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<h1 class="title toc-ignore">References analysis</h1>
<h4 class="author">Olivier Rué</h4>
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<h4 class="date">2021-09-30</h4>
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<pre class="r"><code>ggd &lt;- read.delim(&quot;REFERENCES/ALL_26jan2021.tsv&quot;, sep=&quot;\t&quot;, header=T, stringsAsFactors = F)
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ggd &lt;- ggd %&gt;% as_tibble() </code></pre>
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<div id="assignations-of-references-against-main-databases" class="section level1">
<h1>Assignations of references against main databases</h1>
<p>The 142 sequences were compared to those present in commonly used databanks:</p>
<ul>
<li>UNITE 8.2 for ITS1 and ITS2</li>
<li>SILVA 28S v138 for D1D2</li>
<li>nt (nt_2021-07-30) for RPB2</li>
</ul>
<p>The best hit from blast output is kept and % of coverage and % of identity are ploted for each marker:</p>
<pre class="r"><code>its1 &lt;- read.delim(&quot;REFERENCES/ALL_ITS1.blast_vs_UNITE&quot;, sep=&quot;\t&quot;, header=F)
colnames(its1) &lt;- c(&quot;Strain&quot;, &quot;sseqid&quot;, &quot;pident&quot;, &quot;length&quot;, &quot;mismatch&quot;, &quot;gapopen&quot;, &quot;qstart&quot;, &quot;qend&quot;, &quot;sstart&quot;, &quot;send&quot;, &quot;evalue&quot;, &quot;bitscore&quot;, &quot;qlen&quot;,&quot;taxonomy&quot;)
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t_its1 &lt;- its1 %&gt;% as_tibble() %&gt;% mutate(pcov = length/qlen)%&gt;% mutate(pident = pident/100) %&gt;% mutate(marker = &quot;ITS1&quot;) %&gt;% separate(taxonomy, &quot;;(?=[\\S])&quot;, into = c(&quot;Ssss&quot;, &quot;SKingdom&quot;,&quot;SPhylum&quot;,&quot;SClass&quot;,&quot;SOrder&quot;,&quot;SFamily&quot;,&quot;SGenus&quot;,&quot;SSpecies&quot;), remove = TRUE) %&gt;% mutate(SSpecies = gsub(&quot;\\[.*&quot;,&quot;&quot;,SSpecies)) %&gt;% mutate(SSpecies = gsub(&quot;s__&quot;,&quot;&quot;,SSpecies)) %&gt;% mutate(SSpecies = gsub(&quot;_&quot;,&quot; &quot;,trimws(SSpecies)))
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its2 &lt;- read.delim(&quot;REFERENCES/ALL_ITS2.blast_vs_UNITE&quot;, sep=&quot;\t&quot;, header=F)
colnames(its2) &lt;- c(&quot;Strain&quot;, &quot;sseqid&quot;, &quot;pident&quot;, &quot;length&quot;, &quot;mismatch&quot;, &quot;gapopen&quot;, &quot;qstart&quot;, &quot;qend&quot;, &quot;sstart&quot;, &quot;send&quot;, &quot;evalue&quot;, &quot;bitscore&quot;, &quot;qlen&quot;, &quot;taxonomy&quot;)
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t_its2 &lt;- its2 %&gt;% as_tibble() %&gt;% mutate(pcov = length/qlen)%&gt;% mutate(pident = pident/100) %&gt;% mutate(marker = &quot;ITS2&quot;) %&gt;% separate(taxonomy, &quot;;(?=[\\S])&quot;, into = c(&quot;Ssss&quot;, &quot;SKingdom&quot;,&quot;SPhylum&quot;,&quot;SClass&quot;,&quot;SOrder&quot;,&quot;SFamily&quot;,&quot;SGenus&quot;,&quot;SSpecies&quot;), remove = TRUE) %&gt;% mutate(SSpecies = gsub(&quot;\\[.*&quot;,&quot;&quot;,SSpecies)) %&gt;% mutate(SSpecies = gsub(&quot;s__&quot;,&quot;&quot;,SSpecies)) %&gt;% mutate(SSpecies = gsub(&quot;_&quot;,&quot; &quot;,trimws(SSpecies)))
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d1d2 &lt;- read.delim(&quot;REFERENCES/ALL_D1D2.blast_vs_SILVA138-28S&quot;, sep=&quot;\t&quot;, header=F)
