Construction and EST sequencing of full-length, drought stress cDNA libraries for common beans (Phaseolus vulgaris L.)
Background: Common bean is an important legume crop with only a moderate number of short expressed sequence tags (ESTs) made with traditional methods. The goal of this research was to use full-length cDNA technology to develop ESTs that would overlap with the beginning of open reading frames and the...
| Autores principales: | , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2011
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/43300 |
| _version_ | 1855526901176598528 |
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| author | Blair, Matthew W. Fernández, A.C. Ishitani, Manabu Moreta Mejia, DE Seki, M. Ayling, S. Shinozaki, Kazuo |
| author_browse | Ayling, S. Blair, Matthew W. Fernández, A.C. Ishitani, Manabu Moreta Mejia, DE Seki, M. Shinozaki, Kazuo |
| author_facet | Blair, Matthew W. Fernández, A.C. Ishitani, Manabu Moreta Mejia, DE Seki, M. Ayling, S. Shinozaki, Kazuo |
| author_sort | Blair, Matthew W. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Background:
Common bean is an important legume crop with only a moderate number of short expressed sequence tags (ESTs) made with traditional methods. The goal of this research was to use full-length cDNA technology to develop ESTs that would overlap with the beginning of open reading frames and therefore be useful for gene annotation of genomic sequences. The library was also constructed to represent genes expressed under drought, low soil phosphorus and high soil aluminum toxicity. We also undertook comparisons of the full-length cDNA library to two previous non-full clone EST sets for common bean.
Results:
Two full-length cDNA libraries were constructed: one for the drought tolerant Mesoamerican genotype BAT477 and the other one for the acid-soil tolerant Andean genotype G19833 which has been selected for genome sequencing. Plants were grown in three soil types using deep rooting cylinders subjected to drought and non-drought stress and tissues were collected from both roots and above ground parts. A total of 20,000 clones were selected robotically, half from each library. Then, nearly 10,000 clones from the G19833 library were sequenced with an average read length of 850 nucleotides. A total of 4,219 unigenes were identified consisting of 2,981 contigs and 1,238 singletons. These were functionally annotated with gene ontology terms and placed into KEGG pathways. Compared to other EST sequencing efforts in common bean, about half of the sequences were novel or represented the 5' ends of known genes.
Conclusions:
The present full-length cDNA libraries add to the technological toolbox available for common bean and our sequencing of these clones substantially increases the number of unique EST sequences available for the common bean genome. All of this should be useful for both functional gene annotation, analysis of splice site variants and intron/exon boundary determination by comparison to soybean genes or with common bean whole-genome sequences. In addition the library has a large number of transcription factors and will be interesting for discovery and validation of drought or abiotic stress related genes in common bean. |
| format | Journal Article |
| id | CGSpace43300 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2011 |
| publishDateRange | 2011 |
| publishDateSort | 2011 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace433002025-03-11T12:14:31Z Construction and EST sequencing of full-length, drought stress cDNA libraries for common beans (Phaseolus vulgaris L.) Blair, Matthew W. Fernández, A.C. Ishitani, Manabu Moreta Mejia, DE Seki, M. Ayling, S. Shinozaki, Kazuo beans phaseolus vulgaris drought resistance abiotic stress fríjol resistencia a la sequía estrés abiótico Background: Common bean is an important legume crop with only a moderate number of short expressed sequence tags (ESTs) made with traditional methods. The goal of this research was to use full-length cDNA technology to develop ESTs that would overlap with the beginning of open reading frames and therefore be useful for gene annotation of genomic sequences. The library was also constructed to represent genes expressed under drought, low soil phosphorus and high soil aluminum toxicity. We also undertook comparisons of the full-length cDNA library to two previous non-full clone EST sets for common bean. Results: Two full-length cDNA libraries were constructed: one for the drought tolerant Mesoamerican genotype BAT477 and the other one for the acid-soil tolerant Andean genotype G19833 which has been selected for genome sequencing. Plants were grown in three soil types using deep rooting cylinders subjected to drought and non-drought stress and tissues were collected from both roots and above ground parts. A total of 20,000 clones were selected robotically, half from each library. Then, nearly 10,000 clones from the G19833 library were sequenced with an average read length of 850 nucleotides. A total of 4,219 unigenes were identified consisting of 2,981 contigs and 1,238 singletons. These were functionally annotated with gene ontology terms and placed into KEGG pathways. Compared to other EST sequencing efforts in common bean, about half of the sequences were novel or represented the 5' ends of known genes. Conclusions: The present full-length cDNA libraries add to the technological toolbox available for common bean and our sequencing of these clones substantially increases the number of unique EST sequences available for the common bean genome. All of this should be useful for both functional gene annotation, analysis of splice site variants and intron/exon boundary determination by comparison to soybean genes or with common bean whole-genome sequences. In addition the library has a large number of transcription factors and will be interesting for discovery and validation of drought or abiotic stress related genes in common bean. 2011 2014-09-24T08:41:55Z 2014-09-24T08:41:55Z Journal Article https://hdl.handle.net/10568/43300 en Open Access Springer |
| spellingShingle | beans phaseolus vulgaris drought resistance abiotic stress fríjol resistencia a la sequía estrés abiótico Blair, Matthew W. Fernández, A.C. Ishitani, Manabu Moreta Mejia, DE Seki, M. Ayling, S. Shinozaki, Kazuo Construction and EST sequencing of full-length, drought stress cDNA libraries for common beans (Phaseolus vulgaris L.) |
| title | Construction and EST sequencing of full-length, drought stress cDNA libraries for common beans (Phaseolus vulgaris L.) |
| title_full | Construction and EST sequencing of full-length, drought stress cDNA libraries for common beans (Phaseolus vulgaris L.) |
| title_fullStr | Construction and EST sequencing of full-length, drought stress cDNA libraries for common beans (Phaseolus vulgaris L.) |
| title_full_unstemmed | Construction and EST sequencing of full-length, drought stress cDNA libraries for common beans (Phaseolus vulgaris L.) |
| title_short | Construction and EST sequencing of full-length, drought stress cDNA libraries for common beans (Phaseolus vulgaris L.) |
| title_sort | construction and est sequencing of full length drought stress cdna libraries for common beans phaseolus vulgaris l |
| topic | beans phaseolus vulgaris drought resistance abiotic stress fríjol resistencia a la sequía estrés abiótico |
| url | https://hdl.handle.net/10568/43300 |
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