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Title: Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential

Abstract

There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables. Genes associated with plant interactions highlight the potential use of micromonosporae in agriculture and biotechnology.

Authors:
ORCiD logo [1];  [1];  [2]; ORCiD logo [3];  [4]; ORCiD logo [1]; ORCiD logo [5];  [2];  [6];  [6];  [7]; ORCiD logo [7];  [7];  [7];  [1]; ORCiD logo [3];  [1]
  1. Newcastle Univ., Newcastle upon Tyne (United Kingdom)
  2. Northumbria Univ., Newcastle upon Tyne (United Kingdom)
  3. Leibniz Inst. DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
  4. Universidad de Salamanca (Spain)
  5. Ondokuz Mayis Univ., Kurupelit-Samsun (Turkey)
  6. Pacific Biosciences, Menlo Park, CA (United States)
  7. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1543777
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Carro, Lorena, Nouioui, Imen, Sangal, Vartul, Meier-Kolthoff, Jan P., Trujillo, Martha E., Montero-Calasanz, Maria del Carmen, Sahin, Nevzat, Smith, Darren Lee, Kim, Kristi E., Peluso, Paul, Deshpande, Shweta, Woyke, Tanja, Shapiro, Nicole, Kyrpides, Nikos C., Klenk, Hans-Peter, Göker, Markus, and Goodfellow, Michael. Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. United States: N. p., 2018. Web. doi:10.1038/s41598-017-17392-0.
Carro, Lorena, Nouioui, Imen, Sangal, Vartul, Meier-Kolthoff, Jan P., Trujillo, Martha E., Montero-Calasanz, Maria del Carmen, Sahin, Nevzat, Smith, Darren Lee, Kim, Kristi E., Peluso, Paul, Deshpande, Shweta, Woyke, Tanja, Shapiro, Nicole, Kyrpides, Nikos C., Klenk, Hans-Peter, Göker, Markus, & Goodfellow, Michael. Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. United States. doi:10.1038/s41598-017-17392-0.
Carro, Lorena, Nouioui, Imen, Sangal, Vartul, Meier-Kolthoff, Jan P., Trujillo, Martha E., Montero-Calasanz, Maria del Carmen, Sahin, Nevzat, Smith, Darren Lee, Kim, Kristi E., Peluso, Paul, Deshpande, Shweta, Woyke, Tanja, Shapiro, Nicole, Kyrpides, Nikos C., Klenk, Hans-Peter, Göker, Markus, and Goodfellow, Michael. Thu . "Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential". United States. doi:10.1038/s41598-017-17392-0. https://www.osti.gov/servlets/purl/1543777.
@article{osti_1543777,
title = {Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential},
author = {Carro, Lorena and Nouioui, Imen and Sangal, Vartul and Meier-Kolthoff, Jan P. and Trujillo, Martha E. and Montero-Calasanz, Maria del Carmen and Sahin, Nevzat and Smith, Darren Lee and Kim, Kristi E. and Peluso, Paul and Deshpande, Shweta and Woyke, Tanja and Shapiro, Nicole and Kyrpides, Nikos C. and Klenk, Hans-Peter and Göker, Markus and Goodfellow, Michael},
abstractNote = {There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables. Genes associated with plant interactions highlight the potential use of micromonosporae in agriculture and biotechnology.},
doi = {10.1038/s41598-017-17392-0},
journal = {Scientific Reports},
number = 1,
volume = 8,
place = {United States},
year = {2018},
month = {1}
}

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