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Title: High quality draft genome sequence of Leucobacter chironomi strain MM2LBT (DSM 19883T) isolated from a Chironomus sp. egg mass

Abstract

Leucobacter chironomi strain MM2LBT (Halpern et al., Int J Syst Evol Microbiol 59:665-70 2009) is a Gram-positive, rod shaped, non-motile, aerobic, chemoorganotroph bacterium. L. chironomi belongs to the family Microbacteriaceae, a family within the class Actinobacteria. Strain MM2LBT was isolated from a chironomid (Diptera; Chironomidae) egg mass that was sampled from a waste stabilization pond in northern Israel. In a phylogenetic tree based on 16S rRNA gene sequences, strain MM2LBT formed a distinct branch within the radiation encompassing the genus Leucobacter. Here we describe the features of this organism, together with the complete genome sequence and annotation. We find that the DNA GC content is 69.90%. The chromosome length is 2,964,712 bp. It encodes 2,690 proteins and 61 RNA genes. L. chironomi genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.

Authors:
 [1];  [2];  [3];  [3];  [3];  [3];  [3];  [4];  [5];  [5];  [3];  [6];  [1]
  1. Univ. of Haifa (Israel)
  2. St. Petersburg Academic Univ. (Russia); St. Petersburg Academic Univ. (Russia)
  3. Dept. of Energy Joint Genome Inst., Walnut Creek, CA (United States)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  5. Leibniz Institute DSMZ, Braunschweig (Germany)
  6. Dept. of Energy Joint Genome Inst., Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1256905
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Leucobacter chironomi; Microbacteriaceae; Chironomid; Chironomus; Egg mass; Hexavalent chromium

Citation Formats

Laviad, Sivan, Lapidus, Alla, Copeland, Alex, Reddy, T. B. K., Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N., Markowitz, Victor M., Pukall, Rüdiger, Klenk, Hans-Peter, Woyke, Tanja, Kyrpides, Nikos C., and Halpern, Malka. High quality draft genome sequence of Leucobacter chironomi strain MM2LBT (DSM 19883T) isolated from a Chironomus sp. egg mass. United States: N. p., 2015. Web. doi:10.1186/s40793-015-0003-3.
Laviad, Sivan, Lapidus, Alla, Copeland, Alex, Reddy, T. B. K., Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N., Markowitz, Victor M., Pukall, Rüdiger, Klenk, Hans-Peter, Woyke, Tanja, Kyrpides, Nikos C., & Halpern, Malka. High quality draft genome sequence of Leucobacter chironomi strain MM2LBT (DSM 19883T) isolated from a Chironomus sp. egg mass. United States. https://doi.org/10.1186/s40793-015-0003-3
Laviad, Sivan, Lapidus, Alla, Copeland, Alex, Reddy, T. B. K., Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N., Markowitz, Victor M., Pukall, Rüdiger, Klenk, Hans-Peter, Woyke, Tanja, Kyrpides, Nikos C., and Halpern, Malka. 2015. "High quality draft genome sequence of Leucobacter chironomi strain MM2LBT (DSM 19883T) isolated from a Chironomus sp. egg mass". United States. https://doi.org/10.1186/s40793-015-0003-3. https://www.osti.gov/servlets/purl/1256905.
@article{osti_1256905,
title = {High quality draft genome sequence of Leucobacter chironomi strain MM2LBT (DSM 19883T) isolated from a Chironomus sp. egg mass},
author = {Laviad, Sivan and Lapidus, Alla and Copeland, Alex and Reddy, T. B. K. and Huntemann, Marcel and Pati, Amrita and Ivanova, Natalia N. and Markowitz, Victor M. and Pukall, Rüdiger and Klenk, Hans-Peter and Woyke, Tanja and Kyrpides, Nikos C. and Halpern, Malka},
abstractNote = {Leucobacter chironomi strain MM2LBT (Halpern et al., Int J Syst Evol Microbiol 59:665-70 2009) is a Gram-positive, rod shaped, non-motile, aerobic, chemoorganotroph bacterium. L. chironomi belongs to the family Microbacteriaceae, a family within the class Actinobacteria. Strain MM2LBT was isolated from a chironomid (Diptera; Chironomidae) egg mass that was sampled from a waste stabilization pond in northern Israel. In a phylogenetic tree based on 16S rRNA gene sequences, strain MM2LBT formed a distinct branch within the radiation encompassing the genus Leucobacter. Here we describe the features of this organism, together with the complete genome sequence and annotation. We find that the DNA GC content is 69.90%. The chromosome length is 2,964,712 bp. It encodes 2,690 proteins and 61 RNA genes. L. chironomi genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.},
doi = {10.1186/s40793-015-0003-3},
url = {https://www.osti.gov/biblio/1256905}, journal = {Standards in Genomic Sciences},
issn = {1944-3277},
number = 1,
volume = 10,
place = {United States},
year = {Fri May 08 00:00:00 EDT 2015},
month = {Fri May 08 00:00:00 EDT 2015}
}

