Together, the combination of the Illumina and

Together, the combination of the Illumina and Crizotinib cost 454 sequencing platforms provided 1,813.8 �� coverage of the genome. The final assembly contained 431,902 pyrosequence and 44,889,308 Illumina reads. Genome annotation Genes were identified using Prodigal [49] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [50]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes �C Expert Review (IMG-ER) platform [51].

Genome properties The genome consists of a 1,843,267 bp long chromosome with a 54.9% G+C content (Table 3 and Figure 3). Of the 2,038 genes predicted, 1,986 were protein-coding genes, and 52 RNAs; 19 pseudogenes were also identified. The majority of the protein-coding genes (54.9%) were assigned a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4. Table 3 Genome Statistics Figure 3 Graphical circular map of the genome. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew. Table 4 Number of genes associated with the general COG functional categories Insights from the genome sequence Table 5 shows the whole-genome distances between P.

fumarii and the other type strains within the order Desulfurococcales [15-21] as calculated using the genome-to-genome distance calculator [52-54]. As expected, the distances to the only other member of the family Pyrodictiaceae, H. butylicus, are lower than those to the members of the Desulfurococcaceae. This does not hold for formula 2, which is affected by saturation: if only HSPs of more strongly conserved genes are obtained, these contain, on average, a higher proportion of identical base pairs [52]. Table 5 Genome-to-genome distances between P. fumarii and the genomes of other type strains within the order* Figure 4 shows a neighbor-joining tree inferred with PAUP* [13] from the logarithmized version of distance 3.

The tree differs from the 16S rRNA-based tree (Figure 1) Batimastat regarding the position of Ignisphaera aggregans, which is placed as sister group of all other Desulfurococcaceae by the 16S rRNA, but of Staphylothermus in the whole-genome tree. Figure 4 GGDC NJ tree inferred from the type strain genomes within the order Desulfurococcales. The fraction of shared genes in the genomes of P. fumarii, its closest neighbor H. butylicus, and as an outgroup I. aggregans (see Figure 1) is shown in a Venn diagram (Figure 5).

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