PMC:3317825 / 10551-12072 JSONTXT

{"project":"2_test","denotations":[{"id":"22272658-16200051-10678874","span":{"begin":927,"end":929},"obj":"16200051"},{"id":"22272658-12044357-10678875","span":{"begin":953,"end":955},"obj":"12044357"},{"id":"22272658-12187379-10678876","span":{"begin":970,"end":972},"obj":"12187379"},{"id":"22272658-9687237-10678877","span":{"begin":1006,"end":1008},"obj":"9687237"},{"id":"22272658-15728743-10678878","span":{"begin":1189,"end":1191},"obj":"15728743"},{"id":"22272658-15728743-10678879","span":{"begin":1257,"end":1259},"obj":"15728743"}],"text":"Genomic features\nRoche/454 pyrosequencing was used to determine the sequence of the Staphylococcus simiae genome. A total of 643168 single-end reads resulted from the GS-20 sequencer for S. simiae. De novo assembly with Newbler yielded 565 contigs for a total genome size of 2,587,121 bp with G + C content of 31.9% and 2592 protein-coding sequences (Table 1) with sequencing coverage of 27.4 (2623 singleton reads). The N50 size of the contigs is 19200.\nGenome size was larger in S. aureus (ranging from to 2.743 Mbp to 2.937 Mbp) than in the other Staphylococcus species (ranging from to 2.220 Mbp to 2.698 Mbp). Genomic G + C content of M. caseolyticus (36.6%), S. pseudintermedius (37.5%), and S. carnosus (34.6%) were higher than those of the other Staphylococcus species (ranging from to 31.3% to 33.9%). Genomic G + C content is a result of mutation and selection [55], involving multiple factors including environment [56], symbiotic lifestyle [57], aerobiosis [58], and nitrogen fixation ability [59]. Bacteria showing evidence of translational selection on synonymous codon usage of highly expressed genes tend to have more rRNA operons, more tRNA genes, and faster growth rate [60]. The strength of translationally selected codon usage bias (S) [60] was significantly higher in S. aureus (median S = 1.56) than in the other Staphylococcus species (median S = 1.42) based on Mann-Whitney test (P \u003c 10-4); S. epidermidis strains RP62A (S = 1.15) and ATCC_12228 (S = 1.12) showed the lowest values of S (Table 1)."}