Flooding and Phytophthora cinnamomi : effects on photosynthesis and chlorophyll fluorescence in shoots of non-grafted Persea americana (Mill.) rootstocks differing in tolerance to Phytophthora root rot

Please read abstract in the article.The Hans-Merensky Foundation and the National Research Fund (NRF) through the THRIP programme (Department of Science and Technology, South Africa).http://www.elsevier.com/locate/sajbhj201

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

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

Phylogenetic and expression analysis of the NPR1-like gene family from Persea americana (Mill.)

The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (NPR1) forms an integral part of the salicylic acid (SA) pathway in plants and is involved in cross-talk between the SA and jasmonic acid/ethylene (JA/ET) pathways. Therefore, NPR1 is essential to the effective response of plants to pathogens. Avocado (Persea americana) is a commercially important crop worldwide. Significant losses in production result from Phytophthora root rot, caused by the hemibiotroph, Phytophthora cinnamomi. This oomycete infects the feeder roots of avocado trees leading to an overall decline in health and eventual death. The interaction between avocado and P. cinnamomi is poorly understood and as such limited control strategies exist. Thus uncovering the role of NPR1 in avocado could provide novel insights into the avocado – P. cinnamomi interaction. A total of five NPR1-like sequences were identified. These sequences were annotated using FGENESH and a maximum-likelihood tree was constructed using 34 NPR1-like protein sequences from other plant species. The conserved protein domains and functional motifs of these sequences were predicted. Reverse transcription quantitative PCR was used to analyze the expression of the five NPR1-like sequences in the roots of avocado after treatment with salicylic and jasmonic acid, P. cinnamomi infection, across different tissues and in P. cinnamomi infected tolerant and susceptible rootstocks. Of the five NPR1-like sequences three have strong support for a defensive role while two are most likely involved in development. Significant differences in the expression profiles of these five NPR1-like genes were observed, assisting in functional classification. Understanding the interaction of avocado and P. cinnamomi is essential to developing new control strategies. This work enables further classification of these genes by means of functional annotation and is a crucial step in understanding the role of NPR1 during P. cinnamomi infection.Student funding was provided by the National Research Foundation and project funding was provided by the Hans Merensky Foundation.http://www.frontiersin.orgam201

Transcriptome responses of an ungrafted Phytophthora root rot tolerant avocado (Persea americana) rootstock to flooding and Phytophthora cinnamomi

BACKGROUND : Avocado (Persea americana Mill.) is a commercially important fruit crop worldwide. A major limitation to production is the oomycete Phytophthora cinnamomi, which causes root rot leading to branch-dieback and tree death. The decline of orchards infected with P. cinnamomi occurs much faster when exposed to flooding, even if flooding is only transient. Flooding is a multifactorial stress compromised of several individual stresses, making breeding and selection for tolerant varieties challenging. With more plantations occurring in marginal areas, with imperfect irrigation and drainage, understanding the response of avocado to these stresses will be important for the industry. RESULTS : Maintenance of energy production was found to be central in the response to flooding, as seen by up-regulation of transcripts related to glycolysis and induction of transcripts related to ethanolic fermentation. Energy-intensive processes were generally down-regulated, as evidenced by repression of transcripts related to processes such as secondary cell-wall biosynthesis as well as defence-related transcripts. Aquaporins were found to be down-regulated in avocado roots exposed to flooding, indicating reduced water-uptake under these conditions. CONCLUSIONS : The transcriptomic response of avocado to flooding and P. cinnamomi was investigated utilizing microarray analysis. Differences in the transcriptome caused by the presence of the pathogen were minor compared to transcriptomic perturbations caused by flooding. The transcriptomic response of avocado to flooding reveals a response to flooding that is conserved in several species. This data could provide key information that could be used to improve selection of stress tolerant rootstocks in the avocado industry.Additional file 1: Table S1. Primers used in the RT-qPCR validation of the microarray data. The putative identities assigned to each transcript are listed in the ‘Gene’ column.Additional file 2: Table S2. RT-qPCR validation of microarray data. Representative arrays chosen for microarray validation. Five transcripts were selected to ensure the microarray data was comparable with other expression profiling methods. Values indicate fold-changes in gene expression.‹Additional file 3: Table S3. Avocado transcripts found to be up-regulated in the infected treatment (I) compared to the control treatment (C) at 48 h-post flooding (8 days post-infection).Additional file 4: Figure S1. Comparison of the repressed avocado transcripts in flooded to non-flooded treatments at 22 h post-flooding (A) and 48 h post-flooding (B). Values for transcripts with more than one probe present on the array were first averaged and then subjected to the thresholds to determine differential expression.Additional file 5: Figure S2. Differential GO-term distribution after enrichment analysis for sequences up-regulated in the 22HF vs. 22HI comparison. The percentages of sequences associated with GO terms showing over-representation in the 22HF vs. 22HI comparison compared to the reference set consisting of all sequences on the array (FDR < 0.05). Only transcripts showing significant differential expression (log2FC > 1, adj. P-value < 0.05) were included in the analysis.Additional file 6: Figure S3. Differential GO-term distribution after enrichment analysis for sequences up-regulated in the 48HFI vs. 48HC comparison. The percentages of sequences associated with GO terms showing over-representation in the 48HFI vs. 48HC comparison compared to the reference set consisting of all sequences on the array (FDR < 0.05). Only transcripts showing significant differential expression (log2FC > 1, adj. P-value < 0.05) were included in the analysis.};})()The Hans Merensky foundation and the THRIP programme (TP14080787841) of the National Research Foundation of South Africa.http://www.biomedcentral.com/bmcplantbiolhttp://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81297am2016Forestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologyPlant Scienc

Bacteria-based self-healing concrete− A life cycle assessment perspective

A life cycle assessment (LCA) was utilised to evaluate the environmental impact of bacteria-based self-healing concretes (BBSHCs), where non-ureolytic bacterial endospores are encapsulated in porous calcium silicate granules. Findings reveal that 1 m3 of BBSHC has an overall 85% higher environmental impact than equivalent conventional concrete, primarily due to calcium nitrate and polyvinyl acetate. Furthermore, BBSHC has a 36% larger embodied carbon footprint (120 kg CO2 eq) and a 51% larger water footprint (260 L). However, by selectively incorporating BBSHC in specific areas of reinforced concrete structures, leveraging its inherent self-healing properties to deliberately allow wider crack widths, and consequently, reduce the amount of non-structural steel needed to control early-age cracking, sustainability improvements ranging from 12% to 50% can be achieved depending on the impact category. In this regard, a BBSHC-structure can potentially save up to 51 kg CO2 eq per m3

KEGG biochemical mappings for <i>Persea americana</i>.

<p>KEGG biochemical mappings for <i>Persea americana</i>.</p

Number of reads and nucleotides produced by three 454 sequencing runs of avocado root cDNA.

<p>*Calculated from the total reads pooled from all libraries.</p

Overview of the <i>Persea americana</i> transcriptome sequencing and assembly.

<p>(A) Size distribution of raw reads. (B) Size distribution of contigs after removal of rRNA and adapter sequences. (C) Size distribution of singletons.</p

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

<div><p>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 <i>Phytophthora cinnamomi</i>. 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 <i>P. cinnamomi</i>, 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.</p></div

Relative expression levels of four avocado genes.

<p><i>Sucrose synthase</i> (A), <i>non-symbiotic hemoglobin</i> (B), <i>pyruvate decarboxylase</i> (C), <i>endochitinase</i> (D). Bars represented with the same letter are not significantly different at P<0.05. The x-axis represents time after flooding was commenced.</p