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Open Access Highly Accessed Research article

Functional annotation of 19,841 Populus nigra full-length enriched cDNA clones

Tokihiko Nanjo1*, Tetsuya Sakurai2, Yasushi Totoki3, Atsushi Toyoda3, Mitsuru Nishiguchi1, Tomoyuki Kado4, Tomohiro Igasaki1, Norihiro Futamura1, Motoaki Seki2, Yoshiyuki Sakaki3, Kazuo Shinozaki2 and Kenji Shinohara1

Author Affiliations

1 Department of Molecular and Cell Biology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Ibaraki 305-8687 JAPAN

2 RIKEN Plant Science Center, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 JAPAN

3 RIKEN Genomic Science Center, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 JAPAN

4 Hayama Center for Advanced Studies (HCAS), The Graduate University for Advanced Studies, Shonan Kokusai-mura, Hayama-cho, Miura, Kanagawa 240-0193 JAPAN

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BMC Genomics 2007, 8:448  doi:10.1186/1471-2164-8-448

Published: 3 December 2007

Abstract

Background

Populus is one of favorable model plants because of its small genome. Structural genomics of Populus has reached a breakpoint as nucleotides of the entire genome have been determined. Reaching the post genome era, functional genomics of Populus 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 Populus full-length enriched cDNA clones as part of functional genomics of tree species.

Results

We have been collecting the full-length enriched cDNA of the female poplar (Populus nigra var. italica) for years. By sequencing P. nigra 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 Populus genome.

Conclusion

Our resource of P. nigra full-length enriched clones is expected to provide valuable tools to gain further insight into genome annotation and functional genomics in Populus.