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Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response

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Title Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response
 
Creator Sakurai, Tetsuya
Plata, German
Rodriguez, Fausto
Seki, Motoali
Salcedo, Andres
Toyoda, Atsushi
Hiwata, Atsushi
Tohme, Joe
Sake, Yoshiyuki
Shinozaki, Kazuo
Ishitani, Manabu
 
Subject MANIHOT ESCULENTA
CLONES
DNA
NUCLEOTIDE SEQUENCE
GENETIC MARKERS
STRESS
MANIHOT ESCULENTA
CLONES
ADN
SECUENCIA NUCLEOTÍDICA
MARCADORES GENÉTICOS
ESTRÉS
 
Description CIAT- Outstanding Research Publication Award (ORPA) - 2007
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.
Peer-reviewed
 
Date 2014-10-02T08:33:13Z
2014-10-02T08:33:13Z
2007
 
Type Journal Article
 
Identifier 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.
1471-2229
https://hdl.handle.net/10568/44088
 
Language en
 
Source BMC Plant Biology