Genome Sequencing and Annotation of Chlamydia-like Bacteria

Bacterial 1 kb insert DNA libraries (Purified Neochlamydia S13 and Protochlamydia R18) were prepared using a genomic DNA Sample Prep Kit (Illumina, San Diego, CA). DNA clusters were generated on a slide using a Cluster Generation Kit (ver. 4) on an Illumina Cluster Station, according to the manufacturer's instructions. Sequencing runs for 81-mer paired-end sequence were performed using an Illumina Genome Analyzer IIx (GA IIx). The 81-mer paired-end reads were assembled (parameters k64, n51, c32.1373) using ABySS-pe v1.2.0 [50] (link). Annotation of genes from the draft genome sequences was performed using Rapid Annotation using Subsystem Technology (RAST: http://rast.nmpdr.org/) [51] (link) with a local manual BLASTp search. Metabolic pathway modules were predicted using the Kyoto Encyclopedia of Genes and Genomes (KEGG: http://www.genome.jp/kegg/) [52] (link). Genome comparison was performed using RAST, and then manually visualized by GenomeMatcher 1.69 (http://www.ige.tohoku.ac.jp/joho/gmProject/gmhome.html) [53] (link).

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Ishida K., Sekizuka T., Hayashida K., Matsuo J., Takeuchi F., Kuroda M., Nakamura S., Yamazaki T., Yoshida M., Takahashi K., Nagai H., Sugimoto C, & Yamaguchi H. (2014). Amoebal Endosymbiont Neochlamydia Genome Sequence Illuminates the Bacterial Role in the Defense of the Host Amoebae against Legionella pneumophila. PLoS ONE, 9(4), e95166.

Publication 2014

genomic DNA Sample Prep Kit Cluster Generation Kit (ver. 4) Cluster Station Genome Analyzer IIx (GA IIx).

Bacterial dna Genes Genes annotation Genome Rast

Corresponding Organization :

Other organizations : Health Sciences University of Hokkaido, Hokkaido University, National Institute of Infectious Diseases, Juntendo University, Osaka University

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Variable analysis

independent variables

Bacterial 1 kb insert DNA libraries (Purified Neochlamydia S13 and Protochlamydia R18)

dependent variables

Draft genome sequences
Annotation of genes
Metabolic pathway modules

control variables

Not explicitly mentioned

controls

None specified

Annotations

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