De Novo Sequencing, Assembly, and Analysis of the Root Transcriptome of Persea americana (Mill.) in Response to Phytophthora cinnamomi and Flooding

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.

Canker and fine‐root loss of Malus sieversii (Ldb.) Roem. caused by Phytophthora plurivora in Xinjiang Province in China

“…In Europe, P. plurivora , P. cambivora and P. cactorum caused a decline of beech trees, with collar cankers and fine‐root loss (Jung, ; Jung et al., ). In France, Spain and Portugal, P. cinnamomi has a broad host range, and it is causing a serious decline of Quercus suber and Q. ilex in those regions (Reeksting, Coetzer, Mahomed, Engelbrecht, & van den Berg, ). Phytophthora cinnamomi may also kill beech, black locust, cedar, Eucalyptus and camellia (Balci & Halmschlager, ,; Hansen & Delatour, ; Ho, Lu, & Gong, ; Shearer & Dillon, ; Shen, Shi, Hong, & Liu, ; Zhou et al., ).…”

Expresión diferencial de genes de defensa en aguacate en respuesta a la infección del viroide de la mancha de sol del aguacate

“…El gen de actina (Reeksting et al, 2014) se usó como gen de referencia. Las secuencias de los against the disease.…”

“…The actin gene (Reeksting et al, 2014) was used as a reference gene. Sequences of the primers were taken from the mentioned references.…”

Factors associated with postharvest ripening heterogeneity of ‘Hass’ avocados (Persea americanaMill)

“…Recently, Reeksting et al [78] reported the massive sequencing of the root transcriptome of avocado exposed to Phytophthora cinnamomi and flooding using new generation sequencing platforms. The sequencing data generated is available at the NCBI database.…”