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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 MIKC C  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.

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