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colnames(d1d2) &lt;- c(&quot;Strain&quot;, &quot;sseqid&quot;, &quot;pident&quot;, &quot;length&quot;, &quot;mismatch&quot;, &quot;gapopen&quot;, &quot;qstart&quot;, &quot;qend&quot;, &quot;sstart&quot;, &quot;send&quot;, &quot;evalue&quot;, &quot;bitscore&quot;, &quot;qlen&quot;, &quot;taxonomy&quot;)
t_d1d2 &lt;- d1d2 %&gt;% as_tibble() %&gt;% mutate(pcov = length/qlen)%&gt;% mutate(pident = pident/100) %&gt;% mutate(marker = &quot;D1D2&quot;)%&gt;% separate(taxonomy, &quot;;(?=[\\S])&quot;, into = c(&quot;Ssss&quot;, &quot;SKingdom&quot;,&quot;SPhylum&quot;,&quot;SClass&quot;,&quot;SOrder&quot;,&quot;SFamily&quot;,&quot;SGenus&quot;,&quot;SSpecies&quot;), remove = TRUE) %&gt;% mutate(SSpecies = gsub(&quot;\\[.*&quot;,&quot;&quot;,SSpecies)) %&gt;% mutate(SSpecies = gsub(&quot;s__&quot;,&quot;&quot;,SSpecies)) %&gt;% mutate(SSpecies = gsub(&quot;_&quot;,&quot; &quot;,trimws(SSpecies)))
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rpb2 &lt;- read.delim(&quot;REFERENCES/ALL_RPB2.blast_vs_NT&quot;, sep=&quot;\t&quot;, header=F)
colnames(rpb2) &lt;- c(&quot;Strain&quot;, &quot;sseqid&quot;, &quot;pident&quot;, &quot;length&quot;, &quot;mismatch&quot;, &quot;gapopen&quot;, &quot;qstart&quot;, &quot;qend&quot;, &quot;sstart&quot;, &quot;send&quot;, &quot;evalue&quot;, &quot;bitscore&quot;, &quot;qlen&quot;, &quot;taxonomy&quot;)
t_rpb2 &lt;- rpb2 %&gt;% as_tibble() %&gt;% mutate(pcov = length/qlen) %&gt;% mutate(pident = pident/100)%&gt;% mutate(marker = &quot;RPB2&quot;) %&gt;%  mutate(SSpecies = sub(&quot;^(\\S*\\s+\\S+).*&quot;, &quot;\\1&quot;, taxonomy))
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t &lt;- bind_rows(t_its1, t_its2, t_d1d2, t_rpb2)</code></pre>
<pre class="r"><code>p &lt;- ggplot(t, aes(x=pident, y=pcov, color=marker)) + geom_point(size = 3, alpha = 0.3)
p + stat_ellipse()</code></pre>
<p><img src="references_files/figure-html/unnamed-chunk-3-1.png" width="1008" /></p>
<pre class="r"><code>#ggplot(t) + geom_violin(aes(x = marker, y = pident, color=marker))
#ggplot(t) + geom_violin(aes(x = marker, y = pcov, color=marker))
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p&lt;-ggplot(t, aes(x=marker, y=pcov, fill=marker)) +
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  geom_boxplot(position=position_dodge(1))
p</code></pre>
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<p><img src="references_files/figure-html/unnamed-chunk-3-2.png" width="1008" /></p>
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<pre class="r"><code>b &lt;- pivot_longer(data = t, cols = c(pident,pcov), names_to = &quot;metric&quot;, values_to = &quot;percent&quot;)
p&lt;-ggplot(b, aes(x=marker, y=percent, fill=metric)) +
  geom_boxplot(position=position_dodge(1))
p</code></pre>
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<p><img src="references_files/figure-html/unnamed-chunk-3-3.png" width="1008" /></p>
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<pre class="r"><code>summary(t %&gt;% filter(marker == &quot;ITS1&quot;) %&gt;% select(pident))
summary(t %&gt;% filter(marker == &quot;ITS2&quot;) %&gt;% select(pident))
summary(t %&gt;% filter(marker == &quot;D1D2&quot;) %&gt;% select(pident))
