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

Teruaki Taji, Tetsuya Sakurai, Keiichi Mochida, Atsushi Ishiwata, Atsushi Kurotani, Yasushi Totoki, Atsushi Toyoda, Yoshiyuki Sakaki, Motoaki Seki, Hirokazu Ono, Yoichi Sakata, Shigeo Tanaka, Kazuo Shinozaki

Research output: Contribution to journalArticle

44 Citations (Scopus)

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.

Original languageEnglish
Article number115
JournalBMC Plant Biology
Volume8
DOIs
Publication statusPublished - 2008
Externally publishedYes

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Halophila
genes
Arabidopsis
genome
expressed sequence tags
freezing
promoter regions
clones
mutants
genetic transformation
dipping
acid treatment
ecotypes
ozone
cDNA libraries
stress tolerance
abiotic stress
salt stress
abscisic acid
life cycle (organisms)

ASJC Scopus subject areas

  • Plant Science

Cite this

Large-scale collection and annotation of full-length enriched cDNAs from a model halophyte, Thellungiella halophila. / Taji, Teruaki; Sakurai, Tetsuya; Mochida, Keiichi; Ishiwata, Atsushi; Kurotani, Atsushi; Totoki, Yasushi; Toyoda, Atsushi; Sakaki, Yoshiyuki; Seki, Motoaki; Ono, Hirokazu; Sakata, Yoichi; Tanaka, Shigeo; Shinozaki, Kazuo.

In: BMC Plant Biology, Vol. 8, 115, 2008.

Research output: Contribution to journalArticle

Taji, T, Sakurai, T, Mochida, K, Ishiwata, A, Kurotani, A, Totoki, Y, Toyoda, A, Sakaki, Y, Seki, M, Ono, H, Sakata, Y, Tanaka, S & Shinozaki, K 2008, 'Large-scale collection and annotation of full-length enriched cDNAs from a model halophyte, Thellungiella halophila', BMC Plant Biology, vol. 8, 115. https://doi.org/10.1186/1471-2229-8-115
Taji, Teruaki ; Sakurai, Tetsuya ; Mochida, Keiichi ; Ishiwata, Atsushi ; Kurotani, Atsushi ; Totoki, Yasushi ; Toyoda, Atsushi ; Sakaki, Yoshiyuki ; Seki, Motoaki ; Ono, Hirokazu ; Sakata, Yoichi ; Tanaka, Shigeo ; Shinozaki, Kazuo. / Large-scale collection and annotation of full-length enriched cDNAs from a model halophyte, Thellungiella halophila. In: BMC Plant Biology. 2008 ; Vol. 8.
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AU - Mochida, Keiichi

AU - Ishiwata, Atsushi

AU - Kurotani, Atsushi

AU - Totoki, Yasushi

AU - Toyoda, Atsushi

AU - Sakaki, Yoshiyuki

AU - Seki, Motoaki

AU - Ono, Hirokazu

AU - Sakata, Yoichi

AU - Tanaka, Shigeo

AU - Shinozaki, Kazuo

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N2 - 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.

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