183 lines
14 KiB
XML
183 lines
14 KiB
XML
<document ID-DOI="10.1093/gbe/evaa212" ID-GBIF-Dataset="f572993a-25e4-44bf-80f8-2b9075a81a29" ID-PMC="PMC7846144" ID-PubMed="33022031" ID-Zenodo-Dep="4561628" approvalRequired="5" approvalRequired_for_document="1" approvalRequired_for_textStreams="4" checkinTime="1614243439518" checkinUser="donat" docAuthor="Chambers, James, Sparks, Natalie, Sydney, Natashia, Livingstone, Paul G, Cookson, Alan R & Whitworth, David E" docDate="2020" docId="03A729036472D737FF37FEB3FD8D0F3D" docLanguage="en" docName="genomeBioEvol.evaa212.pdf" docOrigin="Genome Biology and Evolution 12 (12)" docSource="http://dx.doi.org/10.1093/gbe/evaa212" docTitle="Pyxidicoccus caerfyrddinensis Chambers & Sparks & Sydney & Livingstone & Cookson & Whitworth 2020, sp. nov." docType="treatment" docVersion="6" lastPageNumber="2301" masterDocId="FF9E517B647ED73BFFBDFFC1FFC10B09" masterDocTitle="Comparative Genomics and Pan-Genomics of the Myxococcaceae, including a Description of Five Novel Species: Myxococcus eversor sp. nov., Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis sp. nov., Myxococcus vastator sp. nov., Pyxidicoccus caerfyrddinensis sp. nov., and Pyxidicoccus trucidator sp. nov." masterLastPageNumber="2302" masterPageNumber="2289" pageNumber="2301" updateTime="1668128921393" updateUser="ExternalLinkService" zenodo-license-document="CC-BY-4.0" zenodo-license-treatments="CC0-1.0">
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<mods:mods xmlns:mods="http://www.loc.gov/mods/v3">
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<mods:titleInfo>
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<mods:title>Comparative Genomics and Pan-Genomics of the Myxococcaceae, including a Description of Five Novel Species: Myxococcus eversor sp. nov., Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis sp. nov., Myxococcus vastator sp. nov., Pyxidicoccus caerfyrddinensis sp. nov., and Pyxidicoccus trucidator sp. nov.</mods:title>
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</mods:titleInfo>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Chambers, James</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Sparks, Natalie</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Sydney, Natashia</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Livingstone, Paul G</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Cookson, Alan R</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Whitworth, David E</mods:namePart>
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</mods:name>
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<mods:typeOfResource>text</mods:typeOfResource>
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<mods:relatedItem type="host">
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<mods:titleInfo>
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<mods:title>Genome Biology and Evolution</mods:title>
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</mods:titleInfo>
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<mods:part>
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<mods:date>2020</mods:date>
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<mods:detail type="pubDate">
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<mods:number>2020-10-06</mods:number>
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</mods:detail>
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<mods:detail type="volume">
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<mods:number>12</mods:number>
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</mods:detail>
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<mods:detail type="issue">
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<mods:number>12</mods:number>
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</mods:detail>
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<mods:extent unit="page">
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<mods:start>2289</mods:start>
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<mods:end>2302</mods:end>
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</mods:extent>
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</mods:part>
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</mods:relatedItem>
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<mods:location>
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<mods:url>http://dx.doi.org/10.1093/gbe/evaa212</mods:url>
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</mods:location>
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<mods:classification>journal article</mods:classification>
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<mods:identifier type="DOI">10.1093/gbe/evaa212</mods:identifier>
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<mods:identifier type="GBIF-Dataset">f572993a-25e4-44bf-80f8-2b9075a81a29</mods:identifier>
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<mods:identifier type="PMC">PMC7846144</mods:identifier>
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<mods:identifier type="PubMed">33022031</mods:identifier>
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<mods:identifier type="Zenodo-Dep">4561628</mods:identifier>
