Figure 2 Scanning electron micrograph of H. parasuis 29755 Genome selleck catalog sequencing and annotation Genome project history H. parasuis strain 29755 was selected for sequencing because it has long been used in the study of Gl?sser��s disease. Pyrosequencing (454 Life Sciences) was performed at the State University of New York, University at Buffalo Center of Excellence in Bioinformatics and Life Sciences. The draft genome sequence is deposited in GenBank (“type”:”entrez-nucleotide”,”attrs”:”text”:”NZ_ABKM00000000″,”term_id”:”538043205″,”term_text”:”NZ_ABKM00000000″NZ_ABKM00000000). Summary project information is shown in Table 2 according to the Minimum Information about a Genomic Sequence (MIGS) recommendations [34] and the genome content is summarized in Table 3.

Table 2 Genome sequencing project information Table 3 Genome statistics Growth conditions and DNA isolation H. parasuis 29755 was grown from a frozen seed stock for two days under 5% CO2 at 37��C on Casman Agar Base (BBL) supplemented with 1% (w/v) NAD (Sigma) and 5% GIBCO filtered horse serum (Invitrogen). Following growth, a single colony was used to inoculate 5 ml of brain-heart infusion medium supplemented with 10 ��g/ml NAD and 10 ��g/ml hemin (sBHI) and the culture was incubated overnight at 37��C and 185 rpm. The next day, 2 ml of the culture were added to 100 ml of sBHI and the bacterium was again allowed to grow overnight to stationary phase at 37��C and 185 rpm. Bacterial cells were pelleted by centrifugation at 4000 �� g for 10 minutes.

The pellet was resuspended and used as the source of genomic DNA purified with the QIAGEN Blood & Cell Culture DNA Kit, as recommended by the manufacturer. The final preparation contained 1.12 ��g/ul genomic DNA as determined by UV absorption spectrometry. Genome sequencing and assembly Library preparation yielded 9.65 �� 108 molecules/��l of DNA with a mean size of approximately 600 nucleotides, as determined with a RNA6000 Pico chip on an Agilent 2100 Bioanalyzer. Emulsion PCR was performed at a concentration of 2 molecules per bead. Following sequencing, contigs were assembled using the 454 Newbler assembler. Genome annotation Genes were identified manually using GeneMark and automatically using Glimmer as part of the NCBI draft genome submission pipeline. Translated protein sequences were analyzed using PSORTb v.2.

0 [35] to predict final location within the cell and assigned to COG functional categories (Table 4). Table 4 Number of genes associated with the general COG functional categories Genome properties The GSK-3 draft genome is 2,224,137 bp and is likely comprised of one circular chromosome with a G+C content of approximately 39% (Figure 3). For display, contigs were assembled end-to-end with twenty ��N�� bases between contigs. Orientation and order of contigs will change when the genome sequence is closed. Figure 3 Graphical circular map of the H. parasuis 29755 draft pseudogenome.