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Open Access Highly Accessed Research article

Characterization of expressed sequence tags from a full-length enriched cDNA library of Cryptomeria japonica male strobili

Norihiro Futamura1*, Yasushi Totoki2, Atsushi Toyoda3, Tomohiro Igasaki1, Tokihiko Nanjo1, Motoaki Seki4, Yoshiyuki Sakaki23, Adriano Mari5, Kazuo Shinozaki4 and Kenji Shinohara1

Author Affiliations

1 Department of Molecular and Cell Biology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan

2 Computational and Experimental Systems Biology Group, Genomic Sciences Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan

3 Genome Core Technology Facilities, Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230-0045, Japan

4 Plant Functional Genomics Research Group, Plant Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230-0045, Japan

5 Allergy Data Laboratories sc, Via Malipiero 28, 04100 Latina, Italy

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BMC Genomics 2008, 9:383  doi:10.1186/1471-2164-9-383

Published: 11 August 2008

Abstract

Background

Cryptomeria japonica D. Don is one of the most commercially important conifers in Japan. However, the allergic disease caused by its pollen is a severe public health problem in Japan. Since large-scale analysis of expressed sequence tags (ESTs) in the male strobili of C. japonica should help us to clarify the overall expression of genes during the process of pollen development, we constructed a full-length enriched cDNA library that was derived from male strobili at various developmental stages.

Results

We obtained 36,011 expressed sequence tags (ESTs) from either one or both ends of 19,437 clones derived from the cDNA library of C. japonica male strobili at various developmental stages. The 19,437 cDNA clones corresponded to 10,463 transcripts. Approximately 80% of the transcripts resembled ESTs from Pinus and Picea, while approximately 75% had homologs in Arabidopsis. An analysis of homologies between ESTs from C. japonica male strobili and known pollen allergens in the Allergome Database revealed that products of 180 transcripts exhibited significant homology. Approximately 2% of the transcripts appeared to encode transcription factors. We identified twelve genes for MADS-box proteins among these transcription factors. The twelve MADS-box genes were classified as DEF/GLO/GGM13-, AG-, AGL6-, TM3- and TM8-like MIKCC genes and type I MADS-box genes.

Conclusion

Our full-length enriched cDNA library derived from C. japonica male strobili provides information on expression of genes during the development of male reproductive organs. We provided potential allergens in C. japonica. We also provided new information about transcription factors including MADS-box genes expressed in male strobili of C. japonica. Large-scale gene discovery using full-length cDNAs is a valuable tool for studies of gymnosperm species.