Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response
Background Cassava, an allotetraploid known for its remarkable tolerance to abiotic stresses is an important source of energy for humans and animals and a raw material for many industrial processes. A full-length cDNA library of cassava plants under normal, heat, drought, aluminum and post harvest p...
| Main Authors: | , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer
2007
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/44088 |
| _version_ | 1855532834116075520 |
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| author | Sakurai, Tetsuya Plata, Germán Rodríguez Zapata, Fausto Seki, Motoali Salcedo, Andres Toyoda, Atsushi Hiwata, Atsushi Tohme, Joseph M. Sake, Yoshiyuki Shinozaki, Kazuo Ishitani, Manabu |
| author_browse | Hiwata, Atsushi Ishitani, Manabu Plata, Germán Rodríguez Zapata, Fausto Sake, Yoshiyuki Sakurai, Tetsuya Salcedo, Andres Seki, Motoali Shinozaki, Kazuo Tohme, Joseph M. Toyoda, Atsushi |
| author_facet | Sakurai, Tetsuya Plata, Germán Rodríguez Zapata, Fausto Seki, Motoali Salcedo, Andres Toyoda, Atsushi Hiwata, Atsushi Tohme, Joseph M. Sake, Yoshiyuki Shinozaki, Kazuo Ishitani, Manabu |
| author_sort | Sakurai, Tetsuya |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Background
Cassava, an allotetraploid known for its remarkable tolerance to abiotic stresses is an important source of energy for humans and animals and a raw material for many industrial processes. A full-length cDNA library of cassava plants under normal, heat, drought, aluminum and post harvest physiological deterioration conditions was built; 19968 clones were sequence-characterized using expressed sequence tags (ESTs).
Results
The ESTs were assembled into 6355 contigs and 9026 singletons that were further grouped into 10577 scaffolds; we found 4621 new cassava sequences and 1521 sequences with no significant similarity to plant protein databases. Transcripts of 7796 distinct genes were captured and we were able to assign a functional classification to 78% of them while finding more than half of the enzymes annotated in metabolic pathways in Arabidopsis. The annotation of sequences that were not paired to transcripts of other species included many stress-related functional categories showing that our library is enriched with stress-induced genes. Finally, we detected 230 putative gene duplications that include key enzymes in reactive oxygen species signaling pathways and could play a role in cassava stress response features.
Conclusion
The cassava full-length cDNA library here presented contains transcripts of genes involved in stress response as well as genes important for different areas of cassava research. This library will be an important resource for gene discovery, characterization and cloning; in the near future it will aid the annotation of the cassava genome. |
| format | Journal Article |
| id | CGSpace44088 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2007 |
| publishDateRange | 2007 |
| publishDateSort | 2007 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace440882025-03-11T12:14:31Z Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response Sakurai, Tetsuya Plata, Germán Rodríguez Zapata, Fausto Seki, Motoali Salcedo, Andres Toyoda, Atsushi Hiwata, Atsushi Tohme, Joseph M. Sake, Yoshiyuki Shinozaki, Kazuo Ishitani, Manabu manihot esculenta clones dna nucleotide sequence genetic markers stress adn secuencia nucleotídica marcadores genéticos estrés Background Cassava, an allotetraploid known for its remarkable tolerance to abiotic stresses is an important source of energy for humans and animals and a raw material for many industrial processes. A full-length cDNA library of cassava plants under normal, heat, drought, aluminum and post harvest physiological deterioration conditions was built; 19968 clones were sequence-characterized using expressed sequence tags (ESTs). Results The ESTs were assembled into 6355 contigs and 9026 singletons that were further grouped into 10577 scaffolds; we found 4621 new cassava sequences and 1521 sequences with no significant similarity to plant protein databases. Transcripts of 7796 distinct genes were captured and we were able to assign a functional classification to 78% of them while finding more than half of the enzymes annotated in metabolic pathways in Arabidopsis. The annotation of sequences that were not paired to transcripts of other species included many stress-related functional categories showing that our library is enriched with stress-induced genes. Finally, we detected 230 putative gene duplications that include key enzymes in reactive oxygen species signaling pathways and could play a role in cassava stress response features. Conclusion The cassava full-length cDNA library here presented contains transcripts of genes involved in stress response as well as genes important for different areas of cassava research. This library will be an important resource for gene discovery, characterization and cloning; in the near future it will aid the annotation of the cassava genome. 2007-12 2014-10-02T08:33:13Z 2014-10-02T08:33:13Z Journal Article https://hdl.handle.net/10568/44088 en Open Access Springer Sakurai, Tetsuya; Plata, German; Rodriguez, Fausto; Seki, Motoali; Salcedo, Andres; Toyoda, Atsushi; Hiwata, Atsushi; Tohme, Joe; Sake, Yoshiyuki; Shinozaki, Kazuo; Ishitani, Manabu (2007). Sequencing analysis of 20.000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response. BMC Plant Biology 7:66. |
| spellingShingle | manihot esculenta clones dna nucleotide sequence genetic markers stress adn secuencia nucleotídica marcadores genéticos estrés Sakurai, Tetsuya Plata, Germán Rodríguez Zapata, Fausto Seki, Motoali Salcedo, Andres Toyoda, Atsushi Hiwata, Atsushi Tohme, Joseph M. Sake, Yoshiyuki Shinozaki, Kazuo Ishitani, Manabu Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response |
| title | Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response |
| title_full | Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response |
| title_fullStr | Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response |
| title_full_unstemmed | Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response |
| title_short | Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response |
| title_sort | sequencing analysis of 20 000 full length cdna clones from cassava reveals lineage specific expansions in gene families related to stress response |
| topic | manihot esculenta clones dna nucleotide sequence genetic markers stress adn secuencia nucleotídica marcadores genéticos estrés |
| url | https://hdl.handle.net/10568/44088 |
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