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Title: Genome Sequencing and Comparative Analysis of the Biocontrol Agent Trichoderma harzianum sensu stricto TR274

Abstract

Biological control is a complex process which requires many mechanisms and a high diversity of biochemical pathways. The species of Trichoderma harzianum are well known for their biocontrol activity against many plant pathogens. To gain new insights into the biocontrol mechanism used by T. harzianum, we sequenced the isolate TR274 genome using Illumina. The assembly was performed using AllPaths-LG with a maximum coverage of 100x. The assembly resulted in 2282 contigs with a N50 of 37033bp. The genome size generated was 40.8 Mb and the GC content was 47.7%, similar to other Trichoderma genomes. Using the JGI Annotation Pipeline we predicted 13,932 genes with a high transcriptome support. CEGMA tests suggested 100% genome completeness and 97.9% of RNA-SEQ reads were mapped to the genome. The phylogenetic comparison using orthologous proteins with all Trichoderma genomes sequenced at JGI, corroborates the Trichoderma (T. asperellum and T. atroviride), Longibrachiatum (T. reesei and T. longibrachiatum) and Pachibasium (T. harzianum and T. virens) section division described previously. The comparison between two Trichoderma harzianum species suggests a high genome similarity but some strain-specific expansions. Analyses of the secondary metabolites, CAZymes, transporters, proteases, transcription factors were performed. The Pachybasium section expanded virtually all categories analyzed compared withmore » the other sections, specially Longibrachiatum section, that shows a clear contraction. These results suggests that these proteins families have an important role in their respective phenotypes. Future analysis will improve the understanding of this complex genus and give some insights about its lifestyle and the interactions with the environment.« less

Authors:
; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
Genomics Division
OSTI Identifier:
1235082
Report Number(s):
LBNL-178254
ir:178254
Resource Type:
Conference
Country of Publication:
United States
Language:
English

Citation Formats

Steindorff, Andrei S., Noronha, Elilane F., Ulhoa, Cirano J., Kuo, Alan, Salamov, Asaf A., Haridas, Sajeet, Riley, Robert W., Druzhinina, Irina S., Kubicek, Christian P., and Grigoriev, Igor V. Genome Sequencing and Comparative Analysis of the Biocontrol Agent Trichoderma harzianum sensu stricto TR274. United States: N. p., 2015. Web.
Steindorff, Andrei S., Noronha, Elilane F., Ulhoa, Cirano J., Kuo, Alan, Salamov, Asaf A., Haridas, Sajeet, Riley, Robert W., Druzhinina, Irina S., Kubicek, Christian P., & Grigoriev, Igor V. Genome Sequencing and Comparative Analysis of the Biocontrol Agent Trichoderma harzianum sensu stricto TR274. United States.
Steindorff, Andrei S., Noronha, Elilane F., Ulhoa, Cirano J., Kuo, Alan, Salamov, Asaf A., Haridas, Sajeet, Riley, Robert W., Druzhinina, Irina S., Kubicek, Christian P., and Grigoriev, Igor V. Tue . "Genome Sequencing and Comparative Analysis of the Biocontrol Agent Trichoderma harzianum sensu stricto TR274". United States. doi:. https://www.osti.gov/servlets/purl/1235082.
@article{osti_1235082,
title = {Genome Sequencing and Comparative Analysis of the Biocontrol Agent Trichoderma harzianum sensu stricto TR274},
author = {Steindorff, Andrei S. and Noronha, Elilane F. and Ulhoa, Cirano J. and Kuo, Alan and Salamov, Asaf A. and Haridas, Sajeet and Riley, Robert W. and Druzhinina, Irina S. and Kubicek, Christian P. and Grigoriev, Igor V.},
abstractNote = {Biological control is a complex process which requires many mechanisms and a high diversity of biochemical pathways. The species of Trichoderma harzianum are well known for their biocontrol activity against many plant pathogens. To gain new insights into the biocontrol mechanism used by T. harzianum, we sequenced the isolate TR274 genome using Illumina. The assembly was performed using AllPaths-LG with a maximum coverage of 100x. The assembly resulted in 2282 contigs with a N50 of 37033bp. The genome size generated was 40.8 Mb and the GC content was 47.7%, similar to other Trichoderma genomes. Using the JGI Annotation Pipeline we predicted 13,932 genes with a high transcriptome support. CEGMA tests suggested 100% genome completeness and 97.9% of RNA-SEQ reads were mapped to the genome. The phylogenetic comparison using orthologous proteins with all Trichoderma genomes sequenced at JGI, corroborates the Trichoderma (T. asperellum and T. atroviride), Longibrachiatum (T. reesei and T. longibrachiatum) and Pachibasium (T. harzianum and T. virens) section division described previously. The comparison between two Trichoderma harzianum species suggests a high genome similarity but some strain-specific expansions. Analyses of the secondary metabolites, CAZymes, transporters, proteases, transcription factors were performed. The Pachybasium section expanded virtually all categories analyzed compared with the other sections, specially Longibrachiatum section, that shows a clear contraction. These results suggests that these proteins families have an important role in their respective phenotypes. Future analysis will improve the understanding of this complex genus and give some insights about its lifestyle and the interactions with the environment.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Tue Mar 17 00:00:00 EDT 2015},
month = {Tue Mar 17 00:00:00 EDT 2015}
}

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