Inferring the Minimal Genome of <italic toggle="yes">Mesoplasma florum</italic> by Comparative Genomics and Transposon Mutagenesis

ABSTRACT The creation and comparison of minimal genomes will help better define the most fundamental mechanisms supporting life. Mesoplasma florum is a near-minimal, fast-growing, nonpathogenic bacterium potentially amenable to genome reduction efforts. In a comparative genomic study of 13 M. florum...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Vincent Baby, Jean-Christophe Lachance, Jules Gagnon, Jean-François Lucier, Dominick Matteau, Tom Knight, Sébastien Rodrigue
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	Mesoplasma florum comparative genomics minimal genome transposon mutagenesis Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/1a7fae27dd8140b8b773108b4a75ec92
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:1a7fae27dd8140b8b773108b4a75ec92
record_format	dspace
spelling	oai:doaj.org-article:1a7fae27dd8140b8b773108b4a75ec922021-12-02T19:46:17ZInferring the Minimal Genome of <italic toggle="yes">Mesoplasma florum</italic> by Comparative Genomics and Transposon Mutagenesis10.1128/mSystems.00198-172379-5077https://doaj.org/article/1a7fae27dd8140b8b773108b4a75ec922018-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00198-17https://doaj.org/toc/2379-5077ABSTRACT The creation and comparison of minimal genomes will help better define the most fundamental mechanisms supporting life. Mesoplasma florum is a near-minimal, fast-growing, nonpathogenic bacterium potentially amenable to genome reduction efforts. In a comparative genomic study of 13 M. florum strains, including 11 newly sequenced genomes, we have identified the core genome and open pangenome of this species. Our results show that all of the strains have approximately 80% of their gene content in common. Of the remaining 20%, 17% of the genes were found in multiple strains and 3% were unique to any given strain. On the basis of random transposon mutagenesis, we also estimated that ~290 out of 720 genes are essential for M. florum L1 in rich medium. We next evaluated different genome reduction scenarios for M. florum L1 by using gene conservation and essentiality data, as well as comparisons with the first working approximation of a minimal organism, Mycoplasma mycoides JCVI-syn3.0. Our results suggest that 409 of the 473 M. mycoides JCVI-syn3.0 genes have orthologs in M. florum L1. Conversely, 57 putatively essential M. florum L1 genes have no homolog in M. mycoides JCVI-syn3.0. This suggests differences in minimal genome compositions, even for these evolutionarily closely related bacteria. IMPORTANCE The last years have witnessed the development of whole-genome cloning and transplantation methods and the complete synthesis of entire chromosomes. Recently, the first minimal cell, Mycoplasma mycoides JCVI-syn3.0, was created. Despite these milestone achievements, several questions remain to be answered. For example, is the composition of minimal genomes virtually identical in phylogenetically related species? On the basis of comparative genomics and transposon mutagenesis, we investigated this question by using an alternative model, Mesoplasma florum, that is also amenable to genome reduction efforts. Our results suggest that the creation of additional minimal genomes could help reveal different gene compositions and strategies that can support life, even within closely related species.Vincent BabyJean-Christophe LachanceJules GagnonJean-François LucierDominick MatteauTom KnightSébastien RodrigueAmerican Society for MicrobiologyarticleMesoplasma florumcomparative genomicsminimal genometransposon mutagenesisMicrobiologyQR1-502ENmSystems, Vol 3, Iss 3 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Mesoplasma florum comparative genomics minimal genome transposon mutagenesis Microbiology QR1-502
spellingShingle	Mesoplasma florum comparative genomics minimal genome transposon mutagenesis Microbiology QR1-502 Vincent Baby Jean-Christophe Lachance Jules Gagnon Jean-François Lucier Dominick Matteau Tom Knight Sébastien Rodrigue Inferring the Minimal Genome of <italic toggle="yes">Mesoplasma florum</italic> by Comparative Genomics and Transposon Mutagenesis
