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

Tokihiko Nanjo,Yasushi Totoki,Motoaki Seki,Tomohiro Igasaki,Norihiro Futamura,Mitsuru Nishiguchi,Tetsuya Sakurai,Tomoyuki Kado,Yoshiyuki Sakaki,Kenji Shinohara,Kazuo Shinozaki,Atsushi Toyoda

doi:10.1186/1471-2164-8-448

Abstract

BackgroundPopulus 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.ResultsWe 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.ConclusionOur 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.

Highlights

Populus is one of favorable model plants because of its small genome
To further estimate the distribution of the insert sizes of the PnFL2 clones, we created a histogram showing a length distribution of the P. trichocarpa coding sequences (CDS) that were substituted for the P. nigra expressed sequence tags (ESTs). 18,578 PnFL2 nonredundant clones were corresponded to P. trichocarpa's predicted CDS under conditions as following: 1) both the 5'-end and 3'-end sequences of each PnFL2 clone had to have blastn hit against the P. trichocarpa CDS in their proper orientation; 2) E value of the blastn hit had to be less than 1e-35 of both the 5'-end and 3'-end sequences; 3) E value of the hit had to be less than 1e-50 of the 5'-end or 3'-end sequences
Full-length cDNAs are essential for the correct annotation of genomic sequences and for the functional analysis of genes and their products

Summary

Introduction

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. We promoted collection and annotation of the ESTs from Populus full-length enriched cDNA clones as part of functional genomics of tree species. The use of forest trees as a sustainable environmental resource has underscored the importance of genomics in aiding the genetic modification of trees for preferable performance and the development of DNA markers for selective breeding. In this context, the development of the (page number not for citation purposes). The publicly available EST collections of Populus including poplar, aspen, cottonwood and their hybrids have already grown to 385,000 [13]

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Conclusion