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Volume 152, Issue 9

Prediction of whole-genome DNA–DNA similarity, determination of G+C content and phylogenetic analysis within the family by multilocus sequence analysis (MLSA) Free

Abstract

Genome predictions based on selected genes would be a very welcome approach for taxonomic studies, including DNA–DNA similarity, G+C content and representative phylogeny of bacteria. At present, DNA–DNA hybridizations are still considered the gold standard in species descriptions. However, this method is time-consuming and troublesome, and datasets can vary significantly between experiments as well as between laboratories. For the same reasons, full matrix hybridizations are rarely performed, weakening the significance of the results obtained. The authors established a universal sequencing approach for the three genes , and for the , and determined if the sequences could be used for predicting DNA–DNA relatedness within the family. The sequence-based similarity values calculated using a previously published formula proved most useful for species and genus separation, indicating that this method provides better resolution and no experimental variation compared to hybridization. By this method, cross-comparisons within the family over species and genus borders easily become possible. The three genes also serve as an indicator of the genome G+C content of a species. A mean divergence of around 1 % was observed from the classical method, which in itself has poor reproducibility. Finally, the three genes can be used alone or in combination with already-established 16S rRNA, and gene-sequencing strategies in a multisequence-based phylogeny for the family . It is proposed to use the three sequences as a taxonomic tool, replacing DNA–DNA hybridization.

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): MLSA, multilocus sequence analysis and MLSP, multilocus sequence phylogeny
SGM
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2006-09-01
2024-04-27
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Prediction of whole-genome DNA–DNA similarity, determination of G+C content and phylogenetic analysis within the family Pasteurellaceae by multilocus sequence analysis (MLSA)
Microbiology 152, 2537 (2006); https://doi.org/10.1099/mic.0.28991-0
/content/journal/micro/10.1099/mic.0.28991-0
/content/journal/micro/10.1099/mic.0.28991-0
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