Cassava (Manihot esculenta) transcriptome analysis in response to infection by the fungus Colletotrichum gloeosporioides using an oligonucleotide-DNA microarray

Utsumi, Yoshinori; Tanaka, Maho; Kurotani, Atsushi; Yoshida, Takuhiro; Mochida, Keiichi; Matsui, Atsushi; Ishitani, Manabu; Sraphet, Supajit; Whankaew, Sukhuman; Asvarak, Thipa; Narangajavana, Jarunya; Triwitayakorn, Kanokporn; Sakurai, Tetsuya; Seki, Motoaki

doi:10.1007/s10265-016-0828-x

Cited by 28 publications

(32 citation statements)

References 71 publications

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“…Cassava PR families 2, 5, 7, and 9 are most responsive to biotic stress and hormones Across the many cassava-pest/pathogen/hormone interactions examined in this study, PR families with roles in pathogen cell wall degradation (PR-2, PR-5 and PR-7), as well as host cell wall fortification (PR-9) were the predominant families responding to whiteflies (A. socialis), SA, JA, and most other biotic stresses (mealybugs (P. manihoti), fungi (C. gloeosporioides), bacteria (X. axonopodis), CMV, and CBSV) [26,[28][29][30]33]. PR-2 and PR-5 proteins have been reported as β-1,3-endoglucanases and β-glucanbinding proteins, respectively, with roles in pathogen membrane degradation/permeabilization [60,61].…”

Section: Hormone Regulation Of Whitefly-responsive Pr Genesmentioning

confidence: 61%

“…To more broadly define the responses of cassava's PR genes in pathogen and pest interactions, we compared PR gene expression programs to whiteflies (A. socialis) with five other pathogens/pests: cassava mealybugs (Phenacoccus manihoti), bacteria (X. axonopodis), fungi (C. gloeosporioides), and viruses (South African CMV and CBSV) [26,[28][29][30]33] (Additional file 9; Additional file 1: Table S1; Additional file 3: Tables S3, S7 and S11). Each interaction elicited a different number of DEGs; therefore, to facilitate comparisons, the percent of DEGs from each PR family that responded to each biotic stress was determined (Table 4; Fig.…”

Section: Comparison Of Pr Family Responses To a Spectrum Of Biotic Stmentioning

confidence: 99%

“…Indeed, our analysis of published data for five other cassava-pathogen interactions indicated that PR gene downregulation was common in these other cassava-pathosystems ( Fig. 6) [26][27][28][29][30][31][32][33].…”

Section: Cassava's Pr Gene Responses To Whitefly and Other Pathogensmentioning

confidence: 99%

“…Lastly, PR gene responses to whiteflies were compared to data sets in the literature that documented responses to five other aggressors: the cassava mealybug Phenacoccus manihoti; the bacterial blight pathogen Xanthomonas axonopodis pv. manihotis; the fungus causing cassava anthracnose disease Colletotrichum gloeosporioides, Cassava Mosaic Virus (CMV), and Cassava Brown Streak Virus (CBSV) [26][27][28][29][30][31][32][33]. Together, our integrative analyses defined the core transcriptome response of susceptible cassava to whitefly infestation, and revealed key PR gene families (PR-2, -5, -7 and -9) in the responses of cassava to whiteflies, SA, JA, and a variety of other biotic stresses.…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

et al. 2020

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Background: Whiteflies are a threat to cassava (Manihot esculenta), an important staple food in many tropical/ subtropical regions. Understanding the molecular mechanisms regulating cassava's responses against this pest is crucial for developing control strategies. Pathogenesis-related (PR) protein families are an integral part of plant immunity. With the availability of whole genome sequences, the annotation and expression programs of the full complement of PR genes in an organism can now be achieved. An understanding of the responses of the entire complement of PR genes during biotic stress and to the defense hormones, salicylic acid (SA) and jasmonic acid (JA), is lacking. Here, we analyze the responses of cassava PR genes to whiteflies, SA, JA, and other biotic aggressors. Results: The cassava genome possesses 14 of the 17 plant PR families, with a total of 447 PR genes. A cassava PR gene nomenclature is proposed. Phylogenetic relatedness of cassava PR proteins to each other and to homologs in poplar, rice and Arabidopsis identified cassava-specific PR gene family expansions. The temporal programs of PR gene expression in response to the whitefly (Aleurotrachelus socialis) in four whitefly-susceptible cassava genotypes showed that 167 of the 447 PR genes were regulated after whitefly infestation. While the timing of PR gene expression varied, over 37% of whitefly-regulated PR genes were downregulated in all four genotypes. Notably, whitefly-responsive PR genes were largely coordinately regulated by SA and JA. The analysis of cassava PR gene expression in response to five other biotic stresses revealed a strong positive correlation between whitefly and Xanthomonas axonopodis and Cassava Brown Streak Virus responses and negative correlations between whitefly and Cassava Mosaic Virus responses. Finally, certain associations between PR genes in cassava expansions and response to biotic stresses were observed among PR families. Conclusions: This study represents the first genome-wide characterization of PR genes in cassava. PR gene responses to six biotic stresses and to SA and JA are demonstrably different to other angiosperms. We propose that our approach could be applied in other species to fully understand PR gene regulation by pathogens, pests and the canonical defense hormones SA and JA.

