Comparative genomic analysis of 1047 completely sequenced cDNAs from an Arabidopsis-related model halophyte, <it>Thellungiella halophila</it>
<p>Abstract</p> <p>Background</p> <p><it>Thellungiella halophila </it>(also known as <it>T. salsuginea</it>) is a model halophyte with a small size, short life cycle, and small genome. <it>Thellungiella </it>genes exhibit a high degre...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2010-11-01
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| Series: | BMC Plant Biology |
| Online Access: | http://www.biomedcentral.com/1471-2229/10/261 |
| _version_ | 1819122729706586112 |
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| author | Kobayashi Masatomo Tanaka Shigeo Sakata Yoichi Kawasaki Yoshikazu Katori Taku Komatsu Kenji Taji Teruaki Toyoda Atsushi Seki Motoaki Shinozaki Kazuo |
| author_facet | Kobayashi Masatomo Tanaka Shigeo Sakata Yoichi Kawasaki Yoshikazu Katori Taku Komatsu Kenji Taji Teruaki Toyoda Atsushi Seki Motoaki Shinozaki Kazuo |
| author_sort | Kobayashi Masatomo |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p><it>Thellungiella halophila </it>(also known as <it>T. salsuginea</it>) is a model halophyte with a small size, short life cycle, and small genome. <it>Thellungiella </it>genes exhibit a high degree of sequence identity with Arabidopsis genes (90% at the cDNA level). We previously generated a full-length enriched cDNA library of <it>T. halophila </it>from various tissues and from whole plants treated with salinity, chilling, freezing stress, or ABA. We determined the DNA sequences of 20 000 cDNAs at both the 5'- and 3' ends, and identified 9569 distinct genes.</p> <p>Results</p> <p>Here, we completely sequenced 1047 <it>Thellungiella </it>full-length cDNAs representing abiotic-stress-related genes, transcription factor genes, and protein phosphatase 2C genes. The predicted coding sequences, 5'-UTRs, and 3'-UTRs were compared with those of orthologous genes from Arabidopsis for length, sequence similarity, and structure. The 5'-UTR sequences of <it>Thellungiella </it>and Arabidopsis orthologs shared a significant level of similarity, although the motifs were rearranged. While examining the stress-related <it>Thellungiella </it>coding sequences, we found a short splicing variant of <it>T. halophila </it><it>salt overly sensitive 1 </it>(<it>ThSOS1</it>), designated <it>ThSOS1S</it>. ThSOS1S contains the transmembrane domain of ThSOS1 but lacks the C-terminal hydrophilic region. The expression level of <it>ThSOS1S </it>under normal growth conditions was higher than that of <it>ThSOS1</it>. We also compared the expression levels of Na<sup>+</sup>-transport-system genes between <it>Thellungiella </it>and Arabidopsis by using full-length cDNAs from each species as probes. Several genes that play essential roles in Na<sup>+ </sup>excretion, compartmentation, and diffusion (<it>SOS1</it>, <it>SOS2</it>, <it>NHX1</it>, and <it>HKT1</it>) were expressed at higher levels in <it>Thellungiella </it>than in Arabidopsis.</p> <p>Conclusions</p> <p>The full-length cDNA sequences obtained in this study will be essential for the ongoing annotation of the <it>Thellungiella </it>genome, especially for further improvement of gene prediction. Moreover, they will enable us to find splicing variants such as <it>ThSOS1S </it>(AB562331).</p> |
| first_indexed | 2024-12-22T06:57:05Z |
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| last_indexed | 2024-12-22T06:57:05Z |
