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Characterization of soybean genomic features by analysis of its expressed sequence tags

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Abstract

We analyzed 314,254 soybean expressed sequence tags (ESTs), including 29,540 from our laboratory and 284,714 from GenBank. These ESTs were assembled into 56,147 unigenes. About 76.92% of the unigenes were homologous to genes from Arabidopsis thaliana (Arabidopsis). The putative products of these unigenes were annotated according to their homology with the categorized proteins of Arabidopsis. Genes corresponding to cell growth and/or maintenance, enzymes and cell communication belonged to the slow-evolving class, whereas genes related to transcription regulation, cell, binding and death appeared to be fast-evolving. Soybean unigenes with no match to genes within the Arabidopsis genome were identified as soybean-specific genes. These genes were mainly involved in nodule development and the synthesis of seed storage proteins. In addition, we also identified 61 genes regulated by salicylic acid, 1,322 transcription factor genes and 326 disease resistance-like genes from soybean unigenes. SSR analysis showed that the soybean genome was more complex than the Arabidopsis and the Medicago truncatula genomes. GC content in soybean unigene sequences is similar to that in Arabidopsis and M. truncatula. Furthermore, the combined analysis of the EST database and the BAC-contig sequences revealed that the total gene number in the soybean genome is about 63,501.

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Acknowledgements

This research was supported by National Key Basic Research Special Funds, P.R. China (G1998010209, 2002CB111301).

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Authors and Affiliations

  1. Plant Biotechnology Laboratory, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, 100101, Beijing, China

    Ai-Guo Tian, Bang-Jun Wang, Yong-Jun Wang, Jin-Song Zhang & Shou-Yi Chen

  2. Beijing Genomics Institute, Chinese Academy of Sciences, 101300, Beijing, China

    Jun Wang, Peng Cui, Yu-Jun Han, Hao Xu, Li-Juan Cong, Xian-Gang Huang, Xiao-Ling Wang & Yong-Zhi Jiao

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  1. Ai-Guo Tian
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Correspondence to Jin-Song Zhang or Shou-Yi Chen.

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A.-G. Tian and J. Wang contributed equally to this work.

Communicated by H.F. Linskens

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Tian, AG., Wang, J., Cui, P. et al. Characterization of soybean genomic features by analysis of its expressed sequence tags. Theor Appl Genet 108, 903–913 (2004). https://doi.org/10.1007/s00122-003-1499-2

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