Email updates

Keep up to date with the latest news and content from BMC Plant Biology and BioMed Central.

Open Access Research article

Large-scale collection and annotation of full-length enriched cDNAs from a model halophyte, Thellungiella halophila

Teruaki Taji12, Tetsuya Sakurai3, Keiichi Mochida3, Atsushi Ishiwata3, Atsushi Kurotani3, Yasushi Totoki45, Atsushi Toyoda4, Yoshiyuki Sakaki4, Motoaki Seki3, Hirokazu Ono1, Yoichi Sakata1, Shigeo Tanaka1 and Kazuo Shinozaki23*

Author Affiliations

1 Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan

2 Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan

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

4 RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan

5 MetaSystems Research Team, RIKEN Advanced Science Institute, Yokohama, 230-0045, Japan

For all author emails, please log on.

BMC Plant Biology 2008, 8:115  doi:10.1186/1471-2229-8-115

Published: 12 November 2008

Abstract

Background

Thellungiella halophila (also known as Thellungiella salsuginea) is a model halophyte with a small plant size, short life cycle, and small genome. It easily undergoes genetic transformation by the floral dipping method used with its close relative, Arabidopsis thaliana. Thellungiella genes exhibit high sequence identity (approximately 90% at the cDNA level) with Arabidopsis genes. Furthermore, Thellungiella not only shows tolerance to extreme salinity stress, but also to chilling, freezing, and ozone stress, supporting the use of Thellungiella as a good genomic resource in studies of abiotic stress tolerance.

Results

We constructed a full-length enriched Thellungiella (Shan Dong ecotype) cDNA library from various tissues and whole plants subjected to environmental stresses, including high salinity, chilling, freezing, and abscisic acid treatment. We randomly selected about 20 000 clones and sequenced them from both ends to obtain a total of 35 171 sequences. CAP3 software was used to assemble the sequences and cluster them into 9569 nonredundant cDNA groups. We named these cDNAs "RTFL" (RIKEN Thellungiella Full-Length) cDNAs. Information on functional domains and Gene Ontology (GO) terms for the RTFL cDNAs were obtained using InterPro. The 8289 genes assigned to InterPro IDs were classified according to the GO terms using Plant GO Slim. Categorical comparison between the whole Arabidopsis genome and Thellungiella genes showing low identity to Arabidopsis genes revealed that the population of Thellungiella transport genes is approximately 1.5 times the size of the corresponding Arabidopsis genes. This suggests that these genes regulate a unique ion transportation system in Thellungiella.

Conclusion

As the number of Thellungiella halophila (Thellungiella salsuginea) expressed sequence tags (ESTs) was 9388 in July 2008, the number of ESTs has increased to approximately four times the original value as a result of this effort. Our sequences will thus contribute to correct future annotation of the Thellungiella genome sequence. The full-length enriched cDNA clones will enable the construction of overexpressing mutant plants by introduction of the cDNAs driven by a constitutive promoter, the complementation of Thellungiella mutants, and the determination of promoter regions in the Thellungiella genome.