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Title: Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11 T and Bradyrhizobium yuanmingense CCBAU 10071 T

Abstract

The type strain of the prospective Bradyrhizobium shewense sp. nov. ERR11 T, was isolated from a nodule of the leguminous tree Erythrina brucei native to Ethiopia. The type strain Bradyrhizobium yuanmingense CCBAU 10071 T, was isolated from the nodules of Lespedeza cuneata in Beijing, China. The genomes of ERR11 T and CCBAU 10071 T were sequenced by DOE–JGI and deposited at the DOE–JGI genome portal as well as at the European Nucleotide Archive. The genome of ERR11 T is 9,163,226 bp in length and has 102 scaffolds, containing 8548 protein–coding and 86 RNA genes. The CCBAU 10071 T genome is arranged in 108 scaffolds and consists of 8,201,522 bp long and 7776 protein–coding and 85 RNA genes. Both genomes contain symbiotic genes, which are homologous to the genes found in the complete genome sequence of Bradyrhizobium diazoefficiens USDA110 T. The genes encoding for nodulation and nitrogen fixation in ERR11 T showed high sequence similarity with homologous genes found in the draft genome of peanut–nodulating Bradyrhizobium arachidis LMG 26795 T. The nodulation genes nolYA-nodD2D1YABCSUIJ-nolO-nodZ of ERR11 T and CCBAU 10071 T are organized in a similar way to the homologous genes identified in the genomes of USDA110 T, Bradyrhizobium ottawaense USDAmore » 4 and Bradyrhizobium liaoningense CCBAU 05525. The genomes harbor hupSLCFHK and hypBFDE genes that code the expression of hydrogenase, an enzyme that helps rhizobia to uptake hydrogen released by the N 2-fixation process and genes encoding denitrification functions napEDABC and norCBQD for nitrate and nitric oxide reduction, respectively. The genome of ERR11 T also contains nosRZDFYLX genes encoding nitrous oxide reductase. Based on multilocus sequence analysis of housekeeping genes, the novel species, which contains eight strains formed a unique group close to the B. ottawaense branch. Genome Average Nucleotide Identity (ANI) calculated between the genome sequences of ERR11 T and closely related sequences revealed that strains belonging to B. ottawaense branch (USDA4 and CCBAU15615), were the closest strains to the strain ERR11 T with 95.2% ANI. Type strain ERR11 T showed the highest DDH predicted value with CCBAU15615 (58.5%), followed by USDA 4 (53.1%). Nevertheless, the ANI and DDH values obtained between ERR11 T and CCBAU 15615 or USDA 4 were below the cutoff values (ANI ≥ 96.5%; DDH ≥ 70%) for strains belonging to the same species, suggesting that ERR11 T is a new species. Therefore, based on the phylogenetic analysis, ANI and DDH values, we formally propose the creation of B. shewense sp. nov. with strain ERR11 T (HAMBI 3532 T=LMG 30162 T) as the type strain.« less

Authors:
 [1];  [2];  [2];  [3];  [1]
  1. Univ. of Helsinki (Finland). Dept. of Environmental Sciences
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. Univ. of Georgia, Athens, GA (United States). Dept. of Microbiology, Biological Sciences
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1529250
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
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:
Bradyrhizobium shewense sp. nov. ERR11T; Erythrina brucei; Bradyrhizobium yuanmingense CCBAU 10071T; Symbiotic; Ethiopia; Genome average nucleotide identity; Digital DNA-DNA hybridization

Citation Formats

Aserse, Aregu Amsalu, Woyke, Tanja, Kyrpides, Nikos C., Whitman, William B., and Lindström, Kristina. Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11T and Bradyrhizobium yuanmingense CCBAU 10071T. United States: N. p., 2017. Web. doi:10.1186/s40793-017-0283-x.
Aserse, Aregu Amsalu, Woyke, Tanja, Kyrpides, Nikos C., Whitman, William B., & Lindström, Kristina. Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11T and Bradyrhizobium yuanmingense CCBAU 10071T. United States. doi:10.1186/s40793-017-0283-x.
Aserse, Aregu Amsalu, Woyke, Tanja, Kyrpides, Nikos C., Whitman, William B., and Lindström, Kristina. Tue . "Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11T and Bradyrhizobium yuanmingense CCBAU 10071T". United States. doi:10.1186/s40793-017-0283-x. https://www.osti.gov/servlets/purl/1529250.
@article{osti_1529250,
title = {Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11T and Bradyrhizobium yuanmingense CCBAU 10071T},
author = {Aserse, Aregu Amsalu and Woyke, Tanja and Kyrpides, Nikos C. and Whitman, William B. and Lindström, Kristina},
abstractNote = {The type strain of the prospective Bradyrhizobium shewense sp. nov. ERR11T, was isolated from a nodule of the leguminous tree Erythrina brucei native to Ethiopia. The type strain Bradyrhizobium yuanmingense CCBAU 10071T, was isolated from the nodules of Lespedeza cuneata in Beijing, China. The genomes of ERR11T and CCBAU 10071T were sequenced by DOE–JGI and deposited at the DOE–JGI genome portal as well as at the European Nucleotide Archive. The genome of ERR11T is 9,163,226 bp in length and has 102 scaffolds, containing 8548 protein–coding and 86 RNA genes. The CCBAU 10071T genome is arranged in 108 scaffolds and consists of 8,201,522 bp long and 7776 protein–coding and 85 RNA genes. Both genomes contain symbiotic genes, which are homologous to the genes found in the complete genome sequence of Bradyrhizobium diazoefficiens USDA110T. The genes encoding for nodulation and nitrogen fixation in ERR11T showed high sequence similarity with homologous genes found in the draft genome of peanut–nodulating Bradyrhizobium arachidis LMG 26795T. The nodulation genes nolYA-nodD2D1YABCSUIJ-nolO-nodZ of ERR11T and CCBAU 10071T are organized in a similar way to the homologous genes identified in the genomes of USDA110T, Bradyrhizobium ottawaense USDA 4 and Bradyrhizobium liaoningense CCBAU 05525. The genomes harbor hupSLCFHK and hypBFDE genes that code the expression of hydrogenase, an enzyme that helps rhizobia to uptake hydrogen released by the N2-fixation process and genes encoding denitrification functions napEDABC and norCBQD for nitrate and nitric oxide reduction, respectively. The genome of ERR11T also contains nosRZDFYLX genes encoding nitrous oxide reductase. Based on multilocus sequence analysis of housekeeping genes, the novel species, which contains eight strains formed a unique group close to the B. ottawaense branch. Genome Average Nucleotide Identity (ANI) calculated between the genome sequences of ERR11T and closely related sequences revealed that strains belonging to B. ottawaense branch (USDA4 and CCBAU15615), were the closest strains to the strain ERR11T with 95.2% ANI. Type strain ERR11T showed the highest DDH predicted value with CCBAU15615 (58.5%), followed by USDA 4 (53.1%). Nevertheless, the ANI and DDH values obtained between ERR11T and CCBAU 15615 or USDA 4 were below the cutoff values (ANI ≥ 96.5%; DDH ≥ 70%) for strains belonging to the same species, suggesting that ERR11T is a new species. Therefore, based on the phylogenetic analysis, ANI and DDH values, we formally propose the creation of B. shewense sp. nov. with strain ERR11T (HAMBI 3532T=LMG 30162T) as the type strain.},
doi = {10.1186/s40793-017-0283-x},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 12,
place = {United States},
year = {2017},
month = {12}
}

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