Literature DB >> 15796890

The correlation between genomic G+C and optimal growth temperature of prokaryotes is robust: a reply to Marashi and Ghalanbor.

Hector Musto1, Hugo Naya, Alejandro Zavala, Hector Romero, Fernando Alvarez-Valin, Giorgio Bernardi.   

Abstract

We have recently shown that optimal growth temperature (T(opt)) is one of the factors that influence genomic GC in prokaryotes. Our results have been disputed by Marashi and Ghalanbor, who claim that the correlations we show are not "robust" because the elimination of some points (arbitrarily chosen) leads, in some families, to variations in the correlation coefficients and/or significance of correlations. Here, we test whether the correlation between T(opt) and genomic GC is robust by using two independent approaches: detection of possible outliers (using robust Mahalanobis distance) and usage of a non-parametric correlation coefficient that is not sensitive to the presence of outliers. The results presented here reinforce our previous proposal that T(opt) is correlated with genomic GC in prokaryotes.

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Year:  2005        PMID: 15796890     DOI: 10.1016/j.bbrc.2005.02.133

Source DB:  PubMed          Journal:  Biochem Biophys Res Commun        ISSN: 0006-291X            Impact factor:   3.575


  8 in total

1.  Environments shape the nucleotide composition of genomes.

Authors:  Konrad U Foerstner; Christian von Mering; Sean D Hooper; Peer Bork
Journal:  EMBO Rep       Date:  2005-12       Impact factor: 8.807

2.  Prokaryotes that grow optimally in acid have purine-poor codons in long open reading frames.

Authors:  Feng-Hsu Lin; Donald R Forsdyke
Journal:  Extremophiles       Date:  2006-09-07       Impact factor: 2.395

3.  Genomic adaptation of prokaryotic organisms at high temperature.

Authors:  Surajit Basak; Pamela Mukhopadhyay; Sanjib Kumar Gupta; Tapash Chandra Ghosh
Journal:  Bioinformation       Date:  2010-02-28

4.  Across bacterial phyla, distantly-related genomes with similar genomic GC content have similar patterns of amino acid usage.

Authors:  John Lightfield; Noah R Fram; Bert Ely
Journal:  PLoS One       Date:  2011-03-10       Impact factor: 3.240

5.  A positive correlation between GC content and growth temperature in prokaryotes.

Authors:  En-Ze Hu; Xin-Ran Lan; Zhi-Ling Liu; Jie Gao; Deng-Ke Niu
Journal:  BMC Genomics       Date:  2022-02-09       Impact factor: 3.969

6.  The footprint of metabolism in the organization of mammalian genomes.

Authors:  Luisa Berná; Ankita Chaurasia; Claudia Angelini; Concetta Federico; Salvatore Saccone; Giuseppe D'Onofrio
Journal:  BMC Genomics       Date:  2012-05-08       Impact factor: 3.969

7.  Investigations of oligonucleotide usage variance within and between prokaryotes.

Authors:  Jon Bohlin; Eystein Skjerve; David W Ussery
Journal:  PLoS Comput Biol       Date:  2008-04-18       Impact factor: 4.475

8.  Comparative genomics of Photobacterium species from terrestrial and marine habitats.

Authors:  Sandra Fuertes-Perez; Rudi F Vogel; Maik Hilgarth
Journal:  Curr Res Microb Sci       Date:  2021-11-28
  8 in total

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