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High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia

Identifieur interne : 000A80 ( Main/Exploration ); précédent : 000A79; suivant : 000A81

High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia

Auteurs : Agnieszka Klonowska [France] ; Aline L Pez-L Pez [France] ; Lionel Moulin [France] ; Julie Ardley ; Margaret Gollagher ; Dora Marinova ; Rui Tian ; Marcel Huntemann [États-Unis] ; T. B. K. Reddy [États-Unis] ; Neha Varghese [États-Unis] ; Tanja Woyke [États-Unis] ; Victor Markowitz [États-Unis] ; Natalia Ivanova [États-Unis] ; Rekha Seshadri [États-Unis] ; Mohamed N. Baeshen [Arabie saoudite] ; Nabih A. Baeshen [Arabie saoudite] ; Nikos Kyrpides [États-Unis, Arabie saoudite] ; Wayne Reeve

Source :

RBID : PMC:5240323

Abstract

Rhizobium mesoamericanum STM6155 (INSCD = ATYY01000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as an effective nitrogen fixing microsymbiont of the legume Mimosa pudica L.. STM6155 was isolated in 2009 from a nodule of the trap host M. pudica grown in nickel-rich soil collected near Mont Dore, New Caledonia. R. mesoamericanum STM6155 was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) genome sequencing project. Here we describe the symbiotic properties of R. mesoamericanum STM6155, together with its genome sequence information and annotation. The 6,927,906 bp high-quality draft genome is arranged into 147 scaffolds of 152 contigs containing 6855 protein-coding genes and 71 RNA-only encoding genes. Strain STM6155 forms an ANI clique (ID 2435) with the sequenced R. mesoamericanum strain STM3625, and the nodulation genes are highly conserved in these strains and the type strain of Rhizobium grahamii CCGE501T. Within the STM6155 genome, we have identified a chr chromate efflux gene cluster of six genes arranged into two putative operons and we postulate that this cluster is important for the survival of STM6155 in ultramafic soils containing high concentrations of chromate.

Electronic supplementary material

The online version of this article (doi:10.1186/s40793-016-0212-4) contains supplementary material, which is available to authorized users.


Url:
DOI: 10.1186/s40793-016-0212-4
PubMed: 28116041
PubMed Central: 5240323


Affiliations:


Links toward previous steps (curation, corpus...)


