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Comparison of the Transcript Profiles from the Root and the Nodulating Root of the Model Legume Lotus japonicus by Serial Analysis of Gene Expression

May 2005 , Volume 18 , Number  5
Pages  487 - 498

Erika Asamizu , 1 Yasukazu Nakamura , 1 Shusei Sato , 1 and Satoshi Tabata 1

1Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan

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Accepted 6 January 2005.

We performed a comprehensive transcript analysis on the early stage of root nodulation in the model legume Lotus japonicus by serial analysis of gene expression (SAGE). SAGE libraries were made from uninfected roots and nodulating roots abundant in nodule primordia, and 85,482 and 80,233 SAGE tags were recovered, respectively. Comparison of the tag frequency identified 407 tag species that appeared in significantly greater numbers in the nodulating root than in the uninfected root, and the converse was found for 428 tag species. Gene identification of the tags was performed by matching them to L. japonicus expressed sequence tag sequences. We made several novel findings by applying SAGE to transcript analysis of legume root nodulation. A gene that showed the most significant increase in tag number upon nodulation has not been described previously. Different levels of transcription induction among leghemoglobin gene paralogs were found, indicating the effectiveness of SAGE in discriminating different gene family members. We identified genes for 44 unknown tags by means of reverse SAGE. We found 11 antisense tags that increased during nodulation, indicating that regulation of gene expression by antisense transcripts may occur in an organ-dependent manner.

Additional keywords: RT-PCR , transcriptome .

© 2005 The American Phytopathological Society