summary(t %&gt;% filter(marker == &quot;RPB2&quot;) %&gt;% select(pident))</code></pre>
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<p><strong>Consequently, affiliation may be wrong and assignation at Species level is often not retrieved.</strong></p>
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<div id="closest-reference-in-databases" class="section level1 tabset">
<h1 class="tabset">Closest reference in databases</h1>
<p><strong>Sometimes, affiliation gives the expected Species even if sequence is not exactly present. Nevertheless, affilition at Species may be wrong!</strong></p>
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<div id="its1" class="section level2">
<h2>ITS1</h2>
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<pre class="r"><code>infos &lt;- full_join(t_its1,ggd,by=&quot;Strain&quot;) %&gt;% filter(marker == &quot;ITS1&quot;) %&gt;% select(Species, SSpecies, pident, pcov)
infos %&gt;% datatable()</code></pre>
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class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Species<\/th>\n      <th>SSpecies<\/th>\n      <th>pident<\/th>\n      <th>pcov<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":10,"scrollX":true,"language":{"search":"Filter:"},"dom":"Bfrtip","buttons":["copy","csv","excel","pdf","print"],"columnDefs":[{"className":"dt-right","targets":[3,4]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
<p>83 hits have the same Species.</p>
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</div>
<div id="its2" class="section level2">
<h2>ITS2</h2>
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<pre class="r"><code>infos &lt;- full_join(t_its2,ggd,by=&quot;Strain&quot;) %&gt;% filter(marker == &quot;ITS2&quot;) %&gt;% select(Species, SSpecies, pident, pcov)
infos %&gt;% datatable()</code></pre>
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bruxellensis","Saccharomycetales sp","Schwanniomyces occidentalis","Hanseniaspora opuntiae","Hyphopichia burtonii","Meyerozyma smithsonii","Mrakia frigida","Papiliotrema flavescens","Papiliotrema terrestris","Rhodotorula nothofagi","Schwanniomyces etchellsii","Saccharomycetales sp","Symmetrospora coprosmae","Trigonopsis vinaria","Candida glabrata","Kazachstania unispora","Kluyveromyces marxianus","Lodderomyces elongisporus","Meyerozyma guilliermondii","Millerozyma farinosa","Saccharomycetales sp","Issatchenkia orientalis","Saccharomycetales sp","Rhodotorula mucilaginosa","Debaryomyces hansenii","Aureobasidium leucospermi","Saccharomycetales sp","Clavispora lusitaniae","Zygosaccharomyces rouxii","Saccharomyces paradoxus","Wickerhamomyces anomalus","Aciculoconidium aculeatum","Barnettozyma californica","Dekkera bruxellensis","Cyberlindnera mrakii","Diutina catenulata","Geotrichum klebahnii","Hanseniaspora valbyensis","Kluyveromyces dobzhanskii","Kluyveromyces lactis","Kregervanrija fluxuum","Lachancea fermentati","Lachancea waltii","Naganishia vaughanmartiniae","Nakazawaea holstii","Rhodotorula diobovata","Starmerella lactis-condensi","Candida tropicalis","Lachancea kluyveri","Candida stellata","Candida sake","Rhodotorula glutinis","Sporobolomyces roseus","Citeromyces matritensis","Cystobasidium minuta","Filobasidium magnum","Hanseniaspora guilliermondii","Hanseniaspora osmophila","Hanseniaspora