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<treatment ID-DOI="http://doi.org/10.5281/zenodo.4561649" ID-GBIF-Taxon="179910682" ID-Zenodo-Dep="4561649" LSID="urn:lsid:plazi:treatment:03A729036472D737FF37FEB3FD8D0F3D" httpUri="http://treatment.plazi.org/id/03A729036472D737FF37FEB3FD8D0F3D" lastPageNumber="2301" pageId="12" pageNumber="2301">
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<subSubSection box="[138,545,370,394]" pageId="12" pageNumber="2301" type="nomenclature">
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<paragraph blockId="12.[138,545,370,394]" box="[138,545,370,394]" pageId="12" pageNumber="2301">
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<taxonomicName authority="Chambers & Sparks & Sydney & Livingstone & Cookson & Whitworth, 2020" authorityName="Chambers & Sparks & Sydney & Livingstone & Cookson & Whitworth" authorityYear="2020" box="[138,450,370,394]" class="Deltaproteobacteria" family="Myxococcaceae" genus="Pyxidicoccus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Myxococcales" pageId="12" pageNumber="2301" phylum="Proteobacteria" rank="species" species="caerfyrddinensis" status="sp. nov.">
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<emphasis box="[138,450,370,394]" italics="true" pageId="12" pageNumber="2301">Pyxidicoccus caerfyrddinensis</emphasis>
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</taxonomicName>
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<taxonomicNameLabel box="[458,545,370,394]" pageId="12" pageNumber="2301" rank="species">sp. nov.</taxonomicNameLabel>
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</paragraph>
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</subSubSection>
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<subSubSection pageId="12" pageNumber="2301" type="etymology">
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<paragraph blockId="12.[138,772,413,1076]" pageId="12" pageNumber="2301">
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<taxonomicName authorityName="Chambers & Sparks & Sydney & Livingstone & Cookson & Whitworth" authorityYear="2020" box="[138,436,413,436]" class="Deltaproteobacteria" family="Myxococcaceae" genus="Pyxidicoccus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Myxococcales" pageId="12" pageNumber="2301" phylum="Proteobacteria" rank="species" species="caerfyrddinensis">
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<emphasis box="[138,436,413,436]" italics="true" pageId="12" pageNumber="2301">Pyxidicoccus caerfyrddinensis</emphasis>
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</taxonomicName>
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(caer.fyrdd.in.en’sis N.L. masc. adj.
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<taxonomicName authorityName="Chambers & Sparks & Sydney & Livingstone & Cookson & Whitworth" authorityYear="2020" box="[183,346,445,468]" class="Deltaproteobacteria" family="Myxococcaceae" genus="Pyxidicoccus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Myxococcales" pageId="12" pageNumber="2301" phylum="Proteobacteria" rank="species" species="caerfyrddinensis">
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<emphasis box="[183,346,445,468]" italics="true" pageId="12" pageNumber="2301">caerfyrddinensis</emphasis>
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</taxonomicName>
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from
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<location LSID="urn:lsid:plazi:treatment:03A729036472D737FF37FEB3FD8D0F3D:8ED1CECE6472D737FE21FE7CFDD80ADD" box="[412,537,445,468]" country="United Kingdom" county="Caerfyrddin" latitude="51.86" longLatPrecision="652" longitude="-4.31" municipality="Anglicized" name="Caerfyrddin" pageId="12" pageNumber="2301">Caerfyrddin</location>
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, reflecting its isolation from soil sampled near
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<location LSID="urn:lsid:plazi:treatment:03A729036472D737FF37FEB3FD8D0F3D:8ED1CECE6472D737FEC1FE1CFE380AFD" box="[380,505,477,500]" country="United Kingdom" county="Caerfyrddin" latitude="51.86" longLatPrecision="652" longitude="-4.31" municipality="Anglicized" name="Carmarthen" pageId="12" pageNumber="2301">Carmarthen</location>
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[the
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<collectingMunicipality box="[559,665,477,500]" pageId="12" pageNumber="2301">Anglicized</collectingMunicipality>
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name for
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<collectingCounty box="[138,265,509,532]" pageId="12" pageNumber="2301">Caerfyrddin</collectingCounty>
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],
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<collectingCountry box="[280,343,509,532]" name="United Kingdom" pageId="12" pageNumber="2301">Wales</collectingCountry>
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[
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<geoCoordinate box="[354,444,509,532]" degrees="51.86" direction="north" orientation="latitude" pageId="12" pageNumber="2301" precision="555" value="51.86">51.86 N</geoCoordinate>
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<geoCoordinate box="[451,536,509,532]" degrees="4.31" direction="west" orientation="longitude" pageId="12" pageNumber="2301" precision="555" value="-4.31">4.31 W</geoCoordinate>
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]).
