Abstract
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 branch-dieback 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.
Highlights
Avocado (Persea americana Mill.) is a diploid basal angiosperm within the Lauraceae family and contains 24 chromosomes
Sequencing and assembly In order to obtain an overview of the genes involved in the response of avocado to P. cinnamomi, 15 cDNA libraries from a tolerant avocado rootstock either subjected to P. cinnamomi infection or not were sequenced in three runs on the Roche GS FLX and Titanium platforms (Table S1)
This was because one of the three runs was performed on the GS FLX instrument, which has slightly shorter read lengths when compared to the GS FLX Titanium on which the other two runs were performed
Summary
Avocado (Persea americana Mill.) is a diploid basal angiosperm within the Lauraceae family and contains 24 chromosomes. Phytophthora root rot (PRR) results in damage to the fine feeder roots, causing them to become necrotic and brittle This negatively impacts water and nutrient absorption, leading to wilting, defoliation, reduced yields, and eventual tree death [2]. P. cinnamomi has a wide host range and is likely to infect more than 3000 species, including avocado, pineapple, oak chestnut, eucalyptus, rhododendron and macadamia [1,3]. This wide host range ensures that P. cinnamomi will persist in the environment and remain a threat to production
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