Role of Genomics and RNA-seq in Studies of Fungal Virulence

Riccombeni, Alessandro; Butler, Geraldine

doi:10.1007/s12281-012-0104-z

Cited by 3 publications

(2 citation statements)

References 98 publications

(45 reference statements)

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“…Next-generation sequencing technology (Illumina RNA-seq) enables highly sensitive and accurate quantification of expression, thus providing a myriad of transcript data with high resolution, high quality, and low costs (Riccombeni and Butler, 2012 ). It has been widely applied in non-model and model species, such as, Aspergillus nidulans, Hortaea werneckii , and Wallemia ichthyophaga , examining hundreds of stress-tolerance genes (Redkar et al, 1996 ; Petrovic et al, 2002 ; Zajc et al, 2013 ).…”

Section: Introductionmentioning

confidence: 99%

Morphological and Transcriptomic Analysis Reveals the Osmoadaptive Response of Endophytic Fungus Aspergillus montevidensis ZYD4 to High Salt Stress

et al. 2017

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Halophilic fungi have evolved unique osmoadaptive strategies, enabling them to thrive in hypersaline habitats. Here, we conduct morphological and transcriptomic response of endophytic fungus (Aspergillus montevidensis ZYD4) in both the presence and absence of salt stress. Under salt stress, the colony morphology of the A. montevidensis ZYD4 changed drastically and exhibited decreased colony pigmentation. Extensive conidiophores development was observed under salt stress; conidiophores rarely developed in the absence of salt stress. Under salt stress, yellow cleistothecium formation was inhibited, while glycerol and compatible sugars continued to accumulate. Among differentially expressed unigenes (DEGs), 733 of them were up-regulated while 1,619 unigenes were down-regulated. We discovered that genes involved in the accumulation of glycerol, the storage of compatible sugars, organic acids, pigment production, and asexual sporulation were differentially regulated under salt stress. These results provide further understanding of the molecular basis of osmoadaptive mechanisms of halophilic endophytic fungi.

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Section: Introductionmentioning

confidence: 99%

Morphological and Transcriptomic Analysis Reveals the Osmoadaptive Response of Endophytic Fungus Aspergillus montevidensis ZYD4 to High Salt Stress

et al. 2017

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“…Transcriptome analyses of filamentous fungi also has been widely reported (Kawahara et al, 2012;Riccombeni and Butler, 2012;Wang et al, 2010). A. niger is a kind of filamentous fungi which is widely used in industrial fermentation to produce more than 30 kinds of enzymes including amylase, acid protease, cellulase, pectinase, glucose oxidase, etc.…”

Section: Introductionmentioning

confidence: 96%

An RNA-Sequencing Study of the Genes and Metabolic Pathways Involved inAspergillus nigerWeathering of Potassium Feldspar

Wang

Lian

Pan

2014

Geomicrobiology Journal

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Microbial transformation of potassium feldspar to produce organic composite potassium fertilizer is recognized to be an important method of effective use of the huge reserves of low grade K + -bearing rock in China. The mechanism underlying microbial weathering of silicate minerals is still unclear, and this is an obstacle to practical methods of application. To thoroughly understand the molecular mechanism responsible for the weathering of potassium feldspar by Aspergillus niger at a molecular level, high-throughput RNA-sequencing (RNA-seq) and treatment with different potassium sources (cultured in Czapek medium with K + or potassium feldspar) were used to investigate the differentially expressed genes of A. niger associated with potassium feldspar weathering and the related metabolic pathways. A series of differentially expressed genes related to the synthesis and transportation of organic acids, polysaccharides, and proteins (enzymes) were found to be closely associated with the K + released from minerals Downloaded by [Gebze Yuksek Teknoloji Enstitïsu ] at 06:12 23 December 2014 ACCEPTED MANUSCRIPT ACCEPTED MANUSCRIPT 2through bioinformatic analysis. In addition, 12 genes that showed apparent expression differences by RNA-seq analysis and are relevant to organic acid synthesis, protein modification, maintenance of cellular homeostasis, and material transportation, were selected to be further verified using RT-qPCR. Compared to the fungal samples cultured with soluble K + , those with potassium feldspar have certain genes that are more up-regulated, such as the genes for Na + ,K + -ATPase (447.6 multiples), cystathionine beta-synthase (5.6 multiples), cysteine synthase (9 multiples), and glutathione synthase (3.5 multiples). The analysis indicates that A. niger weathering of potassium feldspar is due to the synergistic effect of many factors including the up-regulation of certain genes and activation of related metabolite pathways. The research improves our understanding of the mechanisms of microbial weathering of silicate minerals.

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Deep mRNA sequencing reveals stage-specific transcriptome alterations during microsclerotia development in the smoke tree vascular wilt pathogen, Verticillium dahliae

Xiong

Wang

et al. 2014

BMC Genomics

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BackgroundVerticillium dahliae is a soil-borne fungus that causes vascular wilt diseases in a wide range of plant hosts. V. dahliae produces multicelled, melanized resting bodies, also known as microsclerotia (MS) that can survive for years in the soil. The MS are the primary source of infection of the Verticillium disease cycle. Thus, MS formation marks an important event in the disease cycle of V. dahliae.ResultsIn this study, next generation sequencing technology of RNA-Seq was employed to investigate the global transcriptomic dynamics of MS development to identify differential gene expression at several stages of MS formation in strain XS11 of V. dahliae, isolated from smoke tree. We observed large-scale changes in gene expression during MS formation, such as increased expression of genes involved in protein metabolism and carbohydrate metabolism. Genes involved in glycolytic pathway and melanin biosynthesis were dramatically up-regulated in MS. Cluster analyses revealed increased expression of genes encoding products involved in primary metabolism and stress responses throughout MS development. Differential expression of ubiquitin-dependent protein catabolism and cell death-associated genes during MS development were revealed. Homologs of genes located in the lineage-specific (LS) regions of V. dahliae strain VdLs.17, were either not expressed or showed low expression. Furthermore, alternative splicing (AS) events were analyzed, revealing that over 95.0% AS events involve retention of introns (RI).ConclusionsThese data reveal the dynamics of transcriptional regulation during MS formation and were used to construct a comprehensive high-resolution gene expression map. This map provides a key resource for understanding the biology and molecular basis of MS development of V. dahliae.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-324) contains supplementary material, which is available to authorized users.

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Role of Genomics and RNA-seq in Studies of Fungal Virulence

Cited by 3 publications

References 98 publications

Morphological and Transcriptomic Analysis Reveals the Osmoadaptive Response of Endophytic Fungus Aspergillus montevidensis ZYD4 to High Salt Stress

Morphological and Transcriptomic Analysis Reveals the Osmoadaptive Response of Endophytic Fungus Aspergillus montevidensis ZYD4 to High Salt Stress

An RNA-Sequencing Study of the Genes and Metabolic Pathways Involved inAspergillus nigerWeathering of Potassium Feldspar

Deep mRNA sequencing reveals stage-specific transcriptome alterations during microsclerotia development in the smoke tree vascular wilt pathogen, Verticillium dahliae

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