Sequencing, Assembly, and Analysis of the Draft Root Transcriptome of Persea americana: Flooding and Phytophthora cinnamomi

Avocado (Persea americana Mill.) is an important commercial fruit crop worldwide. It is a diploid angiosperm that contains 24 chromosomes and has an approximate genome size of 920Mb. Avocado is susceptible to Phytophthora root rot (PRR) which is a serious disease, caused by the oomycete Phytophthora cinnamomi, and results in damage to the feeder roots. This leads to branch-dieback and eventual tree death, leading to severe losses in production. Currently control strategies involve an integrated approach including phosphite trunk injections, use of tolerant rootstocks, and proper nursery management. Avocado has also been found to be susceptible to flooding, and flooding has been found to accelerate the disease progression of PRR. Despite the commercial importance of avocado, genomic resources are currently limited. The aims of this study were to generate sequence data for avocado roots and assess the transcriptomic response of avocado to both infection with P. cinnamomi and flooding. Approximately 124Mb of sequence data was generated from three separate sequencing runs utilizing the 454 platform from Roche. This data was assembled into 7 685 contigs while 106 448 sequences remained as singletons. Contigs had an average length of 614bp. Several genes involved in defence and hypoxia were identified, including phenylalanine ammonia‐lyase, PR-5, sucrose synthase, alcohol dehydrogenase, and pyruvate decarboxylase.