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

Tetsuya Sakurai^*¹ , Germán Plata^*² , Fausto Rodríguez-Zapata^*² , Motoaki Seki³ , Andrés Salcedo² , Atsushi Toyoda⁴ , Atsushi Ishiwata¹ , Joe Tohme² , Yoshiyuki Sakaki⁴ , Kazuo Shinozaki³ and Manabu Ishitani²

¹Metabolomics Research Group, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan

²Agrobiodiversity and Biotechnology Project, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia

³Plant Functional Genomics Research Group, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan

⁴Genome Core Technology Facilities, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan

author email corresponding author email* Contributed equally

BMC Plant Biology 2007, 7:66doi:10.1186/1471-2229-7-66


Published:	20 December 2007

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.