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[Phylogenetic analysis of Nocardiopsis species based on 16S rRNA, gyrB, sod and rpoB gene sequences]

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Abstract

In order to understand the phylogenetic relationships among Nocardiopsis species more rationally, the gyrB, sod and rpoB gene partial sequences of 24 validly published Nocardiopsis species were determined. The phylogenetic trees were reconstructed including 16S rRNA gene and above-mentioned three housekeeping genes. The average similarities of gyrB, sod and rpoB of Nocardiopsis species were 87.7%, 87.3% and 94.1%, respectively. Meanwhile, the average similarity of 16S rRNA gene of Nocardiopsis species was 96.65%. The variabilities of gyrB, sod and rpoB gene in Nocardiospis are greater than that of 16S rRNA gene. By comparing the phylogenetic trees, the topology of gyrB gene tree is almost consistent with that of 16S rRNA gene tree. Consequently, the gyrB gene possesses the superiority in phylogenetic taxonomy of the genus Nocardiopsis.

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... requires a detailed taxonomic classification of Nocardiopsis strains from different habitats. High phylogenetic resolution can be achieved by multilocus sequence analyses, which combine phylogenies of 16S rRNA and functional housekeeping genes such as gyrB, rpoB and sodA [17][18][19] . Previous studies have shown that 16S rRNA gene together with gyrB, rpoB and sodA genes could provide better phylogenetic resolution 20-23 than one single gene. ...
... Candidate strains were purified on inorganic salts-starch agar supplemented with 5% (w/v) NaCl 27 and cultivated using the ISP4 medium (Difco Laboratories, Detroit, Mich) at 37 °C for four weeks 29 . Genomic DNA of the obtained strains was extracted and 16S rRNA genes were PCR amplified 19 . PCR amplification of gyrB, rpoB and sodA genes was performed according to the methods described previously 19 . ...
... Genomic DNA of the obtained strains was extracted and 16S rRNA genes were PCR amplified 19 . PCR amplification of gyrB, rpoB and sodA genes was performed according to the methods described previously 19 . The amplified PCR products were purified using a TaKaRa DNA fragment purification kit (Ver. ...
... requires a detailed taxonomic classification of Nocardiopsis strains from different habitats. High phylogenetic resolution can be achieved by multilocus sequence analyses, which combine phylogenies of 16S rRNA and functional housekeeping genes such as gyrB, rpoB and sodA [17][18][19] . Previous studies have shown that 16S rRNA gene together with gyrB, rpoB and sodA genes could provide better phylogenetic resolution 20-23 than one single gene. ...
... Candidate strains were purified on inorganic salts-starch agar supplemented with 5% (w/v) NaCl 27 and cultivated using the ISP4 medium (Difco Laboratories, Detroit, Mich) at 37 °C for four weeks 29 . Genomic DNA of the obtained strains was extracted and 16S rRNA genes were PCR amplified 19 . PCR amplification of gyrB, rpoB and sodA genes was performed according to the methods described previously 19 . ...
... Genomic DNA of the obtained strains was extracted and 16S rRNA genes were PCR amplified 19 . PCR amplification of gyrB, rpoB and sodA genes was performed according to the methods described previously 19 . The amplified PCR products were purified using a TaKaRa DNA fragment purification kit (Ver. ...
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The genus Nocardiopsis is a widespread group within the phylum Actinobacteria and has been isolated from various salty environments worldwide. However, little is known about whether biogeography affects Nocardiopsis distribution in various hypersaline environments. Such information is essential for understanding the ecology of Nocardiopsis. Here we analyzed 16S rRNA, gyrB, rpoB and sodA genes of 78 Nocardiopsis strains isolated from hypersaline environments in Yunnan and Xinjiang Provinces of western China. The obtained Nocardiopsis strains were classified into five operational taxonomic units, each comprising location-specific phylo- and genotypes. Statistical analyses showed that spatial distance and environmental factors substantially influenced Nocardiopsis distribution in hypersaline environments: the former had stronger influence at large spatial scales, whereas the latter was more influential at small spatial scales.
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