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

<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^Cgenes 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

Functional annotation of 19,841 <it>Populus nigra </it>full-length enriched cDNA clones

<p>Abstract</p> <p>Background</p> <p><it>Populus </it>is one of favorable model plants because of its small genome. Structural genomics of <it>Populus </it>has reached a breakpoint as nucleotides of the entire genome have been determined. Reaching the post genome era, functional genomics of <it>Populus </it>is getting more important for well-comprehended plant science. Development of bioresorce serving functional genomics is making rapid progress. Huge efforts have achieved deposits of expressed sequence tags (ESTs) in various plant species consequently accelerating functional analysis of genes. ESTs from full-length cDNA clones are especially powerful for accurate molecular annotation. We promoted collection and annotation of the ESTs from <it>Populus </it>full-length enriched cDNA clones as part of functional genomics of tree species.</p> <p>Results</p> <p>We have been collecting the full-length enriched cDNA of the female poplar (<it>Populus nigra </it>var. <it>italica</it>) for years. By sequencing <it>P. nigra </it>full-length (PnFL) cDNA libraries, we generated about 116,000 5'-end or 3'-end ESTs corresponding to 19,841 nonredundant PnFL clones. Population of PnFL cDNA clones represents 44% of the predicted genes in the <it>Populus </it>genome.</p> <p>Conclusion</p> <p>Our resource of <it>P. nigra </it>full-length enriched clones is expected to provide valuable tools to gain further insight into genome annotation and functional genomics in <it>Populus</it>.</p

Distribution of the predicted insert size in the second version of the full-length cDNA library (PnFL2)

<p><b>Copyright information:</b></p><p>Taken from "Functional annotation of 19,841 full-length enriched cDNA clones"</p><p>http://www.biomedcentral.com/1471-2164/8/448</p><p>BMC Genomics 2007;8():448-448.</p><p>Published online 3 Dec 2007</p><p>PMCID:PMC2222646.</p><p></p> The fragment sizes of 17,273 CDS that were substituted for the ESTs were determined

The putative physical distribution of PnFL clones in 19 chromosomes (top: north; bottom: south)

<p><b>Copyright information:</b></p><p>Taken from "Functional annotation of 19,841 full-length enriched cDNA clones"</p><p>http://www.biomedcentral.com/1471-2164/8/448</p><p>BMC Genomics 2007;8():448-448.</p><p>Published online 3 Dec 2007</p><p>PMCID:PMC2222646.</p><p></p> Each red pixel shows a locus that corresponds to a PnFL clone. The number underneath each chromosome is the chromosome number and that above is the distribution index (see )