The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights
Abstract Background Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antim...
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ftdatacite:10.6084/m9.figshare.c.3667393.v1 2023-05-15T13:58:07+02:00 The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights Bosi, Emanuele Fondi, Marco Orlandini, Valerio Perrin, Elena Maida, Isabel Pascale, Donatella De Tutino, Maria Parrilli, Ermenegilda Giudice, Angelina Lo Filloux, Alain Fani, Renato 2017 https://dx.doi.org/10.6084/m9.figshare.c.3667393.v1 https://figshare.com/collections/The_pangenome_of_Antarctic_Pseudoalteromonas_bacteria_evolutionary_and_functional_insights/3667393/1 unknown Figshare https://dx.doi.org/10.1186/s12864-016-3382-y https://dx.doi.org/10.6084/m9.figshare.c.3667393 CC BY 4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Microbiology FOS Biological sciences Genetics Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Marine Biology 110309 Infectious Diseases FOS Health sciences Collection article 2017 ftdatacite https://doi.org/10.6084/m9.figshare.c.3667393.v1 https://doi.org/10.1186/s12864-016-3382-y https://doi.org/10.6084/m9.figshare.c.3667393 2021-11-05T12:55:41Z Abstract Background Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis. Results Here, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds. Conclusions This study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation of their biotechnological potential. Article in Journal/Newspaper Antarc* Antarctic Antarctica DataCite Metadata Store (German National Library of Science and Technology) Antarctic |
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Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Microbiology FOS Biological sciences Genetics Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Marine Biology 110309 Infectious Diseases FOS Health sciences |
spellingShingle |
Microbiology FOS Biological sciences Genetics Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Marine Biology 110309 Infectious Diseases FOS Health sciences Bosi, Emanuele Fondi, Marco Orlandini, Valerio Perrin, Elena Maida, Isabel Pascale, Donatella De Tutino, Maria Parrilli, Ermenegilda Giudice, Angelina Lo Filloux, Alain Fani, Renato The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights |
topic_facet |
Microbiology FOS Biological sciences Genetics Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Marine Biology 110309 Infectious Diseases FOS Health sciences |
description |
Abstract Background Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis. Results Here, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds. Conclusions This study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation of their biotechnological potential. |
format |
Article in Journal/Newspaper |
author |
Bosi, Emanuele Fondi, Marco Orlandini, Valerio Perrin, Elena Maida, Isabel Pascale, Donatella De Tutino, Maria Parrilli, Ermenegilda Giudice, Angelina Lo Filloux, Alain Fani, Renato |
author_facet |
Bosi, Emanuele Fondi, Marco Orlandini, Valerio Perrin, Elena Maida, Isabel Pascale, Donatella De Tutino, Maria Parrilli, Ermenegilda Giudice, Angelina Lo Filloux, Alain Fani, Renato |
author_sort |
Bosi, Emanuele |
title |
The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights |
title_short |
The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights |
title_full |
The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights |
title_fullStr |
The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights |
title_full_unstemmed |
The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights |
title_sort |
pangenome of (antarctic) pseudoalteromonas bacteria: evolutionary and functional insights |
publisher |
Figshare |
publishDate |
2017 |
url |
https://dx.doi.org/10.6084/m9.figshare.c.3667393.v1 https://figshare.com/collections/The_pangenome_of_Antarctic_Pseudoalteromonas_bacteria_evolutionary_and_functional_insights/3667393/1 |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic Antarctica |
genre_facet |
Antarc* Antarctic Antarctica |
op_relation |
https://dx.doi.org/10.1186/s12864-016-3382-y https://dx.doi.org/10.6084/m9.figshare.c.3667393 |
op_rights |
CC BY 4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.c.3667393.v1 https://doi.org/10.1186/s12864-016-3382-y https://doi.org/10.6084/m9.figshare.c.3667393 |
_version_ |
1766266201927843840 |