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</paragraph>
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</subSubSection>
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<subSubSection pageId="12" pageNumber="2301" type="description">
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<paragraph blockId="12.[138,772,413,1076]" pageId="12" pageNumber="2301">
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Vegetative cells are Gram-negative bacilli tapering slightly at the ends, measuring
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<quantity box="[382,479,573,597]" metricMagnitude="-1" metricUnit="m" metricValue="7.5" metricValueMax="8.0" metricValueMin="7.0" pageId="12" pageNumber="2301" unit="m" value="0.75" valueMax="0.8" valueMin="0.7">
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0.7–0.8
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<emphasis bold="true" box="[466,479,573,597]" pageId="12" pageNumber="2301">m</emphasis>
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</quantity>
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m 3.0–8.0
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<emphasis bold="true" box="[616,629,573,597]" pageId="12" pageNumber="2301">m</emphasis>
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m in electron micrographs. Colonies exhibit swarming motility and appear pale brown on VY-2 agar (w/v 0.5% dried baker’s yeast, 0.1% CaCl
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<subScript attach="left" box="[257,267,679,694]" fontSize="6" pageId="12" pageNumber="2301">2</subScript>
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2H
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<subScript attach="both" box="[304,314,679,694]" fontSize="6" pageId="12" pageNumber="2301">2</subScript>
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O, and 1.5% agar). Fruiting bodies are irregular spheroids, orange in color. Aerobic growth was observed at 30–40 C and at pH 6.0–9.0. Growth was unaffected by the addition of 1–3% NaCl. Hydrolyzes arginine, esculin, gelatin,
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<emphasis box="[386,399,797,820]" italics="true" pageId="12" pageNumber="2301">p</emphasis>
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-nitrophenyl-
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<emphasis box="[532,546,798,821]" italics="true" pageId="12" pageNumber="2301">B</emphasis>
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-
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<subScript attach="none" box="[554,565,803,819]" fontSize="7" pageId="12" pageNumber="2301">D-</subScript>
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galactopyranoside, and urea. Cells prey efficiently on
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<taxonomicName authority="DSM" authorityName="DSM" box="[532,766,829,852]" family="Microbacteriaceae" genus="Clavibacter" kingdom="Bacteria" order="Actinomycetales" pageId="12" pageNumber="2301" phylum="Actinobacteria" rank="species" species="nebraskensis">
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<emphasis box="[532,702,829,852]" italics="true" pageId="12" pageNumber="2301">Cl. nebraskensis</emphasis>
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DSM
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</taxonomicName>
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7483, and with low efficiency upon
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<taxonomicName authority="TOP" authorityName="TOP" box="[561,690,861,884]" class="Gammaproteobacteria" family="Enterobacteriaceae" genus="Escherichia" kingdom="Bacteria" order="Enterobacteriales" pageId="12" pageNumber="2301" phylum="Proteobacteria" rank="species" species="coli">
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<emphasis box="[561,629,861,884]" italics="true" pageId="12" pageNumber="2301">E. coli</emphasis>
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TOP
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</taxonomicName>
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10 and
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<taxonomicName authority="DSM" authorityName="DSM" box="[138,300,893,916]" class="Ustilaginomycetes" family="Ustilaginaceae" genus="Ustilago" kingdom="Chromista" order="Ustilaginales" pageId="12" pageNumber="2301" phylum="Basidiomycota" rank="species" species="maydis">
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<emphasis box="[138,241,893,916]" italics="true" pageId="12" pageNumber="2301">U. maydis</emphasis>
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<accessionNumber box="[249,381,893,916]" httpUri="http://www.ncbi.nlm.nih.gov/protein/DSM14603" pageId="12" pageNumber="2301">DSM 14603</accessionNumber>
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</taxonomicName>
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.
