From outside to the center:

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 Insight into the genome sequence Comparative genomics Lacking an available genome sequence of Deferribacter abyssi, the species yielding the highest score, the following comparative analyses were done with D. desulfuricans [14] (GenBank “type”:”entrez-nucleotide”,”attrs”:”text”:”AP011529″,”term_id”:”290753135″,”term_text”:”AP011529″AP011529, “type”:”entrez-nucleotide”,”attrs”:”text”:”AP011530″,”term_id”:”290755253″,”term_text”:”AP011530″AP011530) and Calditerrivibrio nitroreducens (GenBank “type”:”entrez-nucleotide”,”attrs”:”text”:”CP002347″,”term_id”:”312938725″,”term_text”:”CP002347″CP002347, “type”:”entrez-nucleotide”,”attrs”:”text”:”CP002348″,”term_id”:”312940771″,”term_text”:”CP002348″CP002348) [16], the phylogenetically closest organisms for which a genome sequence was available.

The genomes of F. sinusarabici, D. desulfuricans and C. nitroreducens are similar in sizes (2.5 Mb, 2.5 Mb and 2.2 Mb, respectively) and have a similar, quite low G+C content (38%, 30% and 36%, respectively). Whereas F. sinusarabici has no plasmid, D. desulfuricans harbors a 5.9 kb plasmid; C. nitroreducens contains a 30.8 kb megaplasmid. An estimate of the overall similarity between the three genomes was generated with the GGDC-Genome-to-Genome Distance Calculator [40,41].

This system calculates the distances by comparing the genomes to obtain HSPs (high-scoring segment pairs) and inferring distances from a set of formulas (1, HSP length / total length; 2, identities / HSP length; 3, identities / total length). Table 5 shows the results of the pairwise comparison between the three genomes. Table 5 Pairwise comparison of F. sinusarabici, D. desulfuricans and C. nitroreducens using the GGDC-Calculator. The comparison of the F. sinusarabici and D. desulfuricans genomes revealed that 5.9% of the average of both genome lengths are covered with HSPs. The identity within these HSPs was 83.2%, whereas the identity over the whole genome was only 4.9%. Similar results were inferred for F. sinusarabici and C. nitroreducens (Table 5). The genomes of D. desulfuricans and C.

nitroreducens show a significantly higher degree of similarity with 9.9% of the average of both genomes are covered with HSPs of 83.3% Dacomitinib identity. The identity over the whole length of the genomes was 8.3%. These values corroborate the relationship between the three organisms as shown in the 16S rRNA-based phylogenetic tree in Figure 1, as there is no bootstrap support that F. sinusarabici is closer related to either C. nitroreducens or D. desulfuricans. The fraction of shared genes in the three genomes is shown in a Venn diagram (Figure 4).

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