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Research article
Wei Zhou
Hunan Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-5715-6079
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This work is licensed under a CC BY 4.0 License. Read Full License
Background Sphingobacterium is a class of Gram-negative, non-fermentative bacilii, and rarely involved in human infections. It is characterized by a large number of cellular membrane sphingophospolipids. Due to its wide ecological distribution and oil degradation ability, environmental microbiologists have paid much attention to it.
Results A novel gram-negative bacterium, designated CZ-2 T , was isolated from a sample of tobacco leaves infected with wildfire disease in Guiyang County, Chenzhou City, Hunan Province, China, and its phylogenetic position was investigated by GC content determination, PCR amplification, sequencing and phylogenetic analysis. Growth occurred on TGY medium at 30 °C and pH 7.0. The GC content of the DNA of strain CZ-2 T is 40.68 mol%. Genome relatedness, rDNA phylogeny and chemotaxonomic characteristics all indicate that strain CZ-2 T represents a novel species of the genus Sphingobacterium . We propose the name Sphingobacterium. tobaci sp. nov., with CZ-2 T as the type strain. Third-generation sequencing (TGS) and next-generation sequencing (NGS) were used to derive a finished genome sequence for strain CZ-2 T , consisting of a circular chromosome 3,925,977 bp in size. The genome of strain CZ-2 T features 3,462 protein-encoding and 50 tRNA-encoding genes. Unigenes were annotated by matching against Clusters of Orthologous Groups of proteins (COG; 2,021 genes), Gene Ontology (GO; 1,952 genes) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases (1,380 genes). Comparison of the predicted proteome of CZ-2 T with those of other Sphingobacterium identified 677 species-specific proteins that may contribute to the adaptation of CZ-2 T to its native environment.
Conclusions As the first report of a Sphingobacterium genome sequenced by NGS and TGS, our work will serve as a useful reference for subsequent sequencing and mapping efforts for additional strains and species within this genus.
Keywords
Sphingobacterium sp., PacBio and Illumina sequencing, Evolution, Cluster of Orthologous, Gene Ontology, KEGG, Comparative genomics
Figure 1
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This is a list of supplementary files associated with this preprint. Click to download.
- TableS4.COGannotationandsummary.xlsx
- FigureS3.NRGOCOGKEGGSWSS.venn.pdf
- TableS1.tRNAannotatedinCZ2Tstraingenome.xlsx
- renamed47305.xlsx
- TableS5.KEGGpathway.xlsx
- FigureS2.GOfunctionalcategories.pdf
- FigureS1.ReadslengthdistributionofPacBiodatainCZ2T.pdf
- TableS2.rRNAannotatedinCZ2Tstraingenome.xlsx
- ChecklistforsubmissionGENG.docx
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A new preprint design is coming!
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This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Research article
Wei Zhou
Hunan Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-5715-6079
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 27 Sep, 2019
No community comments so far
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Applied & Industrial Microbiology
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background Sphingobacterium is a class of Gram-negative, non-fermentative bacilii, and rarely involved in human infections. It is characterized by a large number of cellular membrane sphingophospolipids. Due to its wide ecological distribution and oil degradation ability, environmental microbiologists have paid much attention to it.
Results A novel gram-negative bacterium, designated CZ-2 T , was isolated from a sample of tobacco leaves infected with wildfire disease in Guiyang County, Chenzhou City, Hunan Province, China, and its phylogenetic position was investigated by GC content determination, PCR amplification, sequencing and phylogenetic analysis. Growth occurred on TGY medium at 30 °C and pH 7.0. The GC content of the DNA of strain CZ-2 T is 40.68 mol%. Genome relatedness, rDNA phylogeny and chemotaxonomic characteristics all indicate that strain CZ-2 T represents a novel species of the genus Sphingobacterium . We propose the name Sphingobacterium. tobaci sp. nov., with CZ-2 T as the type strain. Third-generation sequencing (TGS) and next-generation sequencing (NGS) were used to derive a finished genome sequence for strain CZ-2 T , consisting of a circular chromosome 3,925,977 bp in size. The genome of strain CZ-2 T features 3,462 protein-encoding and 50 tRNA-encoding genes. Unigenes were annotated by matching against Clusters of Orthologous Groups of proteins (COG; 2,021 genes), Gene Ontology (GO; 1,952 genes) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases (1,380 genes). Comparison of the predicted proteome of CZ-2 T with those of other Sphingobacterium identified 677 species-specific proteins that may contribute to the adaptation of CZ-2 T to its native environment.
Conclusions As the first report of a Sphingobacterium genome sequenced by NGS and TGS, our work will serve as a useful reference for subsequent sequencing and mapping efforts for additional strains and species within this genus.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
This is a list of supplementary files associated with this preprint. Click to download.
- TableS4.COGannotationandsummary.xlsx
- FigureS3.NRGOCOGKEGGSWSS.venn.pdf
- TableS1.tRNAannotatedinCZ2Tstraingenome.xlsx
- renamed47305.xlsx
- TableS5.KEGGpathway.xlsx
- FigureS2.GOfunctionalcategories.pdf
- FigureS1.ReadslengthdistributionofPacBiodatainCZ2T.pdf
- TableS2.rRNAannotatedinCZ2Tstraingenome.xlsx
- ChecklistforsubmissionGENG.docx
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