori Y, Komiyama M, Tashiro H, Tanigami A, Fujiwara T, Ono T, Yamada K, Fujii Y, Ozaki K, Hirao M, Ohmori Y, Kawabata A, Hikiji T, Kobatake N, Inagaki H, Ikema Y, Okamoto S, Okitani R, Kawakami T, Noguchi S, Itoh T, Shigeta K, Senba T, Matsumura K, Nakajima Y, Mizuno T, Morinaga M, Sasaki M, Togashi T, Oyama M, Hata H, Watanabe M, Komatsu T, Mizushima-Sugano J, Satoh T, Shirai Y, Takahashi Y, Nakagawa K, Okumura K, Nagase T, Nomura N, Kikuchi H, Masuho Y, Yamashita R, Nakai K, Yada T, Nakamura Y, Ohara O, Isogai T, Sugano S (2004) Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet 36:40–45

    Article  PubMed  Google Scholar 

  • Panaud O, Vitte C, Hivert J, Muzlak S, Talag J, Brar D, Sarr A (2002) Characterization of transposable elements in the genome of rice (Oryza sativa L.) using representational difference analysis (RDA). Mol Gen Genomics 268:113–121

    Article  CAS  Google Scholar 

  • Paterson AH, Freeling M, Sasaki T (2005) Grains of knowledge: genomics of model cereals. Genome Res 15:1643–1650

    Article  PubMed  CAS  Google Scholar 

  • Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J (2003) TIGR gene indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19:651–652

    Article  PubMed  CAS  Google Scholar 

  • Rensink WA, Buell CR (2004) Arabidopsis to rice. Applying knowledge from a weed to enhance our understanding of a crop species. Plant Physiol 135:622–629

    Article  PubMed  CAS  Google Scholar 

  • Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16:276–277

    Article  PubMed  CAS  Google Scholar 

  • Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Katayose Y, Wu J, Niimura Y, Cheng Z, Nagamura Y, Antonio BA, Kanamori H, Hosokawa S, Masukawa M, Arikawa K, Chiden Y, Hayashi M, Okamoto M, Ando T, Aoki H, Arita K, Hamada M, Harada C, Hijishita S, Honda M, Ichikawa Y, Idonuma A, Iijima M, Ikeda M, Ikeno M, Ito S, Ito T, Ito Y, Ito Y, Iwabuchi A, Kamiya K, Karasawa W, Katagiri S, Kikuta A, Kobayashi N, Kono I, Machita K, Maehara T, Mizuno H, Mizubayashi T, Mukai Y, Nagasaki H, Nakashima M, Nakama Y, Nakamichi Y, Nakamura M, Namiki N, Negishi M, Ohta I, Ono N, Saji S, Sakai K, Shibata M, Shimokawa T, Shomura A, Song J, Takazaki Y, Terasawa K, Tsuji K, Waki K, Yamagata H, Yamane H, Yoshiki S, Yoshihara R, Yukawa K, Zhong H, Iwama H, Endo T, Ito H, Hahn JH, Kim HI, Eun MY, Yano M, Jiang J, Gojobori T (2002) The genome sequence and structure of rice chromosome 1. Nature 420:312–316

    Article  PubMed  CAS  Google Scholar 

  • Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, Sakurai T, Nakajima M, Enju A, Akiyama K, Oono Y, Muramatsu M, Hayashizaki Y, Kawai J, Carninci P, Itoh M, Ishii Y, Arakawa T, Shibata K, Shinagawa A, Shinozaki K (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science 296:141–145

    Article  PubMed  Google Scholar 

  • Sogawa K, Li Y, Zhang J, Liu G, Yao H (2003) Genealogical analysis of resistance to the whitebacked planthipper Sogatella furcifera in Chinese japonica rice Chunjiang 06. Chinese J Rice Sci 17:67–72

    Google Scholar 

  • Soltis DE, Soltis PS (2003) The role of phylogenetics in comparative genetics. Plant Physiol 132:1790–1800

    Article  PubMed  CAS  Google Scholar 

  • Stapleton M, Carlson J, Brokstein P, Yu C, Champe M, George R, Guarin H, Kronmiller B, Pacleb J, Park S, Wan K, Rubin GM, Celniker SE (2002) A Drosophila full-length cDNA resource. Genome Biol 312:research0080.1–0080.8

    Google Scholar 

  • Suyama M, Torrents D, Bork P (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 34:W609–W612

    Article  PubMed  CAS  Google Scholar 

  • Suzuki Y, Taira H, Tsunoda T, Mizushima-Sugano J, Sese J, Hata H, Ota T, Isogai T, Tanaka T, Morishita S, Okubo K, Sakaki Y, Nakamura Y, Suyama A, Sugano S (2001) Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. EMBO Rep 2:388–393

    PubMed  CAS  Google Scholar 

  • Suzuki Y, Yamashita R, Nakai K, Sugano S (2002) DBTSS: database of human transcriptional start sites and full-length cDNAs. Nucleic Acids Res 30:328–331

    Article  PubMed  CAS  Google Scholar 

  • The Rice Chromosome 10 Sequencing Consortium (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300:1566–1569

    Article  Google Scholar 

  • The Rice Full-Length cDNA Consortium (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301:376–379

    Article  Google Scholar 

  • The RIKEN genome exploration research group phase II team, the FANTOM consortium (2001) Functional annotation of a full-length mouse cDNA collection. Nature 409:685–690

