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

Norihiro Futamura,Yasushi Totoki,Adriano Mari,Kenji Shinohara,Atsushi Toyoda,Motoaki Seki,Tomohiro Igasaki,Yoshiyuki Sakaki,Kazuo Shinozaki,Tokihiko Nanjo

doi:10.1186/1471-2164-9-383

Abstract

BackgroundCryptomeria 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.ResultsWe 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.ConclusionOur 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.

Highlights

We found that 2,131 expressed sequence tags (ESTs) (11.5%) derived from 5'-terminal sequences of cDNAs exhibited strong homology (E-value < 1e-10) to protein-coding regions in the Arabidopsis genome
Our results suggest that homologs of stamen- and pollen-specific transcripts of Arabidopsis are expressed in the male strobili of C. japonica
As a result of a search for sequence similarity between ESTs from C. japonica male strobili and the 37 identified Pfam domains, we identified a total of 207 (2.0%) unique transcripts that encoded putative transcription factors, which could be assigned to 29 protein families (Table 6)

Summary

Introduction

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. Molecular studies of angiosperm model plants have identified large numbers of genes that are expressed during stamen and pollen development. The B-class MADS-box genes, which in angiosperms determine petal and stamen identities, and C-class genes that control the identities of stamens and carpels have been identified in conifers [4,5,6,7]. The Norway spruce gene DAL1, belongs to the AGL6 subfamily and DAL10, belongs to gymnosperm-specific subgroup were identified as other MADS-box genes in conifers [8,9]. Available information about transcripts that are expressed in the male reproductive structures of the gymnosperms is still limited [14]

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Discussion

Conclusion