Dual RNA-seq analysis provides new insights into interactions between Norway spruce and necrotrophic pathogen Heterobasidion annosum s.l.

Kovalchuk, Andriy; Zeng, Zhen; Ghimire, Rajendra P.; Kivimäenpää, Minna; Raffaello, Tommaso; Liu, Mengxia; Mukrimin, Mukrimin; Kasanen, Risto; Sun, Hui; Julkunen‐Tiitto, Riitta; Holopainen, Jarmo K.; Asiegbu, Fred O.

doi:10.1186/s12870-018-1602-0

Cited by 39 publications

(20 citation statements)

References 71 publications

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“…Phenylpropanoid pathway intermediates, like 4-hydroxybenzoate, cinnamic acid, ferulic acid, and caffeic acid, were highly accumulated in the resistant soybean line against Sclerotinia sclerotiorum infection [35]. Moreover, in trees displaying symptoms of wood decay, large amounts of lignans were observed [36]. Mulberry trees contain large quantities of flavonoids and other secondary metabolites, such as phenylpropanoids and alkaloids, which have wide roles in defenses against biotic and abiotic stresses [26] and have long been used in Chinese traditional medicine for human disease treatment [37].…”

Section: Discussionmentioning

confidence: 99%

Integrated Transcriptomic and Un-Targeted Metabolomics Analysis Reveals Mulberry Fruit (Morus atropurpurea) in Response to Sclerotiniose Pathogen Ciboria shiraiana Infection

Bao

Gao

Zheng

et al. 2020

IJMS

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Mulberry sclerotiniose caused by Ciboria shiraiana is a devastating disease of mulberry (Morus alba L.) fruit in Northwest China. At present, no disease-resistant varieties are used in production, as the molecular mechanisms of this disease are not well understood. In this study, to explore new prevention methods and provide direction for molecular breeding, transcriptomic sequencing and un-targeted metabolomics were performed on healthy (CK), early-stage diseased (HB1), and middle-stage diseased (HB2) mulberry fruits. Functional annotation, gene ontology, a Kyoto encyclopedia of genes and genomes (KEGG) analysis, and a Mapman analysis of the differentially expressed genes revealed differential regulation of genes related to plant hormone signal transduction, transcription factors, and phenylpropanoid biosynthesis. A correspondence between the transcript pattern and metabolite profile was observed in the phenylpropanoid biosynthesis pathway. It should be noted that the log2 ratio of eugenol (isoeugenol) in HB1 and HB2 are 85 times and 23 times higher than CK, respectively. Our study shows that phenylpropanoid biosynthesis may play an essential role in response to sclerotiniose pathogen infection and eugenol(isoeugenol) enrichment in mulberry fruit, which may provide a novel method for mulberry sclerotiniose control.

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Section: Discussionmentioning

confidence: 99%

Integrated Transcriptomic and Un-Targeted Metabolomics Analysis Reveals Mulberry Fruit (Morus atropurpurea) in Response to Sclerotiniose Pathogen Ciboria shiraiana Infection

Bao

Gao

Zheng

et al. 2020

IJMS

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“…Another structural defense induced in conifers is early fibers lignification to arrest hyphal penetration at the site of infection. Previous studies of plants challenged with pathogens have shown the induction of genes involved in lignin biosynthesis [ 29 , 30 , 31 , 37 ]. In P. pinea , the main enzymes involved in the lignin biosynthesis were induced by F. circinatum infection, including two dirigent-like disease resistance predicted proteins that are associated with lignin biosynthesis and response to pathogens [ 74 ].…”

Section: Discussionmentioning

confidence: 99%

“…In the last decade, an increased number of studies have examined the pathosystems of several forest trees at the transcriptional level [ 27 , 28 , 29 , 30 , 31 , 32 ]. The development of NGS and associated bioinformatics pipelines have made feasible the application of high-throughput transcriptomic analysis to unsequenced species, allowing a deep description of the transcriptional mechanisms implied in plant fungal defense [ 33 , 34 , 35 , 36 , 37 ]. Specifically, some studies have examined the response of different pine species to F. circinatum .…”

Section: Introductionmentioning

confidence: 99%

Dual RNA-Sequencing Analysis of Resistant (Pinus pinea) and Susceptible (Pinus radiata) Hosts during Fusarium circinatum Challenge

