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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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K-means clustering of differentially expressed genes identified as CAZymes (summarized in Table 3).
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pone-0088689-g006: K-means clustering of differentially expressed genes identified as CAZymes (summarized in Table 3).

Mentions: To identify the transcriptomic responses under each condition, we analyzed the distribution of the genes that were identified as being differentially expressed. Pairwise comparisons of the subsets indicated the total number of genes that were overexpressed under each condition. The classification of differentially expressed contigs allowed us to determine the set of genes for carbohydrate-active enzymes that were upregulated in each group (Table 3, Figure 6 and 7).


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)

K-means clustering of differentially expressed genes identified as CAZymes (summarized in Table 3).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0088689-g006: K-means clustering of differentially expressed genes identified as CAZymes (summarized in Table 3).
Mentions: To identify the transcriptomic responses under each condition, we analyzed the distribution of the genes that were identified as being differentially expressed. Pairwise comparisons of the subsets indicated the total number of genes that were overexpressed under each condition. The classification of differentially expressed contigs allowed us to determine the set of genes for carbohydrate-active enzymes that were upregulated in each group (Table 3, Figure 6 and 7).

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