Cargando…
Collection and Comparative Analysis of 1888 Full-length cDNAs from Wild Rice Oryza rufipogon Griff. W1943
A huge amount of cDNA and EST resources have been developed for cultivated rice species Oryza sativa; however, only few cDNA resources are available for wild rice species. In this study, we isolated and completely sequenced 1888 putative full-length cDNA (FLcDNA) clones from wild rice Oryza rufipogo...
Autores principales: | , , , , , , , , |
---|---|
Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2008
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2575888/ https://www.ncbi.nlm.nih.gov/pubmed/18687674 http://dx.doi.org/10.1093/dnares/dsn018 |
_version_ | 1782160359490060288 |
---|---|
author | Lu, Tingting Yu, Shuliang Fan, Danlin Mu, Jie Shangguan, Yingying Wang, Zixuan Minobe, Yuzo Lin, Zhixin Han, Bin |
author_facet | Lu, Tingting Yu, Shuliang Fan, Danlin Mu, Jie Shangguan, Yingying Wang, Zixuan Minobe, Yuzo Lin, Zhixin Han, Bin |
author_sort | Lu, Tingting |
collection | PubMed |
description | A huge amount of cDNA and EST resources have been developed for cultivated rice species Oryza sativa; however, only few cDNA resources are available for wild rice species. In this study, we isolated and completely sequenced 1888 putative full-length cDNA (FLcDNA) clones from wild rice Oryza rufipogon Griff. W1943 for comparative analysis between wild and cultivated rice species. Two cDNA libraries were constructed from 3-week-old leaf samples under either normal or cold-treated conditions. Homology searching of these cDNA sequences revealed that >96.8% of the wild rice cDNAs were matched to the cultivated rice O. sativa ssp. japonica cv. Nipponbare genome sequence. However, <22% of them were fully matched to the cv. Nipponbare genome sequence. The comparative analysis showed that O. rufipogon W1943 had greater similarity to O. sativa ssp. japonica than to ssp. indica cultivars. In addition, 17 novel rice cDNAs were identified, and 41 putative tissue-specific expression genes were defined through searching the rice massively parallel signature-sequencing database. In conclusion, these FLcDNA clones are a resource for further function verification and could be broadly utilized in rice biological studies. |
format | Text |
id | pubmed-2575888 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-25758882009-04-13 Collection and Comparative Analysis of 1888 Full-length cDNAs from Wild Rice Oryza rufipogon Griff. W1943 Lu, Tingting Yu, Shuliang Fan, Danlin Mu, Jie Shangguan, Yingying Wang, Zixuan Minobe, Yuzo Lin, Zhixin Han, Bin DNA Res Full Papers A huge amount of cDNA and EST resources have been developed for cultivated rice species Oryza sativa; however, only few cDNA resources are available for wild rice species. In this study, we isolated and completely sequenced 1888 putative full-length cDNA (FLcDNA) clones from wild rice Oryza rufipogon Griff. W1943 for comparative analysis between wild and cultivated rice species. Two cDNA libraries were constructed from 3-week-old leaf samples under either normal or cold-treated conditions. Homology searching of these cDNA sequences revealed that >96.8% of the wild rice cDNAs were matched to the cultivated rice O. sativa ssp. japonica cv. Nipponbare genome sequence. However, <22% of them were fully matched to the cv. Nipponbare genome sequence. The comparative analysis showed that O. rufipogon W1943 had greater similarity to O. sativa ssp. japonica than to ssp. indica cultivars. In addition, 17 novel rice cDNAs were identified, and 41 putative tissue-specific expression genes were defined through searching the rice massively parallel signature-sequencing database. In conclusion, these FLcDNA clones are a resource for further function verification and could be broadly utilized in rice biological studies. Oxford University Press 2008-10 2008-08-06 /pmc/articles/PMC2575888/ /pubmed/18687674 http://dx.doi.org/10.1093/dnares/dsn018 Text en © The Author 2008. Kazusa DNA Research Institute |
spellingShingle | Full Papers Lu, Tingting Yu, Shuliang Fan, Danlin Mu, Jie Shangguan, Yingying Wang, Zixuan Minobe, Yuzo Lin, Zhixin Han, Bin Collection and Comparative Analysis of 1888 Full-length cDNAs from Wild Rice Oryza rufipogon Griff. W1943 |
title | Collection and Comparative Analysis of 1888 Full-length cDNAs from Wild Rice Oryza rufipogon Griff. W1943 |
title_full | Collection and Comparative Analysis of 1888 Full-length cDNAs from Wild Rice Oryza rufipogon Griff. W1943 |
title_fullStr | Collection and Comparative Analysis of 1888 Full-length cDNAs from Wild Rice Oryza rufipogon Griff. W1943 |
title_full_unstemmed | Collection and Comparative Analysis of 1888 Full-length cDNAs from Wild Rice Oryza rufipogon Griff. W1943 |
title_short | Collection and Comparative Analysis of 1888 Full-length cDNAs from Wild Rice Oryza rufipogon Griff. W1943 |
title_sort | collection and comparative analysis of 1888 full-length cdnas from wild rice oryza rufipogon griff. w1943 |
topic | Full Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2575888/ https://www.ncbi.nlm.nih.gov/pubmed/18687674 http://dx.doi.org/10.1093/dnares/dsn018 |
work_keys_str_mv | AT lutingting collectionandcomparativeanalysisof1888fulllengthcdnasfromwildriceoryzarufipogongriffw1943 AT yushuliang collectionandcomparativeanalysisof1888fulllengthcdnasfromwildriceoryzarufipogongriffw1943 AT fandanlin collectionandcomparativeanalysisof1888fulllengthcdnasfromwildriceoryzarufipogongriffw1943 AT mujie collectionandcomparativeanalysisof1888fulllengthcdnasfromwildriceoryzarufipogongriffw1943 AT shangguanyingying collectionandcomparativeanalysisof1888fulllengthcdnasfromwildriceoryzarufipogongriffw1943 AT wangzixuan collectionandcomparativeanalysisof1888fulllengthcdnasfromwildriceoryzarufipogongriffw1943 AT minobeyuzo collectionandcomparativeanalysisof1888fulllengthcdnasfromwildriceoryzarufipogongriffw1943 AT linzhixin collectionandcomparativeanalysisof1888fulllengthcdnasfromwildriceoryzarufipogongriffw1943 AT hanbin collectionandcomparativeanalysisof1888fulllengthcdnasfromwildriceoryzarufipogongriffw1943 |