Zamora-Ballesteros

Pinto

Amaral

et al. 2021

IJMS

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Fusarium circinatum causes one of the most important diseases of conifers worldwide, the pine pitch canker (PPC). However, no effective field intervention measures aiming to control or eradicate PPC are available. Due to the variation in host genetic resistance, the development of resistant varieties is postulated as a viable and promising strategy. By using an integrated approach, this study aimed to identify differences in the molecular responses and physiological traits of the highly susceptible Pinus radiata and the highly resistant Pinus pinea to F. circinatum at an early stage of infection. Dual RNA-Seq analysis also allowed to evaluate pathogen behavior when infecting each pine species. No significant changes in the physiological analysis were found upon pathogen infection, although transcriptional reprogramming was observed mainly in the resistant species. The transcriptome profiling of P. pinea revealed an early perception of the pathogen infection together with a strong and coordinated defense activation through the reinforcement and lignification of the cell wall, the antioxidant activity, the induction of PR genes, and the biosynthesis of defense hormones. On the contrary, P. radiata had a weaker response, possibly due to impaired perception of the fungal infection that led to a reduced downstream defense signaling. Fusarium circinatum showed a different transcriptomic profile depending on the pine species being infected. While in P. pinea, the pathogen focused on the degradation of plant cell walls, active uptake of the plant nutrients was showed in P. radiata. These findings present useful knowledge for the development of breeding programs to manage PPC.

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“…3 ). A previous study in Arabidopsis evidenced that different RNA binding proteins play a role in response to drought stress [ 41 ].…”

Section: Discussionmentioning

confidence: 99%

Physiological and transcriptional response to drought stress among bioenergy grass Miscanthus species

Vega

Teshome

Klaas

et al. 2021

Biotechnol Biofuels

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Background Miscanthus is a commercial lignocellulosic biomass crop owing to its high biomass productivity, resilience and photosynthetic capacity at low temperature. These qualities make Miscanthus a particularly good candidate for temperate marginal land, where yields can be limited by insufficient or excessive water supply. Differences in response to water stress have been observed among Miscanthus species, which correlated to origin. In this study, we compared the physiological and molecular responses among Miscanthus species under excessive (flooded) and insufficient (drought) water supply in glasshouse conditions. Results A significant biomass loss was observed under drought conditions in all genotypes. M. x giganteus showed a lower reduction in biomass yield under drought conditions compared to the control than the other species. Under flooded conditions, biomass yield was as good as or better than control conditions in all species. 4389 of the 67,789 genes (6.4%) in the reference genome were differentially expressed during drought among four Miscanthus genotypes from different species. We observed the same biological processes were regulated across Miscanthus species during drought stress despite the DEGs being not similar. Upregulated differentially expressed genes were significantly involved in sucrose and starch metabolism, redox, and water and glycerol homeostasis and channel activity. Multiple copies of the starch metabolic enzymes BAM and waxy GBSS-I were strongly up-regulated in drought stress in all Miscanthus genotypes, and 12 aquaporins (PIP1, PIP2 and NIP2) were also up-regulated in drought stress across genotypes. Conclusions Different phenotypic responses were observed during drought stress among Miscanthus genotypes from different species, supporting differences in genetic adaption. The low number of DEGs and higher biomass yield in flooded conditions supported Miscanthus use in flooded land. The molecular processes regulated during drought were shared among Miscanthus species and consistent with functional categories known to be critical during drought stress in model organisms. However, differences in the regulated genes, likely associated with ploidy and heterosis, highlighted the value of exploring its diversity for breeding.

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Dual RNA-seq analysis provides new insights into interactions between Norway spruce and necrotrophic pathogen Heterobasidion annosum s.l.

Cited by 39 publications

References 71 publications

Integrated Transcriptomic and Un-Targeted Metabolomics Analysis Reveals Mulberry Fruit (Morus atropurpurea) in Response to Sclerotiniose Pathogen Ciboria shiraiana Infection

Integrated Transcriptomic and Un-Targeted Metabolomics Analysis Reveals Mulberry Fruit (Morus atropurpurea) in Response to Sclerotiniose Pathogen Ciboria shiraiana Infection

Dual RNA-Sequencing Analysis of Resistant (Pinus pinea) and Susceptible (Pinus radiata) Hosts during Fusarium circinatum Challenge

Physiological and transcriptional response to drought stress among bioenergy grass Miscanthus species

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