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Title: High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia

Abstract

Rhizobium mesoamericanum STM6155 (INSCD=ATYY01000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as an effective nitrogen fixing microsymbiont of the legume Mimosa pudica L.. STM6155 was isolated in 2009 from a nodule of the trap host M. pudica grown in nickel-rich soil collected near Mont Dore, New Caledonia. R. mesoamericanum STM6155 was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) genome sequencing project. Here we describe the symbiotic properties of R. mesoamericanum STM6155, together with its genome sequence information and annotation. The 6,927,906bp high-quality draft genome is arranged into 147 scaffolds of 152 contigs containing 6855 protein-coding genes and 71 RNA-only encoding genes. Strain STM6155 forms an ANI clique (ID 2435) with the sequenced R. mesoamericanum strain STM3625, and the nodulation genes are highly conserved in these strains and the type strain of Rhizobium grahamii CCGE501 T . Within the STM6155 genome, we have identified a chr chromate efflux gene cluster of six genes arranged into two putative operons and we postulate that this cluster is important for the survival of STM6155 in ultramafic soils containing high concentrations of chromate.

Authors:
 [1];  [2];  [1]; ORCiD logo [3];  [4];  [4];  [3];  [5];  [5];  [5];  [5];  [6];  [5];  [5];  [7];  [8];  [9];  [3]
  1. Univ. of Montpellier (France); Lab. of Tropical and Mediterranean Symbioses (UMR-LSTM), Montpellier (France)
  2. Lab. of Tropical and Mediterranean Symbioses (UMR-LSTM), Montpellier (France)
  3. Murdoch Univ., WA (Australia). School of Veterinary and Life Sciences
  4. Curtin Univ., Bentley, WA (United States). Curtin Univ. Sustainability Policy Inst.
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  6. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center
  7. Univ. of Jeddah (Saudi Arabia). Dept. of Biology
  8. King Abdulaziz Univ., Jeddah (Saudi Arabia). Dept. of Biological Sciences
  9. King Abdulaziz Univ., Jeddah (Saudi Arabia). Dept. of Biological Sciences; USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1379683
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; root-nodule bacteria; nitrogen fixation; rhizobium; alphaproteobacteria; mimosa

Citation Formats

Klonowska, Agnieszka, López-López, Aline, Moulin, Lionel, Ardley, Julie, Gollagher, Margaret, Marinova, Dora, Tian, Rui, Huntemann, Marcel, Reddy, T. B. K., Varghese, Neha, Woyke, Tanja, Markowitz, Victor, Ivanova, Natalia, Seshadri, Rekha, Baeshen, Mohamed N., Baeshen, Nabih A., Kyrpides, Nikos, and Reeve, Wayne. High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia. United States: N. p., 2017. Web. doi:10.1186/s40793-016-0212-4.
Klonowska, Agnieszka, López-López, Aline, Moulin, Lionel, Ardley, Julie, Gollagher, Margaret, Marinova, Dora, Tian, Rui, Huntemann, Marcel, Reddy, T. B. K., Varghese, Neha, Woyke, Tanja, Markowitz, Victor, Ivanova, Natalia, Seshadri, Rekha, Baeshen, Mohamed N., Baeshen, Nabih A., Kyrpides, Nikos, & Reeve, Wayne. High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia. United States. doi:10.1186/s40793-016-0212-4.
Klonowska, Agnieszka, López-López, Aline, Moulin, Lionel, Ardley, Julie, Gollagher, Margaret, Marinova, Dora, Tian, Rui, Huntemann, Marcel, Reddy, T. B. K., Varghese, Neha, Woyke, Tanja, Markowitz, Victor, Ivanova, Natalia, Seshadri, Rekha, Baeshen, Mohamed N., Baeshen, Nabih A., Kyrpides, Nikos, and Reeve, Wayne. Tue . "High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia". United States. doi:10.1186/s40793-016-0212-4. https://www.osti.gov/servlets/purl/1379683.
@article{osti_1379683,
title = {High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia},
author = {Klonowska, Agnieszka and López-López, Aline and Moulin, Lionel and Ardley, Julie and Gollagher, Margaret and Marinova, Dora and Tian, Rui and Huntemann, Marcel and Reddy, T. B. K. and Varghese, Neha and Woyke, Tanja and Markowitz, Victor and Ivanova, Natalia and Seshadri, Rekha and Baeshen, Mohamed N. and Baeshen, Nabih A. and Kyrpides, Nikos and Reeve, Wayne},
abstractNote = {Rhizobium mesoamericanum STM6155 (INSCD=ATYY01000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as an effective nitrogen fixing microsymbiont of the legume Mimosa pudica L.. STM6155 was isolated in 2009 from a nodule of the trap host M. pudica grown in nickel-rich soil collected near Mont Dore, New Caledonia. R. mesoamericanum STM6155 was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) genome sequencing project. Here we describe the symbiotic properties of R. mesoamericanum STM6155, together with its genome sequence information and annotation. The 6,927,906bp high-quality draft genome is arranged into 147 scaffolds of 152 contigs containing 6855 protein-coding genes and 71 RNA-only encoding genes. Strain STM6155 forms an ANI clique (ID 2435) with the sequenced R. mesoamericanum strain STM3625, and the nodulation genes are highly conserved in these strains and the type strain of Rhizobium grahamii CCGE501 T . Within the STM6155 genome, we have identified a chr chromate efflux gene cluster of six genes arranged into two putative operons and we postulate that this cluster is important for the survival of STM6155 in ultramafic soils containing high concentrations of chromate.},
doi = {10.1186/s40793-016-0212-4},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 12,
place = {United States},
year = {Tue Jan 17 00:00:00 EST 2017},
month = {Tue Jan 17 00:00:00 EST 2017}
}

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Works referenced in this record:

Confidence Limits on Phylogenies: An Approach Using the Bootstrap
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