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</paragraph>
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<paragraph blockId="12.[138,772,413,1076]" pageId="12" pageNumber="2301">
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DNA
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<collectionCode box="[229,264,925,948]" country="0" name="Goucher College" pageId="12" pageNumber="2301">GC</collectionCode>
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content is 70.2 mol%. The draft genome sequence of
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<specimenCode box="[259,332,957,980]" collectionCode="CA" country="USA" name="Chicago Academy of Sciences" pageId="12" pageNumber="2301" type="Museum">CA032</specimenCode>
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A
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<superScript attach="left" box="[348,357,952,967]" fontSize="6" pageId="12" pageNumber="2301">
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<collectionCode box="[348,357,952,967]" name="Tavera, Department of Geology and Geophysics" pageId="12" pageNumber="2301">T</collectionCode>
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</superScript>
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is available from GenBank (accession JAAIYA01).
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<subSubSection pageId="12" pageNumber="2301" type="materials_examined">
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<materialsCitation ID-GBIF-Occurrence="3042655301" collectedFrom="isolated from soil" collectionCode="A" country="United Kingdom" latitude="51.86" location="Carmarthen" longLatPrecision="652" longitude="-4.31" pageId="12" pageNumber="2301" specimenCode="CA032" specimenCount="1" typeStatus="type strain">
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The
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<typeStatus box="[312,422,989,1012]" pageId="12" pageNumber="2301">type strain</typeStatus>
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(
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<specimenCode box="[437,511,989,1012]" collectionCode="CA" country="USA" name="Chicago Academy of Sciences" pageId="12" pageNumber="2301" type="Museum">CA032</specimenCode>
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<geologicalTimeScale box="[511,527,989,1012]" pageId="12" pageNumber="2301">A</geologicalTimeScale>
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<superScript attach="left" box="[528,537,984,999]" fontSize="6" pageId="12" pageNumber="2301">T</superScript>
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<emphasis bold="true" box="[546,571,989,1013]" pageId="12" pageNumber="2301">¼</emphasis>
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NCCB 100776
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<superScript attach="left" box="[728,737,984,999]" fontSize="6" pageId="12" pageNumber="2301">T</superScript>
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<emphasis bold="true" box="[747,772,989,1013]" pageId="12" pageNumber="2301">¼</emphasis>
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NBBC 114353
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<superScript attach="none" box="[302,311,1016,1031]" fontSize="6" pageId="12" pageNumber="2301">T</superScript>
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) was
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<collectedFrom box="[404,611,1021,1044]" pageId="12" pageNumber="2301">isolated from soil</collectedFrom>
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collected in
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<location LSID="urn:lsid:plazi:treatment:03A729036472D737FF37FEB3FD8D0F3D:8ED1CECE6472D737FF37FBDCFECA0F3D" box="[138,267,1053,1076]" country="United Kingdom" latitude="51.86" longLatPrecision="652" longitude="-4.31" name="Carmarthen" pageId="12" pageNumber="2301">Carmarthen</location>
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,
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<collectingCountry box="[277,309,1053,1076]" name="United Kingdom" pageId="12" pageNumber="2301">UK</collectingCountry>
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(gridref
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<geoCoordinate box="[398,485,1053,1076]" degrees="51.86" direction="north" orientation="latitude" pageId="12" pageNumber="2301" precision="555" value="51.86">51.86 N</geoCoordinate>
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<geoCoordinate box="[492,577,1053,1076]" degrees="4.31" direction="west" orientation="longitude" pageId="12" pageNumber="2301" precision="555" value="-4.31">4.31 W</geoCoordinate>
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</materialsCitation>
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).
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</subSubSection>
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</paragraph>
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</subSubSection>
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</treatment>
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</document> |