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Section: Hormone Regulation Of Whitefly-responsive Pr Genesmentioning

confidence: 61%

Section: Comparison Of Pr Family Responses To a Spectrum Of Biotic Stmentioning

confidence: 99%

Section: Cassava's Pr Gene Responses To Whitefly and Other Pathogensmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

et al. 2020

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“…Briefly, total RNA was labeled with cyanin-3 (Cy3) using the Quick Amp Labeling kit (Agilent Technologies). Next, the Cy3-labeled cRNA was fragmented and hybridized to the Agilent microarray (GPL14139; Utsumi et al, 2016). After hybridization, the microarrays were washed and immediately scanned on an Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8 × 60 K array slides.…”

Section: Methodsmentioning

confidence: 99%

The Histone Deacetylase Inhibitor Suberoylanilide Hydroxamic Acid Alleviates Salinity Stress in Cassava

et al. 2017

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Cassava (Manihot esculenta Crantz) demand has been rising because of its various applications. High salinity stress is a major environmental factor that interferes with normal plant growth and limits crop productivity. As well as genetic engineering to enhance stress tolerance, the use of small molecules is considered as an alternative methodology to modify plants with desired traits. The effectiveness of histone deacetylase (HDAC) inhibitors for increasing tolerance to salinity stress has recently been reported. Here we use the HDAC inhibitor, suberoylanilide hydroxamic acid (SAHA), to enhance tolerance to high salinity in cassava. Immunoblotting analysis reveals that SAHA treatment induces strong hyper-acetylation of histones H3 and H4 in roots, suggesting that SAHA functions as the HDAC inhibitor in cassava. Consistent with increased tolerance to salt stress under SAHA treatment, reduced Na+ content and increased K+/Na+ ratio were detected in SAHA-treated plants. Transcriptome analysis to discover mechanisms underlying salinity stress tolerance mediated through SAHA treatment reveals that SAHA enhances the expression of 421 genes in roots under normal condition, and 745 genes at 2 h and 268 genes at 24 h under both SAHA and NaCl treatment. The mRNA expression of genes, involved in phytohormone [abscisic acid (ABA), jasmonic acid (JA), ethylene, and gibberellin] biosynthesis pathways, is up-regulated after high salinity treatment in SAHA-pretreated roots. Among them, an allene oxide cyclase (MeAOC4) involved in a crucial step of JA biosynthesis is strongly up-regulated by SAHA treatment under salinity stress conditions, implying that JA pathway might contribute to increasing salinity tolerance by SAHA treatment. Our results suggest that epigenetic manipulation might enhance tolerance to high salinity stress in cassava.

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An optimized isolation protocol yields high‐quality RNA from cassava tissues (Manihot esculenta Crantz)

et al. 2019

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We developed and modified a precise, rapid, and reproducible protocol isolating high‐quality RNA from tissues of multiple varieties of cassava plants (Manihot esculenta Crantz). The resulting method is suitable for use in mini, midi, and maxi preparations and rapidly achieves high total RNA yields (170–600 μg·g−1) using low‐cost chemicals and consumables and with minimal contamination from polysaccharides, polyphenols, proteins, and other secondary metabolites. In particular, A260 : A280 ratios were > 2.0 for RNA from various tissues, and all of the present RNA samples yielded ribosomal integrity number values of greater than six. The resulting high purity and quality of isolated RNA will facilitate downstream applications (quantitative reverse transcriptase‐polymerase chain reaction or RNA sequencing) in cassava molecular breeding.

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Cassava (Manihot esculenta) transcriptome analysis in response to infection by the fungus Colletotrichum gloeosporioides using an oligonucleotide-DNA microarray

Cited by 28 publications

References 71 publications

Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

The Histone Deacetylase Inhibitor Suberoylanilide Hydroxamic Acid Alleviates Salinity Stress in Cassava

An optimized isolation protocol yields high‐quality RNA from cassava tissues (Manihot esculenta Crantz)

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