Avocado is a diploid angiosperm containing 24 chromosomes with a genome estimated to be around 920 Mb. It is an
important fruit crop worldwide but is susceptible to a root rot caused by the ubiquitous oomycete Phytophthora
cinnamomi. Phytophthora root rot (PRR) causes damage to the feeder roots of trees, causing necrosis. This leads to branchdieback
and eventual tree death, resulting in severe losses in production. Control strategies are limited and at present an
integrated approach involving the use of phosphite, tolerant rootstocks, and proper nursery management has shown the
best results. Disease progression of PRR is accelerated under high soil moisture or flooding conditions. In addition, avocado
is highly susceptible to flooding, with even short periods of flooding causing significant losses. Despite the commercial
importance of avocado, limited genomic resources are available. Next generation sequencing has provided the means to
generate sequence data at a relatively low cost, making this an attractive option for non-model organisms such as avocado.
The aims of this study were to generate sequence data for the avocado root transcriptome and identify stress-related genes.
Tissue was isolated from avocado infected with P. cinnamomi, avocado exposed to flooding and avocado exposed to a
combination of these two stresses. Three separate sequencing runs were performed on the Roche 454 platform and
produced approximately 124 Mb of data. This was assembled into 7685 contigs, with 106 448 sequences remaining as
singletons. Genes involved in defence pathways such as the salicylic acid and jasmonic acid pathways as well as genes
associated with the response to low oxygen caused by flooding, were identified. This is the most comprehensive study of
transcripts derived from root tissue of avocado to date and will provide a useful resource for future studies.The Technology and Human Resources Programme (THRIP, grant number TP2011060300010) as an initiative of the
National Research Foundation (NRF), the Hans Merensky Foundation, and the Genomics research institute (GRI) at the University of Pretoria.www.plosone.orgam201