uvarum","Hanseniaspora vineae","Lachancea quebecensis","Metschnikowia sp","Metschnikowia reukaufii","Fungi sp","Papiliotrema laurentii","Pichia eremophila","Pichia terricola","Rhodotorula babjevae","Saccharomycodes ludwigii","Zygotorulaspora florentina","Candida parapsilosis","Torulaspora delbrueckii","Pichia membranifaciens"],[1,0.99669,1,0.99662,0.96633,1,1,0.97106,0.98966,0.98966,0.98294,0.98966,1,0.99315,0.98973,0.99656,0.99313,0.98976,0.99313,0.96939,0.99315,1,0.99313,0.99313,1,1,0.99451,1,0.97765,1,1,1,0.99449,0.98945,1,0.99208,1,0.99743,0.99038,0.99526,0.99419,0.97113,1,1,0.99718,1,0.99602,0.98973,0.99656,0.98625,1,0.98601,0.99462,0.97656,1,0.99642,1,1,0.99308,0.99656,0.97938,1,0.95897,1,1,1,1,0.99365,1,1,1,1,0.99695,1,0.99119,0.99038,1,1,0.98707,1,0.99371,1,1,0.99636,1,0.99719,1,1,1,1,0.97807,0.99667,0.99595,1,0.99363,0.98947,1,1,0.99492,0.98892,0.9878,1,1,1,1,0.96087,1,1,0.99148,1,1,1,1,1,1,1,1,0.98491,1,0.99015,0.98276,1,1,0.99673,0.99381,1,0.99688,0.99469,0.98039,0.99196,1,1,1,0.97594,1,0.98712,1,1,1,1,1,1,1],[0.961661341853035,0.958730158730159,1,1,1,0.875,0.893732970027248,1.00647249190939,0.941558441558442,0.941558441558442,0.951298701298701,0.950819672131147,0.938709677419355,0.938906752411576,0.938906752411576,0.938709677419355,0.938709677419355,0.939102564102564,0.938709677419355,0.951456310679612,0.938906752411576,0.873376623376623,0.938709677419355,0.938709677419355,0.892857142857143,0.882882882882883,0.94300518134715,1,0.895,1,1,0.794425087108014,0.887530562347188,0.913253012048193,1,0.904534606205251,0.779850746268657,0.868303571428571,0.920353982300885,0.861224489795918,0.947658402203857,0.907142857142857,0.906801007556675,0.90126582278481,0.949061662198391,0.902313624678663,0.880701754385965,0.938906752411576,0.938709677419355,0.929712460063898,0.875399361022364,0.88,0.907317073170732,0.962406015037594,0.882175226586103,0.874608150470219,0.875,0.966463414634146,0.926282051282051,0.938709677419355,0.938709677419355,0.905660377358491,1,0.87125748502994,1,0.812698412698413,0.858181818181818,0.94311377245509,0.888571428571429,0.806122448979592,0.193877551020408,0.784671532846715,0.893732970027248,0.974212034383954,0.853383458646617,0.920353982300885,0.897637795275591,0.893175074183976,0.878787878787879,0.892265193370166,0.921739130434783,0.836134453781513,0.889204545454545,0.878594249201278,0.896551724137931,0.929503916449086,0.900510204081633,0.861702127659574,0.884955752212389,0.885964912280702,0.853932584269663,0.977198697068404,0.939163498098859,0.892857142857143,0.920821114369501,0.940594059405941,0.912844036697248,0.818604651162791,0.985,0.94750656167979,0.97910447761194,0.966019417475728,0.88125,0.955089820359281,0.885885885885886,1,0.808823529411765,0.86,0.900255754475703,0.903061224489796,0.82051282051282,0.893258426966292,0.892957746478873,0.970189701897019,0.884955752212389,0.891364902506964,0.792114695340502,0.920138888888889,0.893854748603352,0.838842975206612,0.924302788844621,0.890140845070423,0.889518413597734,0.88953488372093,0.925501432664756,0.9,0.894150417827298,0.989501312335958,0.994428969359331,0.992021276595745,0.957746478873239,1,1,1.01907356948229,0.87962962962963,0.903100775193798,0.838174273858921,0.882022471910112,0.892351274787535,0.879746835443038,0.856088560885609,0.903703703703704,0.86551724137931]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Species<\/th>\n      <th>SSpecies<\/th>\n      <th>pident<\/th>\n      <th>pcov<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":10,"scrollX":true,"language":{"search":"Filter:"},"dom":"Bfrtip","buttons":["copy","csv","excel","pdf","print"],"columnDefs":[{"className":"dt-right","targets":[3,4]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
