Cloning of a novel rice TE and its structural comparison with CACTA elements
The genomic structure of the previously reported Rim 2 element induced by rice blast pathogen Magnaporthe grisea was studied. By using a Rim 2 cDNA probe to screen and subsequently subclone the Rim 2 bacterial artificial chromosome, a genomic clone Rim 2-569 was obtained. Sequence analysis revealed...
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| Format: | Article |
| Language: | English |
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Zhejiang University Press
2004-03-01
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| Series: | 浙江大学学报. 农业与生命科学版 |
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| Online Access: | https://www.academax.com/doi/10.3785/1008-9209.2004.02.0133 |
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| author | TIAN Ping-fang WANG Guo-dong LI Qun LI De-bao HE Zu-hua |
| author_facet | TIAN Ping-fang WANG Guo-dong LI Qun LI De-bao HE Zu-hua |
| author_sort | TIAN Ping-fang |
| collection | DOAJ |
| description | The genomic structure of the previously reported Rim 2 element induced by rice blast pathogen Magnaporthe grisea was studied. By using a Rim 2 cDNA probe to screen and subsequently subclone the Rim 2 bacterial artificial chromosome, a genomic clone Rim 2-569 was obtained. Sequence analysis revealed that Rim 2-569 possesses the fundamental structure of Class 2 transposable elements, with perfect terminal inverted repeats in both ends, direct and inverted sub-terminal repeats, along with 3 bp target site duplication. The sequence ‘CACTG’ in the terminal inverted repeats distinguishes it from reported CACTA elements. The element has a open reading frame encoding a putative transposase that shares low similarity with TNP2, TNPD and other putative transposases of CACTA elements. No open reading frame encoding TNP1/TNPA-like DNA binding protein were found in this element. Southern hybridization showed the ubiquitous distribution of Rim 2 elements in rice varieties of different origins, along with data mining, indicating plentiful copies of the element family. These features attest this Rim 2 element belonging to a novel transposon family different from the reported CACTA elements. |
| format | Article |
| id | doaj-art-e15e39d53e4e4cc3bb8579d955689af5 |
| institution | Matheson Library |
| issn | 1008-9209 2097-5155 |
| language | English |
| publishDate | 2004-03-01 |
| publisher | Zhejiang University Press |
| record_format | Article |
| series | 浙江大学学报. 农业与生命科学版 |
| spelling | doaj-art-e15e39d53e4e4cc3bb8579d955689af52025-08-01T05:38:40ZengZhejiang University Press浙江大学学报. 农业与生命科学版1008-92092097-51552004-03-013013314010.3785/1008-9209.2004.02.013310089209Cloning of a novel rice TE and its structural comparison with CACTA elementsTIAN Ping-fangWANG Guo-dongLI QunLI De-baoHE Zu-huaThe genomic structure of the previously reported Rim 2 element induced by rice blast pathogen Magnaporthe grisea was studied. By using a Rim 2 cDNA probe to screen and subsequently subclone the Rim 2 bacterial artificial chromosome, a genomic clone Rim 2-569 was obtained. Sequence analysis revealed that Rim 2-569 possesses the fundamental structure of Class 2 transposable elements, with perfect terminal inverted repeats in both ends, direct and inverted sub-terminal repeats, along with 3 bp target site duplication. The sequence ‘CACTG’ in the terminal inverted repeats distinguishes it from reported CACTA elements. The element has a open reading frame encoding a putative transposase that shares low similarity with TNP2, TNPD and other putative transposases of CACTA elements. No open reading frame encoding TNP1/TNPA-like DNA binding protein were found in this element. Southern hybridization showed the ubiquitous distribution of Rim 2 elements in rice varieties of different origins, along with data mining, indicating plentiful copies of the element family. These features attest this Rim 2 element belonging to a novel transposon family different from the reported CACTA elements.https://www.academax.com/doi/10.3785/1008-9209.2004.02.0133rice<italic>Rim 2 element</italic>genomic sequencemolecular structure |
| spellingShingle | TIAN Ping-fang WANG Guo-dong LI Qun LI De-bao HE Zu-hua Cloning of a novel rice TE and its structural comparison with CACTA elements 浙江大学学报. 农业与生命科学版 rice <italic>Rim 2 element</italic> genomic sequence molecular structure |
| title | Cloning of a novel rice TE and its structural comparison with CACTA elements |
| title_full | Cloning of a novel rice TE and its structural comparison with CACTA elements |
| title_fullStr | Cloning of a novel rice TE and its structural comparison with CACTA elements |
| title_full_unstemmed | Cloning of a novel rice TE and its structural comparison with CACTA elements |
| title_short | Cloning of a novel rice TE and its structural comparison with CACTA elements |
| title_sort | cloning of a novel rice te and its structural comparison with cacta elements |
| topic | rice <italic>Rim 2 element</italic> genomic sequence molecular structure |
| url | https://www.academax.com/doi/10.3785/1008-9209.2004.02.0133 |
| work_keys_str_mv | AT tianpingfang cloningofanovelriceteanditsstructuralcomparisonwithcactaelements AT wangguodong cloningofanovelriceteanditsstructuralcomparisonwithcactaelements AT liqun cloningofanovelriceteanditsstructuralcomparisonwithcactaelements AT lidebao cloningofanovelriceteanditsstructuralcomparisonwithcactaelements AT hezuhua cloningofanovelriceteanditsstructuralcomparisonwithcactaelements |