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Title: Genome analysis of Daldinia eschscholtzii strains UM 1400 and UM 1020, wood-decaying fungi isolated from human hosts

Abstract

Background: Daldinia eschscholtzii is a wood-inhabiting fungus that causes wood decay under certain conditions. It has a broad host range and produces a large repertoire of potentially bioactive compounds. However, there is no extensive genome analysis on this fungal species. Results: Two fungal isolates (UM 1400 and UM 1020) from human specimens were identified as Daldinia eschscholtzii by morphological features and ITS-based phylogenetic analysis. Both genomes were similar in size with 10,822 predicted genes in UM 1400 (35.8 Mb) and 11,120 predicted genes in UM 1020 (35.5 Mb). A total of 751 gene families were shared among both UM isolates, including gene families associated with fungus-host interactions. In the CAZyme comparative analysis, both genomes were found to contain arrays of CAZyme related to plant cell wall degradation. Genes encoding secreted peptidases were found in the genomes, which encode for the peptidases involved in the degradation of structural proteins in plant cell wall. In addition, arrays of secondary metabolite backbone genes were identified in both genomes, indicating of their potential to produce bioactive secondary metabolites. Both genomes also contained an abundance of gene encoding signaling components, with three proposed MAPK cascades involved in cell wall integrity, osmoregulation, and mating/filamentation. Besides genomicmore » evidence for degrading capability, both isolates also harbored an array of genes encoding stress response proteins that are potentially significant for adaptation to living in the hostile environments. In conclusion: Our genomic studies provide further information for the biological understanding of the D. eschscholtzii and suggest that these wood-decaying fungi are also equipped for adaptation to adverse environments in the human host.« less

Authors:
 [1];  [1];  [2];  [1];  [3];  [3];  [3];  [1]
  1. Univ. of Malaya, Kual Lumpur (Malaysia). Department of Medical Microbiology
  2. Univ. Tunku Abdul Rahman, Bandar Sungai Long, Selangor (Malaysia)
  3. Codon Genomics, Jalan Dutamas, Selangor Darul Ehsan (Malaysia)
Publication Date:
Research Org.:
Univ. of Malaya, Kual Lumpur (Malaysia). Department of Medical Microbiology
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1241130
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 16; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Genome sequencing; Daldinia eschscholtzii; Wood-inhabiting endophyte; Wood-decaying fungi

Citation Formats

Chan, Chai Ling, Yew, Su Mei, Ngeow, Yun Fong, Na, Shiang Ling, Lee, Kok Wei, Hoh, Chee-Choong, Yee, Wai-Yan, and Ng, Kee Peng. Genome analysis of Daldinia eschscholtzii strains UM 1400 and UM 1020, wood-decaying fungi isolated from human hosts. United States: N. p., 2015. Web. doi:10.1186/s12864-015-2200-2.
Chan, Chai Ling, Yew, Su Mei, Ngeow, Yun Fong, Na, Shiang Ling, Lee, Kok Wei, Hoh, Chee-Choong, Yee, Wai-Yan, & Ng, Kee Peng. Genome analysis of Daldinia eschscholtzii strains UM 1400 and UM 1020, wood-decaying fungi isolated from human hosts. United States. doi:10.1186/s12864-015-2200-2.
Chan, Chai Ling, Yew, Su Mei, Ngeow, Yun Fong, Na, Shiang Ling, Lee, Kok Wei, Hoh, Chee-Choong, Yee, Wai-Yan, and Ng, Kee Peng. Wed . "Genome analysis of Daldinia eschscholtzii strains UM 1400 and UM 1020, wood-decaying fungi isolated from human hosts". United States. doi:10.1186/s12864-015-2200-2. https://www.osti.gov/servlets/purl/1241130.
@article{osti_1241130,
title = {Genome analysis of Daldinia eschscholtzii strains UM 1400 and UM 1020, wood-decaying fungi isolated from human hosts},
author = {Chan, Chai Ling and Yew, Su Mei and Ngeow, Yun Fong and Na, Shiang Ling and Lee, Kok Wei and Hoh, Chee-Choong and Yee, Wai-Yan and Ng, Kee Peng},
abstractNote = {Background: Daldinia eschscholtzii is a wood-inhabiting fungus that causes wood decay under certain conditions. It has a broad host range and produces a large repertoire of potentially bioactive compounds. However, there is no extensive genome analysis on this fungal species. Results: Two fungal isolates (UM 1400 and UM 1020) from human specimens were identified as Daldinia eschscholtzii by morphological features and ITS-based phylogenetic analysis. Both genomes were similar in size with 10,822 predicted genes in UM 1400 (35.8 Mb) and 11,120 predicted genes in UM 1020 (35.5 Mb). A total of 751 gene families were shared among both UM isolates, including gene families associated with fungus-host interactions. In the CAZyme comparative analysis, both genomes were found to contain arrays of CAZyme related to plant cell wall degradation. Genes encoding secreted peptidases were found in the genomes, which encode for the peptidases involved in the degradation of structural proteins in plant cell wall. In addition, arrays of secondary metabolite backbone genes were identified in both genomes, indicating of their potential to produce bioactive secondary metabolites. Both genomes also contained an abundance of gene encoding signaling components, with three proposed MAPK cascades involved in cell wall integrity, osmoregulation, and mating/filamentation. Besides genomic evidence for degrading capability, both isolates also harbored an array of genes encoding stress response proteins that are potentially significant for adaptation to living in the hostile environments. In conclusion: Our genomic studies provide further information for the biological understanding of the D. eschscholtzii and suggest that these wood-decaying fungi are also equipped for adaptation to adverse environments in the human host.},
doi = {10.1186/s12864-015-2200-2},
journal = {BMC Genomics},
number = 1,
volume = 16,
place = {United States},
year = {2015},
month = {11}
}

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