Pan-genome analyses of 24 Shewanella strains re-emphasize the diversification of their functions yet evolutionary dynamics of metal-reducing pathway

Biotechnology for Biofuels
Chaofang ZhongKang Ning

Abstract

Shewanella strains are important dissimilatory metal-reducing bacteria which are widely distributed in diverse habitats. Despite efforts to genomically characterize Shewanella, knowledge of the molecular components, functional information and evolutionary patterns remain lacking, especially for their compatibility in the metal-reducing pathway. The increasing number of genome sequences of Shewanella strains offers a basis for pan-genome studies. A comparative pan-genome analysis was conducted to study genomic diversity and evolutionary relationships among 24 Shewanella strains. Results revealed an open pan-genome of 13,406 non-redundant genes and a core-genome of 1878 non-redundant genes. Selective pressure acted on the invariant members of core genome, in which purifying selection drove evolution in the housekeeping mechanisms. Shewanella strains exhibited extensive genome variability, with high levels of gene gain and loss during the evolution, which affected variable gene sets and facilitated the rapid evolution. Additionally, genes related to metal reduction were diversely distributed in Shewanella strains and evolved under purifying selection, which highlighted the basic conserved functionality and specificity of respirato...Continue Reading

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Citations

Jan 11, 2020·FEMS Microbiology Reviews·Olivier N LemaireChantal Iobbi-Nivol
Aug 2, 2020·Applied and Environmental Microbiology·Bridget E ConleyJeffrey A Gralnick
Jul 14, 2019·Applied and Environmental Microbiology·Olivier N LemaireChantal Iobbi-Nivol
Jul 25, 2020·Scientific Reports·Silvia J Salgar-ChaparroLaura L Machuca
Apr 13, 2021·Computational and Structural Biotechnology Journal·Chaofang ZhongKang Ning
Jan 12, 2022·MSystems·Alejandro PalomoBarth F Smets

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Methods Mentioned

BETA
protein folding

Software Mentioned

InterProScan
BLASTp
Hmmscan
GBlock
CAFE
Phylip
OrthoMCL
PAML
Codeml
BLAST

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