| Summary: | <p>Abstract</p> <p>Background</p> <p><it>Cryptomeria japonica </it>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 <it>C. japonica </it>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.</p> <p>Results</p> <p>We obtained 36,011 expressed sequence tags (ESTs) from either one or both ends of 19,437 clones derived from the cDNA library of <it>C. japonica </it>male strobili at various developmental stages. The 19,437 cDNA clones corresponded to 10,463 transcripts. Approximately 80% of the transcripts resembled ESTs from <it>Pinus </it>and <it>Picea</it>, while approximately 75% had homologs in <it>Arabidopsis</it>. An analysis of homologies between ESTs from <it>C. japonica </it>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 <it>DEF/GLO/GGM13-, AG-, AGL6-, TM3- </it>and <it>TM8</it>-like MIKC<sup>C </sup>genes and type I MADS-box genes.</p> <p>Conclusion</p> <p>Our full-length enriched cDNA library derived from <it>C. japonica </it>male strobili provides information on expression of genes during the development of male reproductive organs. We provided potential allergens in <it>C. japonica</it>. We also provided new information about transcription factors including MADS-box genes expressed in male strobili of <it>C. japonica</it>. Large-scale gene discovery using full-length cDNAs is a valuable tool for studies of gymnosperm species.</p>
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