Using evolutionary genomics, transcriptomics, and systems biology to reveal gene networks underlying fungal development

Wang, Zheng; Gudibanda, Aditya; Ugwuowo, Ugochukwu; Trail, Frances; Townsend, Jeffrey P.

doi:10.1016/j.fbr.2018.02.001

Cited by 21 publications

(13 citation statements)

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“…solani (FSSC) species complexes are among the most agriculturally important and species-rich lineages within the genus (O’Donnell et al, 2013). In prior research, we studied the homothallic, cereal pathogen F. graminearum (FSAMSC) with particular emphasis on development and function of perithecia, as well as production of mycotoxins and other secondary metabolites (Gaffoor et al, 2005; Sikhakolli et al, 2012; Wang et al, 2012, 2018; Trail et al, 2017; Kim et al, 2018). Recently, we began a study of perithecium development in homothallic F. neocosmosporiellum (formerly Neocosmospora vasinfecta ; Geiser et al, 2013), a member of the FSSC that is reported to be pathogenic on peanut and soybean (Dau et al, 2010; Pan et al, 2010; Sun et al, 2014; Greer et al, 2015), and an opportunistic pathogen of humans (Cornely et al, 2001; Gabriel et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Comparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus Fusarium neocosmosporiellum

et al. 2019

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Fusarium neocosmosporiellum (formerly Neocosmospora vasinfecta ) is a cosmopolitan fungus that has been reported from soil, herbivore dung, and as a fruit- and root-rot pathogen of numerous field crops, although it is not known to cause significant losses on any crop. Taking advantage of the fact that this species produces prolific numbers of perithecia in culture, the genome of F. neocosmosporiellum was sequenced and transcriptomic analysis across five stages of perithecium development was performed to better understand the metabolic potential for sexual development and gain insight into its life history. Perithecium morphology together with the genome and transcriptome were compared with those of the plant pathogen F. graminearum , a model for studying perithecium development. Larger ascospores of F. neocosmosporiellum and their tendency to discharge as a cluster demonstrated a duality of dispersal: the majority are passively dispersed through the formation of cirrhi, while a minority of spores are shot longer distances than those of F. graminearum. The predicted gene number in the F. neocosmosporiellum genome was similar to that in F. graminearum , but F. neocosmosporiellum had more carbohydrate metabolism-related and transmembrane transport genes. Many transporter genes were differentially expressed during perithecium development in F. neocosmosporiellum , which may account for its larger perithecia. Comparative analysis of the secondary metabolite gene clusters identified several polyketide synthase genes that were induced during later stages of perithecium development. Deletion of a polyketide synthase gene in F. neocosmosporiellum resulted in a defective perithecium phenotype, suggesting an important role of the corresponding metabolite, which has yet to be identified, in perithecium development. Results of this study have provided novel insights into the genomic underpinning of development in F. neocosmosporiellum , which may help elucidate its ability to occupy diverse ecological niches.

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Section: Introductionmentioning

confidence: 99%

Comparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus Fusarium neocosmosporiellum

et al. 2019

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“…( Surhio et al, 2017;. Flammulinavelutipes Immunomodulatory (Wang et al, 2018). (Darwesh et al, 2018).…”

Section: Lachnumspmentioning

confidence: 99%

Characterization and biological activities of polysaccharides extracted from the filamentous fungal cell wall: an updated literature review

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et al. 2020

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Filamentous fungi are eukaryotic organisms with several industrial and pharmaceutical applications. Polysaccharides are the principal components of cell walls from Fungi and other organisms like diatoms, and have been reported in the industrial and medical fields as products with a huge number of different biological activities and applications. The objectives of this narrative review were to assess the characterization methods and and biological activities of polysaccharides extracted from the filamentous fungal cell wall. Glucans, chitin and galactomannans are the most common polysaccharide often found in the cell walls of fungi. These polysaccharides can contain different glycosidic linkage either an α or β-configuration and at various positions, such as (1-3,1-4, 1-6), as well as several molecular sizes. This leads to an almost limitless diversity in their structure and biological activity. There are many methods for polysaccharides characterization, among them; the methods commonly used involve Infrared Spectrometry (FT-IR), Nuclear Magnetic Resonance Spectroscopy (MRS), and gas chromatography-mass spectrometry (CG-MS). Typically, cell wall polysaccharides from filamentous fungi have been shown to possess complex, important and multifaceted biological activities including mainly antioxidant, anti-inflammatory, immunomodulatory, antinociceptive, antitumor and hypoglycemic activities. Due to the large number of filamentous fungi genus and species capable of producing useful polysaccharides, perform scientific researches, and produce novel scientific knowledge and information are particularly interesting in order to identify polysaccharides with potential biological activity and that can be used for medicinal purposes.

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“…Although the rDNA markers are relatively short in length, there is evidence of a relatively high level of homoplasy at least in eukaryotes [ 29 ], probably because of the internal heterogeneity among the several copies of these loci [ 30 , 31 ]. Even though species delimitation is moving rapidly to genomic based approaches [ 22 , 32 , 33 , 34 ], most of the everyday taxonomic practice makes use of one or few markers from these loci, that are also particularly abundant in reference databases. In this context, we took into consideration two loci to analyse the patterns of homoplasy variations in defined and well explored groups of yeasts.…”

Section: Introductionmentioning

confidence: 99%

Homoplasy as an Auxiliary Criterion for Species Delimitation

et al. 2021

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Homoplasy is a sort of noise in phylogenetic reconstructions, due to the accumulation of backmutations, convergent evolution and horizontal gene transfer (HGT), which is considered the major trigger of homoplasy in microorganism for its massive presence. It is also known that homoplasy increases with the complexity of the tree with both real and simulated data. In this paper, we analyzed the variation of homoplasy with the two widely used taxonomic markers ITS and LSU in four taxonomic models characterized by differences in the intra-specific distances. An algorithm (HomoDist) was developed to analyze the homoplasy index (HI) variation upon addition of a single element (strain or species) in increasing distance from a starting element. This algorithm allows to follow changes of the consistency index (CI), complementary to the HI, with the increase of the number of taxa and with the increase of the distance among elements. Results show that homoplasy increases—as expected—with the number of taxa, but also as a function of the overall distance among species, often with an almost linear relationship between distance and HI. No HI change was observed in trees with few taxa spanning through short distances, indicating that this noise is not prohibitive in this context, although the analysis of the ratio between HI and distance can be recommended as a criterion for tree acceptance. The absence of large changes of the HI within the species, and its increase when new species are added by HomoDist, suggest that homoplasy variation can be used as an auxiliary test in distance-based species delimitation with any type of marker.

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Using evolutionary genomics, transcriptomics, and systems biology to reveal gene networks underlying fungal development

Cited by 21 publications

References 181 publications

Comparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus Fusarium neocosmosporiellum

Comparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus Fusarium neocosmosporiellum

Characterization and biological activities of polysaccharides extracted from the filamentous fungal cell wall: an updated literature review

Homoplasy as an Auxiliary Criterion for Species Delimitation

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