POSTER NO: 75

Gene Identification and Expression Profiling of 77,150 ESTs from the Rice Oryza sativa L. ssp. indica

¹Yan Zhou, ²Michael G. Walker, ³Liping Wei, ¹Jun Wang, ¹Songnian Hu, ¹Jian Wang, ¹Jun Yu, ¹Huanming Yang, ¹Guyang Matthew Huang
¹Beijing Genomics Institute/Center of Genomics and Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China, ²Stanford University, Stanford, CA 94305, USA, ³Nexus Genomics, Inc., Mountain View, CA 94043, USA

Expressed Sequence Tag (EST) analysis has pioneered genome-wide gene discovery and expression profiling (Adams et al., 1992; Adams et al., 1995; Rounsley et al., 1996). In order to establish a gene expression index in the rice cultivar indica, for which we have surveyed its genome sequence, we sequenced and analyzed 77,150 ESTs from ten rice cDNA libraries from the super hybrid cultivar LYP9 and its parental cultivars. We found very little sequence variation among ESTs from these cultivars and from japonica. Also alternative splicing is rare in rice. Therefore we assembled these ESTs into 13,232 contigs and leave 8,976 singletons. Overall, 7,497 sequences are found similar to existing sequences in GenBank and 14,711 are novel. These sequences are classified by their molecular function, biological process and pathways according to the Gene Ontology (Ashburner et al., 2000).

We compared our newly sequenced ESTs with the publically available 95,000 ESTs from japonica, and found little sequence variation, despite the large difference between their genome sequences. We then assembled the combined 173,000 rice ESTs for further analysis. Over 90% of ESTs were aligned to the available rice genome sequences, with very few alternative splicing events. Using the pooled ESTs, we compared gene expression in carbon fixation pathway between rice and Arabidopsis. With our ESTs, we further profiled gene expression patterns in different tissues, developmental stages, and in a conditional sterile mutant. The expression difference between LYP9 and its parental cultivars reveals that the high-yield breed may have an energy-saving mechanism. We also identified a number of enzymes and transcription factors that contribute to rice development.

References:

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Adams, M. D., Kerlavage, A. R., et al. (1995). Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature, 377, 3-174.

Ashburner, M., Ball, C. A., et al. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet, 25, 25-9.

Rounsley, S. D., Glodek, A., et al. (1996). The construction of Arabidopsis expressed sequence tag assemblies. A new resource to facilitate gene identification. Plant Physiol, 112, 1177-83.