<p>83 hits have the same Species.</p>
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</div>
<div id="d1d2" class="section level2">
<h2>D1D2</h2>
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<pre class="r"><code>infos &lt;- full_join(t_d1d2,ggd,by=&quot;Strain&quot;) %&gt;% filter(marker == &quot;D1D2&quot;) %&gt;% select(Species, SSpecies, pident, pcov) 
infos %&gt;% datatable()</code></pre>
<div id="htmlwidget-79fff9903a22abc5bcab" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-79fff9903a22abc5bcab">{"x":{"filter":"none","data":[["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","23","24","25","26","27","28","29","30","31","32","33","34","35","36","37","38","39","40","41","42","43","44","45","46","47","48","49","50","51","52","53","54","55","56","57","58","59","60","61","62","63","64","65","66","67","68","69","70","71","72","73","74","75","76","77","78","79","80","81","82","83","84","85","86","87","88","89","90","91","92","93","94","95","96","97","98","99","100","101","102","103","104","105","106","107","108","109","110","111","112","113","114","115","116","117","118","119","120","121","122","123","124","125","126","127","128","129","130","131","132","133","134","135","136","137","138","139","140","141","142","143"],["Aspergillus candidus","Aspergillus ochraceus","Cladosporium allicinum","Cladosporium cladosporioides","Cladosporium sphaerospermum","Eurotium amstelodami","Guehomyces pullulans","Neosartorya fischeri","Penicillium aurantiogriseum","Penicillium bialowiezense","Penicillium brevicompactum","Penicillium chermesinum","Penicillium chrysogenum_F7M11","Penicillium commune","Penicillium crustosum","Penicillium dipodomyicola","Penicillium expansum","Penicillium gladioli","Penicillium nordicum","Penicillium olsonii","Penicillium palitans","Penicillium salamii","Penicillium verrucosum","Penicillium viridicatum","Rhodotorula mucilaginosa","Torulopsis candida","Yarrowia alimentaria","Yarrowia bubula","Yarrowia lipolytica","Yarrowia porcina","Candida aaseri","Candida apicola","Kazachstania saulgeensis","Saccharomyces bayanus","Saccharomyces pastorianus","Saccharomyces uvarum","Saturnispora diversa","Schizosaccharomyces japonicus","Candida carpophila","Hyphopichia pseudoburtonii","Kazachstania barnettii","Kazachstania bozae","Kazachstania bulderi","Kazachstania exigua","Kazachstania humilis","Kazachstania servazzii","Pichia norvegensis","Penicillium camemberti var. camemberti","Penicillium nalgiovense","Penicillium solitum","Aspergillus fumigatus","Cyberlindnera jadinii","Geotrichum candidum","Lichtheimia corymbifera","Mucor circinelloides","Mucor fuscus","Mucor lanceolatus","Mucor racemosus","Penicillium antarcticum","Penicillium chrysogenum_CBS","Penicillium roqueforti","Trichosporon asahii","Yarrowia deformans","Candida zeylanoides","Candida azyma","Candida metapsilosis","Candida vini","Cryptococcus neoformans","Cystobasidium