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Analysis of genomic regions of Trichoderma harzianum IOC-3844 related to biomass degradation.

Crucello A, Sforça DA, Horta MA, dos Santos CA, Viana AJ, Beloti LL, de Toledo MA, Vincentz M, Kuroshu RM, de Souza AP - PLoS ONE (2015)

Bottom Line: The assembled BAC sequences revealed 232 predicted genes, 31.5% of which were related to catabolic pathways, including those involved in biomass degradation.Thus, we demonstrate a rapid and efficient tool that focuses on specific genomic regions by combining a BAC library with transcriptomic data.This is the first BAC-based structural genomic study of the cellulolytic fungus T. harzianum, and its findings provide new perspectives regarding the use of this species in biomass degradation processes.

View Article: PubMed Central - PubMed

Affiliation: Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.

ABSTRACT
Trichoderma harzianum IOC-3844 secretes high levels of cellulolytic-active enzymes and is therefore a promising strain for use in biotechnological applications in second-generation bioethanol production. However, the T. harzianum biomass degradation mechanism has not been well explored at the genetic level. The present work investigates six genomic regions (~150 kbp each) in this fungus that are enriched with genes related to biomass conversion. A BAC library consisting of 5,760 clones was constructed, with an average insert length of 90 kbp. The assembled BAC sequences revealed 232 predicted genes, 31.5% of which were related to catabolic pathways, including those involved in biomass degradation. An expression profile analysis based on RNA-Seq data demonstrated that putative regulatory elements, such as membrane transport proteins and transcription factors, are located in the same genomic regions as genes related to carbohydrate metabolism and exhibit similar expression profiles. Thus, we demonstrate a rapid and efficient tool that focuses on specific genomic regions by combining a BAC library with transcriptomic data. This is the first BAC-based structural genomic study of the cellulolytic fungus T. harzianum, and its findings provide new perspectives regarding the use of this species in biomass degradation processes.

No MeSH data available.


Related in: MedlinePlus

GO term distribution among the annotated BAC sequences.(A) According to biological processes; (B) According to molecular functions; and (C) According to cellular components.
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pone.0122122.g003: GO term distribution among the annotated BAC sequences.(A) According to biological processes; (B) According to molecular functions; and (C) According to cellular components.

Mentions: Within the 6 assembled T. harzianum IOC-3844 BACs, 232 genes were predicted, with an average of 38.6 genes per BAC. The average length of the predicted genes was 1,408 bp. These sequences comprise 37% of the assembly (1 gene per 3.8 kb). After running Blast2GO, 148 sequences were annotated with GO terms (Fig. 3), and 208 sequences exhibited matches against the InterPro collection of protein signature databases.


Analysis of genomic regions of Trichoderma harzianum IOC-3844 related to biomass degradation.

Crucello A, Sforça DA, Horta MA, dos Santos CA, Viana AJ, Beloti LL, de Toledo MA, Vincentz M, Kuroshu RM, de Souza AP - PLoS ONE (2015)

GO term distribution among the annotated BAC sequences.(A) According to biological processes; (B) According to molecular functions; and (C) According to cellular components.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383378&req=5

pone.0122122.g003: GO term distribution among the annotated BAC sequences.(A) According to biological processes; (B) According to molecular functions; and (C) According to cellular components.
Mentions: Within the 6 assembled T. harzianum IOC-3844 BACs, 232 genes were predicted, with an average of 38.6 genes per BAC. The average length of the predicted genes was 1,408 bp. These sequences comprise 37% of the assembly (1 gene per 3.8 kb). After running Blast2GO, 148 sequences were annotated with GO terms (Fig. 3), and 208 sequences exhibited matches against the InterPro collection of protein signature databases.

Bottom Line: The assembled BAC sequences revealed 232 predicted genes, 31.5% of which were related to catabolic pathways, including those involved in biomass degradation.Thus, we demonstrate a rapid and efficient tool that focuses on specific genomic regions by combining a BAC library with transcriptomic data.This is the first BAC-based structural genomic study of the cellulolytic fungus T. harzianum, and its findings provide new perspectives regarding the use of this species in biomass degradation processes.

View Article: PubMed Central - PubMed

Affiliation: Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.

ABSTRACT
Trichoderma harzianum IOC-3844 secretes high levels of cellulolytic-active enzymes and is therefore a promising strain for use in biotechnological applications in second-generation bioethanol production. However, the T. harzianum biomass degradation mechanism has not been well explored at the genetic level. The present work investigates six genomic regions (~150 kbp each) in this fungus that are enriched with genes related to biomass conversion. A BAC library consisting of 5,760 clones was constructed, with an average insert length of 90 kbp. The assembled BAC sequences revealed 232 predicted genes, 31.5% of which were related to catabolic pathways, including those involved in biomass degradation. An expression profile analysis based on RNA-Seq data demonstrated that putative regulatory elements, such as membrane transport proteins and transcription factors, are located in the same genomic regions as genes related to carbohydrate metabolism and exhibit similar expression profiles. Thus, we demonstrate a rapid and efficient tool that focuses on specific genomic regions by combining a BAC library with transcriptomic data. This is the first BAC-based structural genomic study of the cellulolytic fungus T. harzianum, and its findings provide new perspectives regarding the use of this species in biomass degradation processes.

No MeSH data available.


Related in: MedlinePlus