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| spelling | doaj.art-45843568d7864c049b396d284acb79012022-12-21T18:34:54ZengBMCBMC Plant Biology1471-22292010-11-0110126110.1186/1471-2229-10-261Comparative genomic analysis of 1047 completely sequenced cDNAs from an Arabidopsis-related model halophyte, <it>Thellungiella halophila</it>Kobayashi MasatomoTanaka ShigeoSakata YoichiKawasaki YoshikazuKatori TakuKomatsu KenjiTaji TeruakiToyoda AtsushiSeki MotoakiShinozaki Kazuo<p>Abstract</p> <p>Background</p> <p><it>Thellungiella halophila </it>(also known as <it>T. salsuginea</it>) is a model halophyte with a small size, short life cycle, and small genome. <it>Thellungiella </it>genes exhibit a high degree of sequence identity with Arabidopsis genes (90% at the cDNA level). We previously generated a full-length enriched cDNA library of <it>T. halophila </it>from various tissues and from whole plants treated with salinity, chilling, freezing stress, or ABA. We determined the DNA sequences of 20 000 cDNAs at both the 5'- and 3' ends, and identified 9569 distinct genes.</p> <p>Results</p> <p>Here, we completely sequenced 1047 <it>Thellungiella </it>full-length cDNAs representing abiotic-stress-related genes, transcription factor genes, and protein phosphatase 2C genes. The predicted coding sequences, 5'-UTRs, and 3'-UTRs were compared with those of orthologous genes from Arabidopsis for length, sequence similarity, and structure. The 5'-UTR sequences of <it>Thellungiella </it>and Arabidopsis orthologs shared a significant level of similarity, although the motifs were rearranged. While examining the stress-related <it>Thellungiella </it>coding sequences, we found a short splicing variant of <it>T. halophila </it><it>salt overly sensitive 1 </it>(<it>ThSOS1</it>), designated <it>ThSOS1S</it>. ThSOS1S contains the transmembrane domain of ThSOS1 but lacks the C-terminal hydrophilic region. The expression level of <it>ThSOS1S </it>under normal growth conditions was higher than that of <it>ThSOS1</it>. We also compared the expression levels of Na<sup>+</sup>-transport-system genes between <it>Thellungiella </it>and Arabidopsis by using full-length cDNAs from each species as probes. Several genes that play essential roles in Na<sup>+ </sup>excretion, compartmentation, and diffusion (<it>SOS1</it>, <it>SOS2</it>, <it>NHX1</it>, and <it>HKT1</it>) were expressed at higher levels in <it>Thellungiella </it>than in Arabidopsis.</p> <p>Conclusions</p> <p>The full-length cDNA sequences obtained in this study will be essential for the ongoing annotation of the <it>Thellungiella </it>genome, especially for further improvement of gene prediction. Moreover, they will enable us to find splicing variants such as <it>ThSOS1S </it>(AB562331).</p>http://www.biomedcentral.com/1471-2229/10/261 |
| spellingShingle | Kobayashi Masatomo Tanaka Shigeo Sakata Yoichi Kawasaki Yoshikazu Katori Taku Komatsu Kenji Taji Teruaki Toyoda Atsushi Seki Motoaki Shinozaki Kazuo Comparative genomic analysis of 1047 completely sequenced cDNAs from an Arabidopsis-related model halophyte, <it>Thellungiella halophila</it> BMC Plant Biology |
| title | Comparative genomic analysis of 1047 completely sequenced cDNAs from an Arabidopsis-related model halophyte, <it>Thellungiella halophila</it> |
| title_full | Comparative genomic analysis of 1047 completely sequenced cDNAs from an Arabidopsis-related model halophyte, <it>Thellungiella halophila</it> |
| title_fullStr | Comparative genomic analysis of 1047 completely sequenced cDNAs from an Arabidopsis-related model halophyte, <it>Thellungiella halophila</it> |
| title_full_unstemmed | Comparative genomic analysis of 1047 completely sequenced cDNAs from an Arabidopsis-related model halophyte, <it>Thellungiella halophila</it> |
| title_short | Comparative genomic analysis of 1047 completely sequenced cDNAs from an Arabidopsis-related model halophyte, <it>Thellungiella halophila</it> |
| title_sort | comparative genomic analysis of 1047 completely sequenced cdnas from an arabidopsis related model halophyte it thellungiella halophila it |
| url | http://www.biomedcentral.com/1471-2229/10/261 |
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