description	ABSTRACT The creation and comparison of minimal genomes will help better define the most fundamental mechanisms supporting life. Mesoplasma florum is a near-minimal, fast-growing, nonpathogenic bacterium potentially amenable to genome reduction efforts. In a comparative genomic study of 13 M. florum strains, including 11 newly sequenced genomes, we have identified the core genome and open pangenome of this species. Our results show that all of the strains have approximately 80% of their gene content in common. Of the remaining 20%, 17% of the genes were found in multiple strains and 3% were unique to any given strain. On the basis of random transposon mutagenesis, we also estimated that ~290 out of 720 genes are essential for M. florum L1 in rich medium. We next evaluated different genome reduction scenarios for M. florum L1 by using gene conservation and essentiality data, as well as comparisons with the first working approximation of a minimal organism, Mycoplasma mycoides JCVI-syn3.0. Our results suggest that 409 of the 473 M. mycoides JCVI-syn3.0 genes have orthologs in M. florum L1. Conversely, 57 putatively essential M. florum L1 genes have no homolog in M. mycoides JCVI-syn3.0. This suggests differences in minimal genome compositions, even for these evolutionarily closely related bacteria. IMPORTANCE The last years have witnessed the development of whole-genome cloning and transplantation methods and the complete synthesis of entire chromosomes. Recently, the first minimal cell, Mycoplasma mycoides JCVI-syn3.0, was created. Despite these milestone achievements, several questions remain to be answered. For example, is the composition of minimal genomes virtually identical in phylogenetically related species? On the basis of comparative genomics and transposon mutagenesis, we investigated this question by using an alternative model, Mesoplasma florum, that is also amenable to genome reduction efforts. Our results suggest that the creation of additional minimal genomes could help reveal different gene compositions and strategies that can support life, even within closely related species.
format	article
author	Vincent Baby Jean-Christophe Lachance Jules Gagnon Jean-François Lucier Dominick Matteau Tom Knight Sébastien Rodrigue
author_facet	Vincent Baby Jean-Christophe Lachance Jules Gagnon Jean-François Lucier Dominick Matteau Tom Knight Sébastien Rodrigue
author_sort	Vincent Baby
title	Inferring the Minimal Genome of <italic toggle="yes">Mesoplasma florum</italic> by Comparative Genomics and Transposon Mutagenesis
title_short	Inferring the Minimal Genome of <italic toggle="yes">Mesoplasma florum</italic> by Comparative Genomics and Transposon Mutagenesis
title_full	Inferring the Minimal Genome of <italic toggle="yes">Mesoplasma florum</italic> by Comparative Genomics and Transposon Mutagenesis
title_fullStr	Inferring the Minimal Genome of <italic toggle="yes">Mesoplasma florum</italic> by Comparative Genomics and Transposon Mutagenesis
title_full_unstemmed	Inferring the Minimal Genome of <italic toggle="yes">Mesoplasma florum</italic> by Comparative Genomics and Transposon Mutagenesis
title_sort	inferring the minimal genome of <italic toggle="yes">mesoplasma florum</italic> by comparative genomics and transposon mutagenesis
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/1a7fae27dd8140b8b773108b4a75ec92
work_keys_str_mv	AT vincentbaby inferringtheminimalgenomeofitalictoggleyesmesoplasmaflorumitalicbycomparativegenomicsandtransposonmutagenesis AT jeanchristophelachance inferringtheminimalgenomeofitalictoggleyesmesoplasmaflorumitalicbycomparativegenomicsandtransposonmutagenesis AT julesgagnon inferringtheminimalgenomeofitalictoggleyesmesoplasmaflorumitalicbycomparativegenomicsandtransposonmutagenesis AT jeanfrancoislucier inferringtheminimalgenomeofitalictoggleyesmesoplasmaflorumitalicbycomparativegenomicsandtransposonmutagenesis AT dominickmatteau inferringtheminimalgenomeofitalictoggleyesmesoplasmaflorumitalicbycomparativegenomicsandtransposonmutagenesis AT tomknight inferringtheminimalgenomeofitalictoggleyesmesoplasmaflorumitalicbycomparativegenomicsandtransposonmutagenesis AT sebastienrodrigue inferringtheminimalgenomeofitalictoggleyesmesoplasmaflorumitalicbycomparativegenomicsandtransposonmutagenesis
_version_	1718376010476421120

Inferring the Minimal Genome of <italic toggle="yes">Mesoplasma florum</italic> by Comparative Genomics and Transposon Mutagenesis

Ejemplares similares