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Cited by: 6 works
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Works referenced in this record:

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Leucobacter luti sp. nov., and Leucobacter alluvii sp. nov., two new species of the genus Leucobacter isolated under chromium stress
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Chironomid Egg Masses as a Natural Reservoir of Vibrio cholerae Non-O1 and Non-O139 in Freshwater Habitats
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Culturable and VBNC Vibrio cholerae: Interactions with Chironomid Egg Masses and Their Bacterial Population
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Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass
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Leucobacter denitrificans sp. nov., isolated from cow dung
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Chironomid egg masses and Vibrio cholerae
journal, July 2001


Vibrio cholerae and Aeromonas: do they share a mutual host?
journal, February 2008


The protective role of endogenous bacterial communities in chironomid egg masses and larvae
journal, June 2013


A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
journal, December 2009


The minimum information about a genome sequence (MIGS) specification
journal, May 2008


PICRUSt2 for prediction of metagenome functions
journal, June 2020


High-quality draft assemblies of mammalian genomes from massively parallel sequence data
journal, December 2010


Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990


The DNA Bank Network: The Start from a German Initiative
journal, March 2011


IMG ER: a system for microbial genome annotation expert review and curation
journal, June 2009


Approved Lists of Bacterial Names
journal, January 1980


Leucobacter komagatae gen. nov., sp. nov., a New Aerobic Gram-Positive, Nonsporulating Rod with 2,4-Diaminobutyric Acid in the Cell Wall
journal, October 1996


Proposal for a New Hierarchic Classification System, Actinobacteria classis nov.
journal, April 1997


Leucobacter chironomi sp. nov., a chromate-resistant bacterium isolated from a chironomid egg mass
journal, April 2009


Leucobacter aerolatus sp. nov., from the air of a duck barn
journal, January 2010


Leucobacter celer sp. nov., isolated from Korean fermented seafood
journal, October 2010


Leucobacter tardus sp. nov., isolated from the phyllosphere of Solanum tuberosum L.
journal, November 2008


Leucobacter iarius sp. nov., in the family Microbacteriaceae
journal, April 2007


Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008


Chironomid egg masses harbour the clinical species Aeromonas taiwanensis and Aeromonas sanarellii
journal, October 2012


Dependent population dynamics between chironomids (nonbiting midges) and Vibrio cholerae: Chironomids and Vibrio cholerae
journal, January 2006


The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation
journal, December 2012


Solexa Ltd
journal, June 2004


Bacterial Community Composition Associated with Chironomid Egg Masses
journal, December 2012


Leucobacter exalbidus sp. nov., an actinobacterium isolated from a mixed culture from compost
journal, January 2011


Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects
journal, May 2013


Genome sequence of the chromate-resistant bacterium Leucobacter salsicius type strain M1-8T
journal, December 2013


Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project
journal, December 2013


The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes
journal, July 2009


Works referencing / citing this record:

Exemplar Abstract for Leucobacter chironomi Halpern et al. 2009 emend. Nouioui et al. 2018.
dataset, January 2013


Antibiotic resistance genes in the Actinobacteria phylum
journal, June 2019


High-Quality Draft Genome Sequence of Leucobacter sp. Strain G161, a Distinct and Effective Chromium Reducer
journal, February 2016