Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11T and Bradyrhizobium yuanmingense CCBAU 10071T

Autor: Nikos C. Kyrpides, Tanja Woyke, William B. Whitman, Kristina Lindström, Aregu Amsalu Aserse
Přispěvatelé: Environmental Sciences
Jazyk: angličtina
Rok vydání: 2017
Předmět:
0301 basic medicine
Bradyrhizobium yuanmingense
lcsh:QH426-470
Sequence analysis
030106 microbiology
Bradyrhizobium yuanmingense CCBAU 10071(T)
Biology
Symbiotic
Genome average nucleotide identity
Genome
Bradyrhizobium
03 medical and health sciences
Genetics
Extended Genome Report
ROOT-NODULES
Gene
1183 Plant biology
microbiology
virology
Whole genome sequencing
Phylogenetic tree
MICROBIAL SPECIES DELINEATION
STRAINS
Human Genome
food and beverages
RAIN-FOREST
DENITRIFICATION
Erythrina brucei
biology.organism_classification
Digital DNA-DNA hybridization
Molecular biology
EFFECTIVE NODULES
Housekeeping gene
lcsh:Genetics
030104 developmental biology
ERYTHRINA-BRUCEI
BACTERIUM
Bradyrhizobium yuanmingense CCBAU 10071T
JAPONICUM
GEN. NOV
Biochemistry and Cell Biology
Ethiopia
Bradyrhizobium shewense sp nov ERR11(T)
Bradyrhizobium shewense sp. nov. ERR11T
Zdroj: Standards in Genomic Sciences, Vol 12, Iss 1, Pp 1-14 (2017)
Standards in genomic sciences, vol 12, iss 1
Standards in Genomic Sciences
ISSN: 1944-3277
Popis: The type strain of the prospective 10.1601/nm.30737 sp. nov. ERR11T, was isolated from a nodule of the leguminous tree Erythrina brucei native to Ethiopia. The type strain 10.1601/nm.1463 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 T, was isolated from the nodules of Lespedeza cuneata in Beijing, China. The genomes of ERR11T and 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+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 ERR11T is 9,163,226 bp in length and has 102 scaffolds, containing 8548 protein–coding and 86 RNA genes. The 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+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 10.1601/nm.24498 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+110 T. 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 10.1601/nm.27386 10.1601/strainfinder?urlappend=%3Fid%3DLMG+26795 T. The nodulation genes nolYA-nodD2D1YABCSUIJ-nolO-nodZ of ERR11T and 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 T are organized in a similar way to the homologous genes identified in the genomes of 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+110 T , 10.1601/nm.25806 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+4 and 10.1601/nm.1462 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+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 10.1601/nm.25806 branch. Genome Average Nucleotide Identity (ANI) calculated between the genome sequences of ERR11T and closely related sequences revealed that strains belonging to 10.1601/nm.25806 branch (10.1601/strainfinder?urlappend=%3Fid%3DUSDA+4 and 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+15615), were the closest strains to the strain ERR11T with 95.2% ANI. Type strain ERR11T showed the highest DDH predicted value with 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+15615 (58.5%), followed by 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+4 (53.1%). Nevertheless, the ANI and DDH values obtained between ERR11T and 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+15615 or 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+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 10.1601/nm.30737 sp. nov. with strain ERR11T (10.1601/strainfinder?urlappend=%3Fid%3DHAMBI+3532 T=10.1601/strainfinder?urlappend=%3Fid%3DLMG+30162 T) as the type strain. Electronic supplementary material The online version of this article (10.1186/s40793-017-0283-x) contains supplementary material, which is available to authorized users.
Databáze: OpenAIRE
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