slooffiae","Dekkera bruxellensis","Diutina rugosa","Hanseniaspora occidentalis","Hanseniaspora opuntiae","Hyphopichia burtonii","Meyerozyma caribbica","Mrakia frigida","Papiliotrema flavescens","Papiliotrema terrestris","Rhodotorula nothofagi","Schwanniomyces etchellsii","Starmerella bacillaris","Symmetrospora coprosmae","Trigonopsis vinaria","Candida glabrata","Kazachstania unispora","Kluyveromyces marxianus","Lodderomyces elongisporus","Meyerozyma guilliermondii","Millerozyma farinosa","Pichia fermentans","Pichia kudriavzevii","Pichia occidentalis","Rhodotorula mucilaginosa var. mucilaginosa","Debaryomyces hansenii","Aureobasidium pullulans","Candida intermedia","Clavispora lusitaniae","Zygosaccharomyces rouxii","Saccharomyces cerevisiae","Wickerhamomyces anomalus","Aciculoconidium aculeatum","Barnettozyma californica","Candida santamariae","Cyberlindnera mrakii","Diutina catenulata","Geotrichum klebahnii","Hanseniaspora valbyensis","Kluyveromyces dobzhanskii","Kluyveromyces lactis var. lactis","Kregervanrija fluxuum","Lachancea fermentati","Lachancea waltii","Naganishia globosa","Nakazawaea holstii","Rhodotorula diobovata","Starmerella lactis-condensi","Candida tropicalis","Lachancea kluyveri","Starmerella stellata","Candida sake","Rhodotorula glutinis","Sporobolomyces roseus","Citeromyces matritensis","Cystobasidium minutum","Filobasidium magnum","Filobasidium magnum","Hanseniaspora guilliermondii","Hanseniaspora osmophila","Hanseniaspora uvarum","Hanseniaspora vineae","Lachancea thermotolerans","Metschnikowia pulcherrima","Metschnikowia reukaufii","Naganishia albida","Papiliotrema laurentii","Pichia kluyveri","Pichia terricola","Rhodotorula babjevae","Saccharomycodes ludwigii","Zygotorulaspora florentina","Candida parapsilosis","Torulaspora delbrueckii","Pichia membranifaciens"],["Aspergillus oryzae RIB40","Aspergillus sclerotiorum","Cladosporium allicinum","Cladosporium cladosporioides","Cladosporium sphaerospermum UM 843","Aspergillus cristatus","Mrakia blollopis","Aspergillus fumigatus Af293","Penicillium griseofulvum","Penicillium brevicompactum","Penicillium brevicompactum","Penicillium subrubescens","Penicillium nalgiovense","Penicillium griseofulvum","Penicillium griseofulvum","Penicillium griseofulvum","Penicillium griseofulvum","Penicillium griseofulvum","Penicillium nalgiovense","Penicillium brevicompactum","Penicillium griseofulvum","Penicillium brevicompactum","Penicillium nalgiovense","Penicillium griseofulvum","Alloscardovia sp.","Scheffersomyces shehatae","Yarrowia lipolytica","Yarrowia lipolytica","Yarrowia lipolytica","Yarrowia lipolytica","Yamadazyma sp.","Candida apicola","Kazachstania exigua","Saccharomyces eubayanus","Saccharomyces eubayanus","Saccharomyces uvarum MCYC 623","Saturnispora diversa","Schizosaccharomyces japonicus yFS275","Meyerozyma guilliermondii","Hyphopichia burtonii","Kazachstania barnettii","Kazachstania exigua","Kazachstania barnettii","Kazachstania exigua","Kazachstania barnettii","Kazachstania servazzii","Pichia norvegensis","Penicillium griseofulvum","Penicillium nalgiovense","Penicillium subrubescens","Aspergillus fumigatus Af293","Cyberlindnera jadinii NBRC 0988","Galactomyces candidus","Lichtheimia corymbifera","Lichtheimia ramosa B5399","Mucor irregularis","Mucor racemosus","Mucor