18 research outputs found
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 ā 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 āGeneā 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.ā¹Additional 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 concreteā 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 1Ā 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 (120Ā kg CO2 eq) and a 51% larger water footprint (260Ā 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 51Ā 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