Le document en format XML

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<title xml:lang="en" level="a" type="main">High-quality draft genome sequence of
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strain STM6155, a
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microsymbiont from New Caledonia</title>
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<name sortKey="Klonowska, Agnieszka" sort="Klonowska, Agnieszka" uniqKey="Klonowska A" first="Agnieszka" last="Klonowska">Agnieszka Klonowska</name>
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<name sortKey="Reddy, T B K" sort="Reddy, T B K" uniqKey="Reddy T" first="T. B. K." last="Reddy">T. B. K. Reddy</name>
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<nlm:aff id="Aff6">Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA</nlm:aff>
<country>États-Unis</country>
<placeName>
<region type="state">Californie</region>
</placeName>
<wicri:cityArea>Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley</wicri:cityArea>
</affiliation>
</author>
<author>
<name sortKey="Ivanova, Natalia" sort="Ivanova, Natalia" uniqKey="Ivanova N" first="Natalia" last="Ivanova">Natalia Ivanova</name>
<affiliation wicri:level="2">
<nlm:aff id="Aff5">DOE Joint Genome Institute, Walnut Creek, CA USA</nlm:aff>
<country>États-Unis</country>
<placeName>
<region type="state">Californie</region>
</placeName>
<wicri:cityArea>DOE Joint Genome Institute, Walnut Creek</wicri:cityArea>
</affiliation>
</author>
<author>
<name sortKey="Seshadri, Rekha" sort="Seshadri, Rekha" uniqKey="Seshadri R" first="Rekha" last="Seshadri">Rekha Seshadri</name>
<affiliation wicri:level="2">
<nlm:aff id="Aff5">DOE Joint Genome Institute, Walnut Creek, CA USA</nlm:aff>
<country>États-Unis</country>
<placeName>
<region type="state">Californie</region>
</placeName>
<wicri:cityArea>DOE Joint Genome Institute, Walnut Creek</wicri:cityArea>
</affiliation>
</author>
<author>
<name sortKey="Baeshen, Mohamed N" sort="Baeshen, Mohamed N" uniqKey="Baeshen M" first="Mohamed N." last="Baeshen">Mohamed N. Baeshen</name>
<affiliation wicri:level="1">
<nlm:aff id="Aff7">Department of Biology, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia</nlm:aff>
<country xml:lang="fr">Arabie saoudite</country>
<wicri:regionArea>Department of Biology, Faculty of Science, University of Jeddah, Jeddah</wicri:regionArea>
<wicri:noRegion>Jeddah</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Baeshen, Nabih A" sort="Baeshen, Nabih A" uniqKey="Baeshen N" first="Nabih A." last="Baeshen">Nabih A. Baeshen</name>
<affiliation wicri:level="1">
<nlm:aff id="Aff8">Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia</nlm:aff>
<country xml:lang="fr">Arabie saoudite</country>
<wicri:regionArea>Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah</wicri:regionArea>
<wicri:noRegion>Jeddah</wicri:noRegion>
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</author>
<author>
<name sortKey="Kyrpides, Nikos" sort="Kyrpides, Nikos" uniqKey="Kyrpides N" first="Nikos" last="Kyrpides">Nikos Kyrpides</name>
<affiliation wicri:level="2">
<nlm:aff id="Aff5">DOE Joint Genome Institute, Walnut Creek, CA USA</nlm:aff>
<country>États-Unis</country>
<placeName>
<region type="state">Californie</region>
</placeName>
<wicri:cityArea>DOE Joint Genome Institute, Walnut Creek</wicri:cityArea>
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<affiliation wicri:level="1">
<nlm:aff id="Aff8">Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia</nlm:aff>
<country xml:lang="fr">Arabie saoudite</country>
<wicri:regionArea>Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah</wicri:regionArea>
<wicri:noRegion>Jeddah</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Reeve, Wayne" sort="Reeve, Wayne" uniqKey="Reeve W" first="Wayne" last="Reeve">Wayne Reeve</name>
<affiliation>
<nlm:aff id="Aff3">School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia</nlm:aff>
<wicri:noCountry code="subfield">WA Australia</wicri:noCountry>
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</author>
</analytic>
<series>
<title level="j">Standards in Genomic Sciences</title>
<idno type="eISSN">1944-3277</idno>
<imprint>
<date when="2017">2017</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc>
<textClass></textClass>
</profileDesc>
</teiHeader>
<front>
<div type="abstract" xml:lang="en">
<p>
<italic>Rhizobium mesoamericanum</italic>
STM6155 (INSCD = ATYY01000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as an effective nitrogen fixing microsymbiont of the legume
<italic>Mimosa pudica</italic>
L.. STM6155 was isolated in 2009 from a nodule of the trap host
<italic>M. pudica</italic>
grown in nickel-rich soil collected near Mont Dore, New Caledonia.
<italic>R. mesoamericanum</italic>
STM6155 was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) genome sequencing project. Here we describe the symbiotic properties of
<italic>R. mesoamericanum</italic>
STM6155, together with its genome sequence information and annotation. The 6,927,906 bp high-quality draft genome is arranged into 147 scaffolds of 152 contigs containing 6855 protein-coding genes and 71 RNA-only encoding genes. Strain STM6155 forms an ANI clique (ID 2435) with the sequenced
<italic>R. mesoamericanum</italic>
strain STM3625, and the nodulation genes are highly conserved in these strains and the type strain of
<italic>Rhizobium grahamii</italic>
CCGE501
<sup>T</sup>
. Within the STM6155 genome, we have identified a
<italic>chr</italic>
chromate efflux gene cluster of six genes arranged into two putative operons and we postulate that this cluster is important for the survival of STM6155 in ultramafic soils containing high concentrations of chromate.</p>
<sec>
<title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/s40793-016-0212-4) contains supplementary material, which is available to authorized users.</p>
</sec>
</div>
</front>
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<name sortKey="Klonowska, Agnieszka" sort="Klonowska, Agnieszka" uniqKey="Klonowska A" first="Agnieszka" last="Klonowska">Agnieszka Klonowska</name>
</region>
<name sortKey="Klonowska, Agnieszka" sort="Klonowska, Agnieszka" uniqKey="Klonowska A" first="Agnieszka" last="Klonowska">Agnieszka Klonowska</name>
<name sortKey="L Pez L Pez, Aline" sort="L Pez L Pez, Aline" uniqKey="L Pez L Pez A" first="Aline" last="L Pez-L Pez">Aline L Pez-L Pez</name>
<name sortKey="Moulin, Lionel" sort="Moulin, Lionel" uniqKey="Moulin L" first="Lionel" last="Moulin">Lionel Moulin</name>
<name sortKey="Moulin, Lionel" sort="Moulin, Lionel" uniqKey="Moulin L" first="Lionel" last="Moulin">Lionel Moulin</name>
</country>
<country name="États-Unis">
<region name="Californie">
<name sortKey="Huntemann, Marcel" sort="Huntemann, Marcel" uniqKey="Huntemann M" first="Marcel" last="Huntemann">Marcel Huntemann</name>
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<name sortKey="Ivanova, Natalia" sort="Ivanova, Natalia" uniqKey="Ivanova N" first="Natalia" last="Ivanova">Natalia Ivanova</name>
<name sortKey="Kyrpides, Nikos" sort="Kyrpides, Nikos" uniqKey="Kyrpides N" first="Nikos" last="Kyrpides">Nikos Kyrpides</name>
<name sortKey="Markowitz, Victor" sort="Markowitz, Victor" uniqKey="Markowitz V" first="Victor" last="Markowitz">Victor Markowitz</name>
<name sortKey="Reddy, T B K" sort="Reddy, T B K" uniqKey="Reddy T" first="T. B. K." last="Reddy">T. B. K. Reddy</name>
<name sortKey="Seshadri, Rekha" sort="Seshadri, Rekha" uniqKey="Seshadri R" first="Rekha" last="Seshadri">Rekha Seshadri</name>
<name sortKey="Varghese, Neha" sort="Varghese, Neha" uniqKey="Varghese N" first="Neha" last="Varghese">Neha Varghese</name>
<name sortKey="Woyke, Tanja" sort="Woyke, Tanja" uniqKey="Woyke T" first="Tanja" last="Woyke">Tanja Woyke</name>
</country>
<country name="Arabie saoudite">
<noRegion>
<name sortKey="Baeshen, Mohamed N" sort="Baeshen, Mohamed N" uniqKey="Baeshen M" first="Mohamed N." last="Baeshen">Mohamed N. Baeshen</name>
</noRegion>
<name sortKey="Baeshen, Nabih A" sort="Baeshen, Nabih A" uniqKey="Baeshen N" first="Nabih A." last="Baeshen">Nabih A. Baeshen</name>
<name sortKey="Kyrpides, Nikos" sort="Kyrpides, Nikos" uniqKey="Kyrpides N" first="Nikos" last="Kyrpides">Nikos Kyrpides</name>
</country>
</tree>
</affiliations>
</record>

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