Members of the genus
The genus
Species in this genus have been collected from geographically diverse ecosystems. The wide spread of
Despite the potential importance of
For the extraction of genomic DNA (gDNA), strain 56AF was grown in nutrient broth medium (Difco Laboratories, USA) at 25°C with shaking at 150 rpm for 24 h. The gDNA was extracted using the PureLink Genomic DNA kit (Thermo Fisher Scientific, USA) according to the manufacturer’s instructions. gDNA quantification was performed with a Qubit® fluorometer (Thermo Fisher Scientific).
After the description of new
Digital DNA-DNA hybridization (dDDH) values between the genome sequences of
The genome of strain 56AF was prepared using the Nextera DNA Library Preparation Kit (Illumina Inc., USA) and sequenced using a paired-end approach on the Illumina MiSeq platform. The average insert length was ~550 bp. Reads were trimmed and filtered with Trimmomatic software (version 0.32) [
Trimmed reads were assembled de novo with Velvet software (version 1.2.10) [
This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number MTBD00000000. The version described in this paper is the first version, MTBD01000000.
ORFs were predicted using the RAST server databases. Additional functional annotations were performed with the SEED database and Kyoto Encyclopedia of Genes and Genomes (KEGG). Additionally, gene discovery was performed with Prodigal software [
The
The phylogenetic position of
Maximum likelihood phylogenetic tree showing the evolutionary position of
The
The
(a) Circular map of the draft genome of
Comparison of the genomic properties of
Size (Mb) | Contig | GC (%) | Gene | rRNA | tRNA | Other RNA | Reference | |
---|---|---|---|---|---|---|---|---|
4,56 | 141 | 62 | 4,294 | 8 | 89 | 1 | This study | |
4,75 | 1 | 64.8 | 4,438 | 25 | 98 | 5 | [ | |
5,03 | 67 | 62.8 | 4,595 | 13 | 57 | 4 | [ | |
4,09 | 223 | 62.6 | 3,916 | 4 | 81 | 1 | [ | |
4,67 | 152 | 64.9 | 4,313 | 77 | 4 | [ | ||
C. |
4,97 | 152 | 64.44 | 4463 | 6 | 74 | 4 | [ |
4.77 | 1,63 | 64.8 | 4492 | 33 | 4 | [ | ||
4.63 | 326 | 64.7 | 4404 | 33 | 5 | [ |
SEED subsystems distribution of the
Subsystem category | Subsystem feature counts |
---|---|
Sulfur metabolism | 32 |
Phosphorus metabolism | 47 |
Carbohydrates | 242 |
Amino acids and derivatives | 417 |
Fatty acids, lipid, and isoprenoids | 103 |
Metabolism secondary | 4 |
Nitrogen metabolism | 13 |
Metabolism of aromatic compounds | 24 |
Cofactors, vitamins, prosthetic groups, and pigments | 242 |
Nucleosides and nucleotides | 90 |
Dormancy and sporulation | 1 |
Respiration | 133 |
Stress response | 134 |
DNA metabolism | 99 |
Membrane transport | 156 |
Regulation and cell signaling | 88 |
Motility and chemotaxis | 176 |
Cell division and cell cycle | 35 |
Protein metabolism | 298 |
RNA metabolism | 135 |
Iron acquisition and metabolism | 34 |
Phages, prophages, transposable elements and plasmids | 65 |
Miscellaneous | 45 |
Photosynthesis | 0 |
Potassium metabolism | 20 |
Virulence, disease, and defense | 88 |
Cell wall and capsule | 166 |
Among the predicted genes present in the genome of
A number of potential
There are five well-studied double-membrane-spanning secretion systems (T1SS, T2SS, T3SS, T4SS, and T6SS) present in a wide variety of pathogenic and nonpathogenic gram-negative bacteria. These systems secrete products with diverse functions, such as those involved in adhesion, pathogenicity, adaptation, and survival [
In gram-negative bacteria, T1SS is composed of three membrane proteins, two in the inner membrane belonging to the ABC transporter and membrane fusion protein (MFP) families and a third porin-like protein in the outer membrane [
T2SS consists of a large multiprotein machinery with 12–15 components known as general secretion pathway (Gsp) proteins [
T3SS is found in a large number of gram-negative pathogens and symbionts [
T4SS is found in both gram-negative and gram-positive bacteria and in some archaea and allows the translocation of DNA and proteins into target cells, playing an important role in the pathogenesis of a wide range of bacteria [
Finally, T6SS is broadly distributed among Proteobacteria. It translocates toxic effector proteins into eukaryotic and prokaryotic cells and has an important role in pathogenesis, bacterial communication, and interactions with the environment [
Toxins can be identified by the presence of a variety of proteins, such as hemolysins, hemolytic enterotoxins, colicin V, lytic proteins, and Nudix hydrolases. These toxins are associated with pathogenic bacteria [
Important virulence factors for host cell invasion were found, for example, CDSs encoding a hydrolase cell-wall associated protein, metalloproteases, lypolitic proteins, collagenases, and the proteolytic enzymes KpSS and KpSC. The last two are conserved proteins involved in capsular polysaccharides assembly systems [
Unlike other
A set of genes with potential roles in multiple antibiotic resistance were identified in the
Additionally, the annotation of the
Based on orthologous groups (OGs) analysis, the eight
Distribution of orthologous groups (OGs) among the genomes of
Open reading frames
Genomic DNA
Digital DNA-DNA hybridization
Kyoto Encyclopedia of Genes and Genomes
Clusters of Orthologous Groups
Orthologous groups
Type secretion system.
The authors declare no conflict of interests.
This work and publication were supported by the grants from the Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG, APQ 00801/12 and APQ-00463-13), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES).
Table S1: misassembly report based on the alignment of