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

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.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.Among starch producing crops, cassava (Manihot esculenta Crantz, Euphorbiaceae) has a higher carbohydrate production than rice or maize under suboptimal conditions [1]; more than 163 million tons are produced in the world each year and about 84% of them are used for direct human consumption and animal feed [2]. Cassava starch is used as a raw material for a wide range of food products and industrial goods, including paper, cardboard, textile, plywood, glue and alcohol [3]. Moreover, because starch production from cassava is cheap compared to other crops, it is gaining attention as a biomass source for fuel production [4]. The growing interest in cassava as an energy crop is evidenced by a genome sequencing project [5] and the increasing production and technical advancements in tropical countries; for instance, cassava fresh root producti