    Article  Google Scholar 

  • Town CD, Cheung F, Maiti R, Crabtree J, Haas BJ, Wortman JR, Hine EE, Althoff R, Arbogast TS, Tallon LJ, Vigouroux M, Trick M, Bancroft I (2006) Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 18:1348–1359

    Article  PubMed  CAS  Google Scholar 

  • Vandepoele K, Van de Peer Y (2005) Exploring the plant transcriptome through phylogenetic profiling. Plant Physiol 137:31–42

    Article  PubMed  CAS  Google Scholar 

  • Vitte C, Ishii T, Lamy F, Brar D, Panaud O (2004) Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.). Mol Gen Genomics 272:504–511

    Article  CAS  Google Scholar 

  • Wang BB, Brendel V (2006) Genome wide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci USA 103:7175–7180

    Article  PubMed  CAS  Google Scholar 

  • Wei C, Lamesch P, Arumugam M, Rosenberg J, Hu P, Vidal M, Brent MR (2005) Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions. Genome Res 15:577–582

    Article  PubMed  CAS  Google Scholar 

  • Windsor AJ, Mitchell-Olds T (2006) Comparative genomics as a tool for gene discovery. Curr Opin Biotec 17:1–7

    Article  Google Scholar 

  • Wu J, Maehara T, Shimokawa T, Yamamoto S, Harada C, Takazaki Y, Ono N, Mukai Y, Koike K, Yazaki J, Fujii F, Shomura A, Ando T, Kono I, Waki K, Yamamoto K, Yano M, Matsumoto T, Sasaki T (2002) A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 14:525–535

    Article  PubMed  CAS  Google Scholar 

  • Xie K, Zhang J, Xiang Y, Feng Q, Han B, Chu Z, Wang S, Zhang Q, Xiong L (2005) Isolation and annotation of 10828 putative full length cDNAs from indica rice. Sci China Ser C Life Sci 48:445–451

    Article  CAS  Google Scholar 

  • Yuan Q, Ouyang S, Liu J, Suh B, Cheung F, Sultana R, Lee D, Quackenbush J, Buell CR (2003) The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res 31:229–233

    Article  PubMed  CAS  Google Scholar 

  • 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, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, 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, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang 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, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome Oryza sativa L. ssp. indica. Science 296:92–100

    Article  PubMed  Google Scholar 

  • 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 S, Li X, Zheng H, Cong L, Lin L, Yin J, Geng J, Li G, Shi J, Liu J, Lv H, Li J, Wang J, Deng Y, Ran L, Shi X, Wang X, Wu Q, Li C, Ren X, Wang J, Wang 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, Liu J, Xiao Y, Bu D, Tan J, Yang L, Ye C, Zhang J, 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, Zhang Z, Zhang Y, Huang X, Su Z, Tong W, Li J,Tong Z, Li S, Ye J, Wang L, Fang L, Lei T, Chen C, Chen H, Xu Z, Li H, Huang H, Zhang F, Xu H, Li N, Zhao C, Li S, Dong L, Huang Y, Li L, Xi Y, Qi Q, Li W, Zhang B, Hu W, Zhang Y, 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, Wang J, Wong GK, Yang H (2005) The genomes of Oryza sativa: a history of duplications. PloS Biology 32:e38

    Article  Google Scholar 

  • Zhang J, Feng Q, Jin C, Qiu D, Zhang L, Xie K, Yuan D, Han B, Zhang Q, Wang S (2005) Features of the expressed sequences revealed by a large-sale analysis of ESTs from a normalized cDNA library of the elite indica rice cultivar Minghui 63. Plant J 42:772–780

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

We thank Robin Buell for critical comments on the manuscript. This research was supported by the grants from the Ministry of Science and Technology of China (The China Rice Functional Genomics Programs, grant no. 2002AA2Z1003/2006AA10A102), the Chinese Academy of Sciences (grant no. 038019315), and the National Natural Science Foundatation (grant no. 30325014).

Author information

Authors and Affiliations

  1. National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China

    Xiaohui Liu, Tingting Lu, Shuliang Yu, Ying Li, Yuchen Huang, Tao Huang, Lei Zhang, Jingjie Zhu, Qiang Zhao, Danlin Fan, Jie Mu, Yingying Shangguan, Qi Feng, Jianping Guan, Kai Ying, Yu Zhang, Yuping Lu & Bin Han

  2. College of Life Science & Biotechnology, Shanghai Jiaotong University, Shanghai, China

    Tingting Lu, Ying Li, Yuchen Huang, Jingjie Zhu, Qiang Zhao, Qi Feng & Zhixin Lin

  3. School of Life Sciences, Fudan University, Shanghai, China

    Shuliang Yu

  4. The State Key Laboratory of Rice Biology, China Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China

    Zongxiu Sun & Qian Qian

Authors
  1. Xiaohui Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tingting Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Shuliang Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ying Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yuchen Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Tao Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Lei Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Jingjie Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Qiang Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Danlin Fan
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Jie Mu
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Yingying Shangguan
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Qi Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Jianping Guan
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Kai Ying
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Yu Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Zhixin Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Zongxiu Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. Qian Qian
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. Yuping Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  21. Bin Han
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Bin Han.

Additional information

Xiaohui Liu, Tingting Lu, Shuliang Yu and Ying Li contributed equally to this work.

Electronic supplementary material

Below is the electronic supplementary material.

ESM 1 (DOC 236 kb)

ESM 2 (GIF 68 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Liu, X., Lu, T., Yu, S. et al. A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies. Plant Mol Biol 65, 403–415 (2007). https://doi.org/10.1007/s11103-007-9174-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11103-007-9174-7

Keywords

Search

Navigation