Dissecting the fungal biology of Bipolaris papendorfii: from phylogenetic to comparative genomic analysis

Kuan, Chee Sian; Yew, Su Mei; Toh, Yue Fen; Chan, Chai Ling; Ngeow, Yun Fong; Lee, Kok Wei; Na, Shiang Ling; Yee, Wai-Yan; Hoh, Chee-Choong; Ng, Kee Peng

doi:10.1093/dnares/dsv007

Cited by 21 publications

(27 citation statements)

References 64 publications

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“…A large-scale DNA extraction was conducted based on a modified method as described in Kuan et al [ 67 ]. The sequencing and assembly of UM 578 genome were carried out as described previously [ 9 ].…”

Section: Methodsmentioning

confidence: 99%

The genome of newly classified Ochroconis mirabilis: Insights into fungal adaptation to different living conditions

et al. 2016

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BackgroundOchroconis mirabilis, a recently introduced water-borne dematiaceous fungus, is occasionally isolated from human skin lesions and nails. We identified an isolate of O. mirabilis from a skin scraping with morphological and molecular studies. Its genome was then sequenced and analysed for genetic features related to classification and biological characteristics.ResultsUM 578 was identified as O. mirabilis based on morphology and internal transcribed spacer (ITS)-based phylogeny. The 34.61 Mb assembled genome with 13,435 predicted genes showed less efficiency of this isolate in plant cell wall degradation. Results from the peptidase comparison analysis with reported keratin-degrading peptidases from dermatophytes suggest that UM 578 is very unlikely to be utilising these peptidases to survive in the host. Nevertheless, we have identified peptidases from M10A, M12A and S33 families that may allow UM 578 to invade its host via extracellular matrix and collagen degradation. Furthermore, the lipases in UM 578 may have a role in supporting the fungus in host invasion. This fungus has the potential ability to synthesise melanin via the 1,8-dihydroxynaphthalene (DHN)-melanin pathway and to produce mycotoxins. The mating ability of this fungus was also inspected in this study and a mating type gene containing alpha domain was identified. This fungus is likely to produce taurine that is required in osmoregulation. The expanded gene family encoding the taurine catabolism dioxygenase TauD/TdfA domain suggests the utilisation of taurine under sulfate starvation. The expanded glutathione-S-transferase domains and RTA1-like protein families indicate the selection of genes in UM 578 towards adaptation in hostile environments.ConclusionsThe genomic analysis of O. mirabilis UM 578 provides a better understanding of fungal survival tactics in different habitats.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2409-8) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

The genome of newly classified Ochroconis mirabilis: Insights into fungal adaptation to different living conditions

et al. 2016

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“…The assembly completeness was also analyzed with Benchmarking Universal Single Copy Orthologs (BUSCO 3.0.1; Waterhouse et al 2017). In addition, 238 whole-genome assemblies of other Dothideomycetes were downloaded from NCBI Gen-Bank and the JGI Genome portal (Additional file 1: Table S1; Galagan et al 2005;Fedorova et al 2008;Sharpton et al 2009;Ellwood et al 2010;Desjardins et al 2011;Goodwin et al 2011;Rouxel et al 2011;Stukenbrock et al 2011;Chan et al 2012;Hu et al 2012;Joardar et al 2012;Ng et al 2012;Ohm et al 2012;Spatafora et al 2012;Blanco-Ulate et al 2013;Condon et al 2013;Lenassi et al 2013;Yew et al 2013;Aragona et al 2014;Bihon et al 2014;Chan et al 2014;Cooke et al 2014;Gao et al 2014;Gostinčar et al, 2014;Han et al 2014;Soliai et al 2014;Sterflinger et al 2014;van der Nest et al 2014;Yang et al 2014;Franco et al 2015;Grandaubert et al 2015;Kuan et al 2015;Morales-Cruz et al 2015;Orner et al 2015;Shaw et al 2015;Shiller et al 2015;…”

Section: Bioinformaticsmentioning

confidence: 99%

Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota)

et al. 2019

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Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces, that have been suggested to be early diverging lineages. We assembled phylogenomic datasets from newly sequenced (4) and previously available genomes (238) of 242 taxa. We explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. Overall, our phylogenetic reconstructions provide consistent and well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class. In addition, many of the major lineages within Dothideomycetes are recovered as monophyletic, and the phylogenomic approach implemented strongly supports their relationships. Ancestral character state reconstruction suggest that the rock-inhabiting lifestyle is ancestral within the class.

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“…Genomic comparison is a powerful tool for understanding differences and evolutionary dynamics among related species [36–38]. Our data show a high similarity between different strains of T. harzianum (IOC3844, B97 and T6776), which indicates that differences in enzyme production and efficiency may be related more to gene regulation mechanisms than differences in the sequence itself.…”

Section: Discussionmentioning

confidence: 71%

“Integrative Genomic Analysis for the Bioprospection of Regulators and Accessory Enzymes Associated with Cellulose Degradation in a Filamentous Fungus (Trichoderma harzianum)”

Filho¹,

Horta

Santos

et al. 2019

Preprint

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27Background: Unveiling fungal genome structure and function reveals the potential 28 biotechnological use of fungi. Trichoderma harzianum is a powerful CAZyme-producing 29 fungus. We studied the genomic regions in T. harzianum IOC3844 containing CAZyme 30 genes, transcription factors and transporters. 31Results: We used bioinformatics tools to mine the T. harzianum genome for potential 32 genomics, transcriptomics, and exoproteomics data and coexpression networks. The DNA 33 was sequenced by PacBio SMRT technology for multi-omics data analysis and integration. In 34 total, 1676 genes were annotated in the genomic regions analyzed; 222 were identified as 35CAZymes in T. harzianum IOC3844. When comparing transcriptome data under cellulose or 36 glucose conditions, 114 genes were differentially expressed in cellulose, with 51 CAZymes. 37 CLR2, a transcription factor physically and phylogenetically conserved in T. harzianum spp., 38 was differentially expressed under cellulose conditions. The genes induced/repressed under 39 cellulose conditions included those important for plant biomass degradation, including CIP2 40 of the CE15 family and a copper-dependent LPMO of the AA9 family. 41 Conclusions:Our results provide new insights into the relationship between genomic 42 organization and hydrolytic enzyme expression and regulation in T. harzianum IOC3844. Our 43 results can improve plant biomass degradation, which is fundamental for developing more 44 efficient strains and/or enzymatic cocktails for the production of hydrolytic enzymes. 45

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Dissecting the fungal biology of Bipolaris papendorfii: from phylogenetic to comparative genomic analysis

Cited by 21 publications

References 64 publications

The genome of newly classified Ochroconis mirabilis: Insights into fungal adaptation to different living conditions

The genome of newly classified Ochroconis mirabilis: Insights into fungal adaptation to different living conditions

Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota)

“Integrative Genomic Analysis for the Bioprospection of Regulators and Accessory Enzymes Associated with Cellulose Degradation in a Filamentous Fungus (Trichoderma harzianum)”

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