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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2007-12

AUTHORS

Tetsuya Sakurai, Germán Plata, Fausto Rodríguez-Zapata, Motoaki Seki, Andrés Salcedo, Atsushi Toyoda, Atsushi Ishiwata, Joe Tohme, Yoshiyuki Sakaki, Kazuo Shinozaki, Manabu Ishitani

ABSTRACT

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. More... »

PAGES

66

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/1471-2229-7-66

    DOI

    http://dx.doi.org/10.1186/1471-2229-7-66

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1020839372

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/18096061


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