racemosus","Penicillium arizonense","Penicillium nalgiovense","Penicillium griseofulvum","Tetradesmus obliquus","Yarrowia lipolytica","Talaromyces marneffei ATCC 18224","Wickerhamiella azyma","Candida orthopsilosis Co 90-125","Kregervanrija fluxuum","Cryptococcus neoformans var. grubii","Cystobasidium laryngis","Brettanomyces bruxellensis","Phaeoacremonium minimum UCRPA7","Hanseniaspora osmophila","Hanseniaspora opuntiae","Dastarcus helophoroides","Meyerozyma guilliermondii ATCC 6260","Mrakia blollopis","Prorocentrum micans","Prorocentrum micans","Leucosporidium creatinivorum","Schwanniomyces etchellsii","Starmerella bacillaris","Cystobasidium laryngis","Trigonopsis vinaria","","Kazachstania unispora","Kluyveromyces marxianus","Lodderomyces elongisporus NRRL YB-4239","Meyerozyma guilliermondii ATCC 6260","Millerozyma farinosa CBS 7064 (Pichia farinosa CBS 7064)","Pichia fermentans","Pichia kudriavzevii","Pichia occidentalis","Alloscardovia sp.","Talaromyces marneffei ATCC 18224","Aureobasidium sp.","","Clavispora lusitaniae","Zygosaccharomyces rouxii","Saccharomyces cerevisiae (baker's yeast)","Wickerhamomyces anomalus","Aciculoconidium aculeatum","Barnettozyma californica","Talaromyces marneffei ATCC 18224","Cyberlindnera mrakii","Spathaspora passalidarum NRRL Y-27907","Galactomyces candidus","Hanseniaspora valbyensis","Kluyveromyces wickerhamii UCD 54-210","Kluyveromyces lactis","Kregervanrija fluxuum","Lachancea fermentati","Lachancea waltii NCYC 2644","unknown species","Nakazawaea holstii","Rhodotorula graminis WP1","Starmerella bombicola","Candida tropicalis","Naumovozyma castellii NRRL Y-12630","Starmerella bacillaris","Scheffersomyces shehatae","Rhodotorula graminis WP1","Alloscardovia sp.","Citeromyces matritensis","Cystobasidium laryngis","Mrakia frigida","Mrakia frigida","Hanseniaspora opuntiae","Hanseniaspora osmophila","Hanseniaspora opuntiae","Hanseniaspora osmophila","Lachancea thermotolerans CBS 6340","Metschnikowia fructicola 277","Metschnikowia reukaufii","unknown species","Papiliotrema laurentii RY1","Pichia kluyveri","Pichia terricola","Rhodotorula graminis WP1","Saccharomycodes ludwigii","Zygotorulaspora mrakii","Candida orthopsilosis Co 90-125","Torulaspora delbrueckii","Pichia membranifaciens"],[0.96769,0.98226,1,1,0.98684,0.99674,0.93344,0.99511,0.99837,0.98377,0.99838,0.9658,0.99837,0.99674,0.99674,1,0.99511,0.99511,0.99674,0.99188,0.99674,0.98379,0.99674,0.99837,1,0.93126,0.88909,0.90597,0.99818,0.9235,0.96341,0.99809,0.9949,1,1,1,0.99819,0.99684,0.99411,0.89672,1,0.99653,0.99491,1,0.97966,1,1,0.99674,1,0.99837,0.99854,0.99355,0.98543,0.95492,0.99714,0.92,0.9171,0.99308,0.9759,0.99837,0.99837,0.93302,0.93807,0.95928,1,0.99397,0.99829,0.99844,0.95639,0.99029,0.85827,0.94127,1,0.99824,0.99187,0.99533,0.96812,0.9689,0.88321,1,0.9981,0.90373,1,1,1,1,1,0.99512,0.99675,1,0.99835,1,1,0.99837,1,0.9911,1,1,1,0.99831,0.98093,1,0.96254,0.99831,0.90256,0.89967,1,0.98299,1,0.99828,1,0.99675,0.93171,1,0.99503,0.90138,1,1,0.92586,0.93301,0.99834,0.8748,1,0.95707,0.98295,0.98333,0.99675,0.99674,0.99187,0.98369,1,0.97601,0.9982,0.91186,0.99842,0.9983,0.99825,0.99834,1,0.95041,0.99184,1,0.99829],[1.00161812297735,1.00323624595469,1,1,1,1,1.0015503875969,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1.0016393442623,1.01851851851852,1.01