Whole-genome sequencing and comparative genomic analysis of potential biotechnological strains of Trichoderma harzianum, Trichoderma atroviride, and Trichoderma reesei

Rosolen, Rafaela Rossi; Horta, Maria Augusta Crivelente; Azevedo, Paulo; Silva, Carla Cristina da; Sforça, Danilo Augusto; Goldman, Gustavo H.; Souza, Anete Pereira de

doi:10.1007/s00438-023-02013-5

Cited by 4 publications

(3 citation statements)

References 104 publications

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“…An integrative analysis of genomic content, enzyme activity, and proteomics data of eight taxonomically close Aspergillus species suggested that fungi with similar genomic potential for PBD could differ dramatically in CAZyme production and overall enzyme activities [ 7 ]. Similar results have been reported for Trichoderma and Penicillium species [ 8 , 9 , 10 , 11 ]. In addition, different species employ different sets of transcription factors (TFs) to regulate the utilization of specific polysaccharides.…”

Section: Introductionsupporting

confidence: 90%

Comparative Genomics and Transcriptomics Analyses Reveal Divergent Plant Biomass-Degrading Strategies in Fungi

Li,

Wiebenga,

Lipzen

et al. 2023

JoF

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Plant biomass is one of the most abundant renewable carbon sources, which holds great potential for replacing current fossil-based production of fuels and chemicals. In nature, fungi can efficiently degrade plant polysaccharides by secreting a broad range of carbohydrate-active enzymes (CAZymes), such as cellulases, hemicellulases, and pectinases. Due to the crucial role of plant biomass-degrading (PBD) CAZymes in fungal growth and related biotechnology applications, investigation of their genomic diversity and transcriptional dynamics has attracted increasing attention. In this project, we systematically compared the genome content of PBD CAZymes in six taxonomically distant species, Aspergillus niger, Aspergillus nidulans, Penicillium subrubescens, Trichoderma reesei, Phanerochaete chrysosporium, and Dichomitus squalens, as well as their transcriptome profiles during growth on nine monosaccharides. Considerable genomic variation and remarkable transcriptomic diversity of CAZymes were identified, implying the preferred carbon source of these fungi and their different methods of transcription regulation. In addition, the specific carbon utilization ability inferred from genomics and transcriptomics was compared with fungal growth profiles on corresponding sugars, to improve our understanding of the conversion process. This study enhances our understanding of genomic and transcriptomic diversity of fungal plant polysaccharide-degrading enzymes and provides new insights into designing enzyme mixtures and metabolic engineering of fungi for related industrial applications.

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Section: Introductionsupporting

confidence: 90%

Comparative Genomics and Transcriptomics Analyses Reveal Divergent Plant Biomass-Degrading Strategies in Fungi

Li,

Wiebenga,

Lipzen

et al. 2023

JoF

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“…For the studied species, the retrieved CAZyme genes represent a tiny fraction of all CAZymes (Kubicek et al, 2011; Filho et al, 2017; Rosolen et al, 2023). Whole-genome analysis has shown that T. reesei genomes present fewer CAZymes than biocontrol strains (Kubicek et al, 2011; Li et al, 2017; Li and Wang, 2021).…”

Section: Discussionmentioning

confidence: 99%

“…A previous study characterized the global transcriptome through transcriptomic profiling, revealing different strategies for carbon utilization (Almeida et al, 2021). As transcriptomic, genomic, and phenotypic variation is common even at the strain level, such differences must be carefully studied to understand their role in the biodegradative process (Hewedy et al, 2020; Almeida et al, 2021; Pachauri et al, 2023; Rosolen et al, 2023). In TA0020, 31 genes showed expression levels greater than 5000 TPM.…”

Section: Discussionmentioning

confidence: 99%

Lignocellulolytic carbohydrate-active enzyme-encoding gene clusters in novelTrichoderma atrovirideandTrichoderma harzianumstrains: A BAC-guided transcriptome analysis

Campiteli,

Rosolen,

Horta

et al. 2023

Preprint

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Lignocellulosic biomass is a challenging substrate for enzymatic hydrolysis and therefore increases the process cost in biorefineries. In nature, filamentous fungi naturally degrade lignocellulose by using an arsenal of hydrolytic and oxidative enzymes, specifically, carbohydrate-active enzymes (CAZymes). These fungi, including those of the genusTrichoderma, produce and secrete an arsenal of CAZymes that act synergistically to efficiently degrade complex and recalcitrant substrates.Trichoderma atrovirideCBMAI-0020 andTrichoderma harzianumCBMAI-0179 are biocontrol strains against important phytopathogens and naturally degrade lignocellulosic substrates. We employed the bacterial artificial chromosome (BAC) methodology together with gene expression data under cellulose degradation conditions to identify novel degradative enzymes, explore their proximal context, and identify CAZyme gene clusters. Using this simple, time-saving, and cost-effective molecular tool, it was possible to identify genomic regions rich in CAZymes. We found important gene clusters related to lignocellulose degradation by inspecting the linear structure and expression data of CAZyme-rich regions. The results offered a genomic perspective of important regions related to carbohydrate metabolism, uncovering novel targets positively regulated in the degradation of lignocellulose and helping to elucidate differences in biomass degradation amongTrichodermaspecies.

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Decrypting biocontrol functions and application modes by genomes data of three Trichoderma Strains/Species

Ji,

Liu,

Han

et al. 2024

Fungal Genetics and Biology

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Whole-genome sequencing and comparative genomic analysis of potential biotechnological strains of Trichoderma harzianum, Trichoderma atroviride, and Trichoderma reesei

Cited by 4 publications

References 104 publications

Comparative Genomics and Transcriptomics Analyses Reveal Divergent Plant Biomass-Degrading Strategies in Fungi

Comparative Genomics and Transcriptomics Analyses Reveal Divergent Plant Biomass-Degrading Strategies in Fungi

Lignocellulolytic carbohydrate-active enzyme-encoding gene clusters in novelTrichoderma atrovirideandTrichoderma harzianumstrains: A BAC-guided transcriptome analysis

Decrypting biocontrol functions and application modes by genomes data of three Trichoderma Strains/Species

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