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Transcriptome profile of Trichoderma harzianum IOC-3844 induced by sugarcane bagasse.

Horta MA, Vicentini R, Delabona Pda S, Laborda P, Crucello A, Freitas S, Kuroshu RM, Polikarpov I, Pradella JG, Souza AP - PLoS ONE (2014)

Bottom Line: De novo assembly resulted in 32,396 contigs, which were submitted for identification and classified according to their identities.This analysis allowed us to define a principal set of T. harzianum genes that are involved in the degradation of cellulose and hemicellulose and the accessory genes that are involved in the depolymerization of biomass.The present study provides valuable information for future studies on biomass degradation and contributes to a better understanding of the role of the genes that are involved in this process.

View Article: PubMed Central - PubMed

Affiliation: Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil.

ABSTRACT
Profiling the transcriptome that underlies biomass degradation by the fungus Trichoderma harzianum allows the identification of gene sequences with potential application in enzymatic hydrolysis processing. In the present study, the transcriptome of T. harzianum IOC-3844 was analyzed using RNA-seq technology. The sequencing generated 14.7 Gbp for downstream analyses. De novo assembly resulted in 32,396 contigs, which were submitted for identification and classified according to their identities. This analysis allowed us to define a principal set of T. harzianum genes that are involved in the degradation of cellulose and hemicellulose and the accessory genes that are involved in the depolymerization of biomass. An additional analysis of expression levels identified a set of carbohydrate-active enzymes that are upregulated under different conditions. The present study provides valuable information for future studies on biomass degradation and contributes to a better understanding of the role of the genes that are involved in this process.

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Molecular functions, biological process distribution and cellular localization of the transcriptome assembly.Contigs were assigned putative classifications based on homology and evaluated for their predicted involvement in molecular functions (A), biological processes (B) and cellular localization (C).
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pone-0088689-g003: Molecular functions, biological process distribution and cellular localization of the transcriptome assembly.Contigs were assigned putative classifications based on homology and evaluated for their predicted involvement in molecular functions (A), biological processes (B) and cellular localization (C).

Mentions: Transcript profiling is an important strategy for studying the expression of large gene sets under particular conditions. To determine the influence of the complex sugarcane bagasse substrate on gene expression, the contigs generated from the de novo assembly of the transcriptome were analyzed. The generated assembly was compared with the archive of the assembly scaffolds for T. harzianum CBS 226.95 [38], which demonstrated a similarity of 96% with the contigs derived from the assembly of the transcriptome. To identify the responses of the transcriptome under the different conditions tested, the contigs were annotated and classified according to their predicted functions (Figure 3).


Transcriptome profile of Trichoderma harzianum IOC-3844 induced by sugarcane bagasse.

Horta MA, Vicentini R, Delabona Pda S, Laborda P, Crucello A, Freitas S, Kuroshu RM, Polikarpov I, Pradella JG, Souza AP - PLoS ONE (2014)

Molecular functions, biological process distribution and cellular localization of the transcriptome assembly.Contigs were assigned putative classifications based on homology and evaluated for their predicted involvement in molecular functions (A), biological processes (B) and cellular localization (C).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3928278&req=5

pone-0088689-g003: Molecular functions, biological process distribution and cellular localization of the transcriptome assembly.Contigs were assigned putative classifications based on homology and evaluated for their predicted involvement in molecular functions (A), biological processes (B) and cellular localization (C).
Mentions: Transcript profiling is an important strategy for studying the expression of large gene sets under particular conditions. To determine the influence of the complex sugarcane bagasse substrate on gene expression, the contigs generated from the de novo assembly of the transcriptome were analyzed. The generated assembly was compared with the archive of the assembly scaffolds for T. harzianum CBS 226.95 [38], which demonstrated a similarity of 96% with the contigs derived from the assembly of the transcriptome. To identify the responses of the transcriptome under the different conditions tested, the contigs were annotated and classified according to their predicted functions (Figure 3).

Bottom Line: De novo assembly resulted in 32,396 contigs, which were submitted for identification and classified according to their identities.This analysis allowed us to define a principal set of T. harzianum genes that are involved in the degradation of cellulose and hemicellulose and the accessory genes that are involved in the depolymerization of biomass.The present study provides valuable information for future studies on biomass degradation and contributes to a better understanding of the role of the genes that are involved in this process.

View Article: PubMed Central - PubMed

Affiliation: Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil.

ABSTRACT
Profiling the transcriptome that underlies biomass degradation by the fungus Trichoderma harzianum allows the identification of gene sequences with potential application in enzymatic hydrolysis processing. In the present study, the transcriptome of T. harzianum IOC-3844 was analyzed using RNA-seq technology. The sequencing generated 14.7 Gbp for downstream analyses. De novo assembly resulted in 32,396 contigs, which were submitted for identification and classified according to their identities. This analysis allowed us to define a principal set of T. harzianum genes that are involved in the degradation of cellulose and hemicellulose and the accessory genes that are involved in the depolymerization of biomass. An additional analysis of expression levels identified a set of carbohydrate-active enzymes that are upregulated under different conditions. The present study provides valuable information for future studies on biomass degradation and contributes to a better understanding of the role of the genes that are involved in this process.

Show MeSH
Related in: MedlinePlus