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Genome sequencing and annotation of Serratia sp. strain TEL.

Lephoto TE, Gray VM - Genom Data (2015)

Bottom Line: We present the annotation of the draft genome sequence of Serratia sp. strain TEL (GenBank accession number KP711410).This organism was isolated from entomopathogenic nematode Oscheius sp. strain TEL (GenBank accession number KM492926) collected from grassland soil and has a genome size of 5,000,541 bp and 542 subsystems.The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession number LDEG00000000.

View Article: PubMed Central - PubMed

Affiliation: Microbiology and Biotechnology Department, School of Molecular and Cell Biology, University of the Witwatersrand, Braamfontein 2050, Johannesburg, South Africa.

ABSTRACT
We present the annotation of the draft genome sequence of Serratia sp. strain TEL (GenBank accession number KP711410). This organism was isolated from entomopathogenic nematode Oscheius sp. strain TEL (GenBank accession number KM492926) collected from grassland soil and has a genome size of 5,000,541 bp and 542 subsystems. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession number LDEG00000000.

No MeSH data available.


Related in: MedlinePlus

The evolutionary history of Serratia sp. TEL (pointed with a red arrow) inferred by using the Maximum Likelihood method based on the Tamura–Nei model on MEGA6 software. The bootstrap consensus tree inferred from 1000 replications.
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f0005: The evolutionary history of Serratia sp. TEL (pointed with a red arrow) inferred by using the Maximum Likelihood method based on the Tamura–Nei model on MEGA6 software. The bootstrap consensus tree inferred from 1000 replications.

Mentions: To isolate the bacterial pathogen, non-feeding infective juveniles were surface sterilized with 0.1% sodium hypochlorite for 4 h and rinsed with autoclaved distilled water. Sterile IJs were carefully suspended in 1 ml of sterile nutrient broth in a microtube and homogenized with a small sterile plastic pestle. The homogenate was streaked onto NBTA and McConkey agar plates and incubated at 25 °C for 24 h in the dark. DNA was extracted from the bright green colonies and pink colonies, pure cultures obtained from the selective media and genomic DNA was extracted using the ZR bacterial DNA miniprep kit (Zymo Research). A polymerase chain reaction was employed to amplify the 16S rRNA gene sequence of the isolated bacterial DNA using EUB968 forward primer 5′-ACGGGCGGTGTGTC-3′ Tm (°C) = 62 and UNIV1382 reverse primer 5′-AACGCGAAGAACCTTAC-3′ Tm (°C) = 66. The same primers were used for the sequencing of this gene. The sequence obtained was subjected to NCBI BLAST under the default settings for highly similar alignments. The analysis revealed that among all the matches for the 16S rRNA gene sequences, the unknown sequence had a high affinity to a novel Serratia species which was then assigned the name Serratia sp. strain TEL. Other high scoring bacteria 16S rRNA sequences were downloaded from GenBank to be used for phylogenetic analysis. The evolutionary relatedness of Serratia sp. strain TEL with several Serratia species was based on the 16S rRNA ITS regions using the Maximum Likelihood method based on the Tamura–Nei model using MEGA6. The bootstrap consensus tree was inferred from 1000 replications and the tree was drawn to scale, with branch lengths measuring the number of substitutions per site (next to the branches) as shown in Fig. 1. Bacteria belonging to the well-known genera Photorhabdus and Xenorhabdus were used as possible out-groups to root the tree and see if there is any significant relationship they might have with the identified Serratia species.


Genome sequencing and annotation of Serratia sp. strain TEL.

Lephoto TE, Gray VM - Genom Data (2015)

The evolutionary history of Serratia sp. TEL (pointed with a red arrow) inferred by using the Maximum Likelihood method based on the Tamura–Nei model on MEGA6 software. The bootstrap consensus tree inferred from 1000 replications.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664685&req=5

f0005: The evolutionary history of Serratia sp. TEL (pointed with a red arrow) inferred by using the Maximum Likelihood method based on the Tamura–Nei model on MEGA6 software. The bootstrap consensus tree inferred from 1000 replications.
Mentions: To isolate the bacterial pathogen, non-feeding infective juveniles were surface sterilized with 0.1% sodium hypochlorite for 4 h and rinsed with autoclaved distilled water. Sterile IJs were carefully suspended in 1 ml of sterile nutrient broth in a microtube and homogenized with a small sterile plastic pestle. The homogenate was streaked onto NBTA and McConkey agar plates and incubated at 25 °C for 24 h in the dark. DNA was extracted from the bright green colonies and pink colonies, pure cultures obtained from the selective media and genomic DNA was extracted using the ZR bacterial DNA miniprep kit (Zymo Research). A polymerase chain reaction was employed to amplify the 16S rRNA gene sequence of the isolated bacterial DNA using EUB968 forward primer 5′-ACGGGCGGTGTGTC-3′ Tm (°C) = 62 and UNIV1382 reverse primer 5′-AACGCGAAGAACCTTAC-3′ Tm (°C) = 66. The same primers were used for the sequencing of this gene. The sequence obtained was subjected to NCBI BLAST under the default settings for highly similar alignments. The analysis revealed that among all the matches for the 16S rRNA gene sequences, the unknown sequence had a high affinity to a novel Serratia species which was then assigned the name Serratia sp. strain TEL. Other high scoring bacteria 16S rRNA sequences were downloaded from GenBank to be used for phylogenetic analysis. The evolutionary relatedness of Serratia sp. strain TEL with several Serratia species was based on the 16S rRNA ITS regions using the Maximum Likelihood method based on the Tamura–Nei model using MEGA6. The bootstrap consensus tree was inferred from 1000 replications and the tree was drawn to scale, with branch lengths measuring the number of substitutions per site (next to the branches) as shown in Fig. 1. Bacteria belonging to the well-known genera Photorhabdus and Xenorhabdus were used as possible out-groups to root the tree and see if there is any significant relationship they might have with the identified Serratia species.

Bottom Line: We present the annotation of the draft genome sequence of Serratia sp. strain TEL (GenBank accession number KP711410).This organism was isolated from entomopathogenic nematode Oscheius sp. strain TEL (GenBank accession number KM492926) collected from grassland soil and has a genome size of 5,000,541 bp and 542 subsystems.The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession number LDEG00000000.

View Article: PubMed Central - PubMed

Affiliation: Microbiology and Biotechnology Department, School of Molecular and Cell Biology, University of the Witwatersrand, Braamfontein 2050, Johannesburg, South Africa.

ABSTRACT
We present the annotation of the draft genome sequence of Serratia sp. strain TEL (GenBank accession number KP711410). This organism was isolated from entomopathogenic nematode Oscheius sp. strain TEL (GenBank accession number KM492926) collected from grassland soil and has a genome size of 5,000,541 bp and 542 subsystems. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession number LDEG00000000.

No MeSH data available.


Related in: MedlinePlus