Dataset Information

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.

SUBMITTER: Reeksting BJ

PROVIDER: S-EPMC3919710 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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De novo sequencing, assembly, and analysis of the root transcriptome of Persea americana (Mill.) in response to Phytophthora cinnamomi and flooding.

Reeksting Bianca J BJ Coetzer Nanette N Mahomed Waheed W Engelbrecht Juanita J van den Berg Noëlani N

PloS one 20140210 2

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 t ...[more]

PMID: 24563685

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Project description:Phlomis plants are a source of biological active substances with potential applications in the control of phytopathogens. Phlomis purpurea (Lamiaceae) is autochthonous of southern Iberian Peninsula and Morocco and was found to be resistant to Phytophthora cinnamomi. Phlomis purpurea has revealed antagonistic effect in the rhizosphere of Quercus suber and Q. ilex against P. cinnamomi. Phlomis purpurea roots produce bioactive compounds exhibiting antitumor and anti-Phytophthora activities with potential to protect susceptible plants. Although these important capacities of P. purpurea have been demonstrated, there is no transcriptomic or genomic information available in public databases that could bring insights on the genes underlying this anti-oomycete activity.Using Illumina technology we obtained a de novo assembly of P. purpurea transcriptome and differential transcript abundance to identify putative defence related genes in challenged versus non-challenged plants. A total of 1,272,600,000 reads from 18 cDNA libraries were merged and assembled into 215,739 transcript contigs. BLASTX alignment to Nr NCBI database identified 124,386 unique annotated transcripts (57.7%) with significant hits. Functional annotation identified 83,550 out of 124,386 unique transcripts, which were mapped to 141 pathways. 39% of unigenes were assigned GO terms. Their functions cover biological processes, cellular component and molecular functions. Genes associated with response to stimuli, cellular and primary metabolic processes, catalytic and transporter functions were among those identified. Differential transcript abundance analysis using DESeq revealed significant differences among libraries depending on post-challenge times. Comparative cyto-histological studies of P. purpurea roots challenged with P. cinnamomi zoospores and controls revealed specific morphological features (exodermal strips and epi-cuticular layer), that may provide a constitutive efficient barrier against pathogen penetration. Genes involved in cutin biosynthesis and in exodermal Casparian strips formation were up-regulated.The de novo assembly of transcriptome using short reads for a non-model plant, P. purpurea, revealed many unique transcripts useful for further gene expression, biological function, genomics and functional genomics studies. The data presented suggest a combination of a constitutive resistance and an increased transcriptional response from P. purpurea when challenged with the pathogen. This knowledge opens new perspectives for the understanding of defence responses underlying pathogenic oomycete/plant interaction upon challenge with P. cinnamomi.

Project description:BACKGROUND: Avocado (Persea americana) belongs to the Lauraceae family and is an important commercial fruit crop in over 50 countries. The most serious pathogen affecting avocado production is Phytophthora cinnamomi which causes Phytophthora root rot (PRR). Root pathogens such as P. cinnamomi and their interactions with hosts are poorly understood and despite the importance of both the avocado crop and the effect Phytophthora has on its cultivation, there is a lack of molecular knowledge underpinning our understanding of defence strategies against the pathogen. In order to initiate a better understanding of host-specific defence we have generated EST data using 454 pyrosequencing and profiled nine defence-related genes from Pc-infected avocado roots. RESULTS: 2.0 Mb of data was generated consisting of ~10,000 reads on a single lane of the GS FLX platform. Using the Newbler assembler 371 contigs were assembled, of which 367 are novel for Persea americana. Genes were classified according to Gene Ontology terms. In addition to identifying root-specific ESTs we were also able to identify and quantify the expression of nine defence-related genes that were differentially regulated in response to P. cinnamomi. Genes such as metallothionein, thaumatin and the pathogenesis related PsemI, mlo and profilin were found to be differentially regulated. CONCLUSIONS: This is the first study in elucidating the avocado root transcriptome as well as identifying defence responses of avocado roots to the root pathogen P. cinnamomi. Our data is currently the only EST data that has been generated for avocado rootstocks, and the ESTs identified in this study have already been useful in identifying defence-related genes as well as providing gene information for other studies looking at processes such as ROS regulation as well as hypoxia in avocado roots. Our EST data will aid in the elucidation of the avocado transcriptome and identification of markers for improved rootstock breeding and screening. The characterization of the avocado transcriptome will furthermore form a basis for functional genomics of basal angiosperms.

