title: Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response.
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.
  
  
  CONCLUSIONS
  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.
authors: Metabolomics Research Group, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan. stetsuya@psc.riken.jp
authors: Tetsuya
authors: T
authors: Sakurai
authors: Germán
authors: G
authors: Plata
authors: Fausto
authors: F
authors: Rodríguez-Zapata
authors: Motoaki
authors: M
authors: Seki
authors: Andrés
authors: A
authors: Salcedo
authors: Atsushi
authors: A
authors: Toyoda
authors: Atsushi
authors: A
authors: Ishiwata
authors: Joe
authors: J
authors: Tohme
authors: Yoshiyuki
authors: Y
authors: Sakaki
authors: Kazuo
authors: K
authors: Shinozaki
authors: Manabu
authors: M
authors: Ishitani
mesh_terms: D001483:Base Sequence; D003001:Cloning, Molecular; D016000:Cluster Analysis; D017931:DNA Primers; D018076:DNA, Complementary / Q000235:genetics*; D017343:Genes, Plant; D002365:Manihot / Q000235:genetics* / Q000378:metabolism; D005810:Multigene Family; D012333:RNA, Messenger / Q000235:genetics; D017382:Reactive Oxygen Species; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers; D018076:DNA, Complementary; D012333:RNA, Messenger; D017382:Reactive Oxygen Species