Project description:The hemibiotrophic plant pathogen Phytophthora cinnamomi Rands is the most devastating pathogen of avocado (Persea americana Mill.) and, as such, causes significant annual losses in the industry. Although the molecular basis of P. cinnamomi resistance in avocado and P. cinnamomi virulence determinants have been the subject of recent research, none have yet attempted to compare the transcriptomic responses of both pathogen and host during their interaction. In the current study, the transcriptomes of both avocado and P. cinnamomi were explored by dual RNA sequencing. The basis for partial resistance was sought by the inclusion of both susceptible (R0.12) and partially resistant (Dusa®) rootstocks sampled at early (6, 12 and 24 hours post-inoculation, hpi) and late time-points (120 hpi). Substantial differences were noted in the number of differentially expressed genes found in Dusa® and R0.12, specifically at 12 and 24 hpi. Here, the partially resistant rootstock perpetuated defense responses initiated at 6 hpi, while the susceptible rootstock abruptly reversed course. Instead, gene ontology enrichment confirmed that R0.12 activated pathways related to growth and development, essentially rendering its response at 12 and 24 hpi no different from that of the mock-inoculated controls. As expected, several classes of P. cinnamomi effector genes were differentially expressed in both Dusa® and R0.12. However, their expression differed between rootstocks, indicating that P. cinnamomi might alter the expression of its effector arsenal based on the rootstock. Based on some of the observed differences, several P. cinnamomi effectors were highlighted as potential candidates for further research. Similarly, the receptor-like kinase (RLK) and apoplastic protease coding genes in avocado were investigated, focusing on their potential role in differing rootstock responses. This study suggests that the basis of partial resistance in Dusa® is predicated on its ability to respond appropriately during the early stages following P. cinnamomi inoculation, and that important components of the first line of inducible defense, apoplastic proteases and RLKs, are likely to be important to the observed outcome.

Project description:Grafting is typically utilized to merge adapted seedling rootstocks with highly productive clonal scions. This process implies the interaction of multiple genomes to produce a unique tree phenotype. However, the interconnection of both genotypes obscures individual contributions to phenotypic variation (rootstock-mediated heritability), hampering tree breeding. Therefore, our goal was to quantify the inheritance of seedling rootstock effects on scion traits using avocado (Persea americana Mill.) cv. Hass as a model fruit tree. We characterized 240 diverse rootstocks from 8 avocado cv. Hass orchards with similar management in three regions of the province of Antioquia, northwest Andes of Colombia, using 13 microsatellite markers simple sequence repeats (SSRs). Parallel to this, we recorded 20 phenotypic traits (including morphological, biomass/reproductive, and fruit yield and quality traits) in the scions for 3 years (2015–2017). Relatedness among rootstocks was inferred through the genetic markers and inputted in a “genetic prediction” model to calculate narrow-sense heritabilities (h2) on scion traits. We used three different randomization tests to highlight traits with consistently significant heritability estimates. This strategy allowed us to capture five traits with significant heritability values that ranged from 0.33 to 0.45 and model fits (r) that oscillated between 0.58 and 0.73 across orchards. The results showed significance in the rootstock effects for four complex harvest and quality traits (i.e., total number of fruits, number of fruits with exportation quality, and number of fruits discarded because of low weight or thrips damage), whereas the only morphological trait that had a significant heritability value was overall trunk height (an emergent property of the rootstock–scion interaction). These findings suggest the inheritance of rootstock effects, beyond root phenotype, on a surprisingly wide spectrum of scion traits in “Hass” avocado. They also reinforce the utility of polymorphic SSRs for relatedness reconstruction and genetic prediction of complex traits. This research is, up to date, the most cohesive evidence of narrow-sense inheritance of rootstock effects in a tropical fruit tree crop. Ultimately, our work highlights the importance of considering the rootstock–scion interaction to broaden the genetic basis of fruit tree breeding programs while enhancing our understanding of the consequences of grafting.

Project description:BackgroundDiscovering a genome-wide set of avocado (Persea americana Mill.) single nucleotide polymorphisms and characterizing the diversity of germplasm collection is a powerful tool for breeding. However, discovery is a costly process, due to loss of loci that are proven to be non-informative when genotyping the germplasm.ResultsOur study on a collection of 100 accessions comprised the three race types, Guatemalan, Mexican, and West Indian. To increase the chances of discovering polymorphic loci, three pools of genomic DNA, one from each race, were sequenced and the reads were aligned to a reference transcriptome. In total, 507,917 polymorphic loci were identified in the entire collection. Of these, 345,617 were observed in all three pools, 117,692 in two pools, 44,552 in one of the pools, and only 56 (0.0001%) were homozygous in the three pools but for different alleles. The polymorphic loci were validated using 192 randomly selected SNPs by genotyping the accessions within each pool. The sensitivity of polymorphic locus prediction ranged from 0.77 to 0.94. The correlation between the allele frequency estimated from the pooled sequences and actual allele frequency from genotype calling of individual accessions was r = 0.8. A subset of 109 SNPs were then used to evaluate the genetic relationships among avocado accessions and the genetic diversity of the collection. The three races were distinctly clustered by projecting the genetic variation on a PCA plot. As expected, by estimating the kinship coefficient for all the accessions, many of the cultivars from the California breeding program were closely related to each other, especially, the Hass-like ones. The green-skin avocados, e.g., 'Bacon', 'Zutano', 'Ettinger' and 'Fuerte' were also closely related to each other.ConclusionsA framework for SNP discovery and genetically characterizing of a breeder's accessions was described. Sequencing pools of gDNA is a cost-effective approach to create a genome-wide stock of polymorphic loci for a breeding program. Reassessing the botanical and the genetic knowledge about the germplasm accessions is valuable for future breeding. Kinship analysis may be used as a first step in finding a parental candidates in a parentage analyses.

Dataset Information

De novo sequencing, assembly, and analysis of the root transcriptome of Persea americana (Mill.) in response to Phytophthora cinnamomi and flooding.

Publications

De novo sequencing, assembly, and analysis of the root transcriptome of Persea americana (Mill.) in response to Phytophthora cinnamomi and flooding.

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