841620626151,1.0018281535649,1.01104972375691,1,1,0.959216965742251,1,1,1,0.958333333333333,1,1,1.00734394124847,0.960848287112561,0.986301369863014,0.960848287112561,0.959216965742251,0.962479608482871,0.960975609756098,0.961352657004831,1,1,1,1.00073099415205,1,1.00182481751825,0.973983739837398,1.00143266475645,1.00415512465374,1.00346620450607,1.00138504155125,1,1,1,1.0015600624025,1.01104972375691,1.00163132137031,0.959731543624161,0.940425531914894,0.960526315789474,1,1,1,0.722960151802656,1.0016339869281,1,1,1.00326264274062,1,0.972267536704731,1,0.682724252491694,0.959216965742251,1.00190476190476,1.00311526479751,0.960132890365448,1,0.960975609756098,1,1,1.00326264274062,1,1,1,1,1,1,1,1.00357142857143,0.957142857142857,1,1,0.961038961038961,0.951612903225806,0.962085308056872,1.00163132137031,0.961102106969206,0.767716535433071,1.0135593220339,0.961038961038961,1,1,0.957236842105263,1,1.00325732899023,0.959438377535101,0.959216965742251,0.933539412673879,0.960227272727273,1,1,1.00381679389313,1.01157024793388,0.933539412673879,1.00326264274062,0.961102106969206,0.936011904761905,0.262686567164179,0.0895522388059701,1,1,1,1,1,1,1,1.0032154340836,0.963358778625954,0.960720130932897,0.959798994974874,0.933539412673879,0.961165048543689,0.968,1,1,0.960591133004926]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Species<\/th>\n      <th>SSpecies<\/th>\n      <th>pident<\/th>\n      <th>pcov<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":10,"scrollX":true,"language":{"search":"Filter:"},"dom":"Bfrtip","buttons":["copy","csv","excel","pdf","print"],"columnDefs":[{"className":"dt-right","targets":[3,4]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
<p>44 hits have the same Species.</p>
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</div>
<div id="rpb2" class="section level2">
<h2>RPB2</h2>
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<pre class="r"><code>infos &lt;- full_join(t_rpb2,ggd,by=&quot;Strain&quot;) %&gt;% filter(marker == &quot;RPB2&quot;) %&gt;% select(Species, SSpecies, pident, pcov) 
infos %&gt;% datatable()</code></pre>
<div id="htmlwidget-81f6c165587d44d87f42" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-81f6c165587d44d87f42">{"x":{"filter":"none","data":[["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","23","24","25","26","27","28","29","30","31","32","33","34","35","36","37","38","39","40","41","42","43","44","45","46","47","48","49","50","51","52","53","54","55","56","57","58","59","60","61","62","63","64","65","66","67","68","69","70","71","72","73","74","75","76","77","78","79","80","81","82","83","84","85","86","87","88","89","90","91","92","93","94","95","96","97","98","99","100","101","102","103","104","105","106","107","108","109","110","111","112","113","114","115","116","117","118","119","120","121","122","123","124","125","126","127","128","129","130","131","132","133","134","135","136","137","138","139"],["Aspergillus candidus","Aspergillus ochraceus","Cladosporium allicinum","Cladosporium cladosporioides","Cladosporium sphaerospermum","Eurotium amstelodami","Guehomyces pullulans","Neosartorya fischeri","Penicillium aurantiogriseum","Penicillium bialowiezense","Penicillium brevicompactum","Penicillium chermesinum","Penicillium chrysogenum_F7M11","Penicillium commune","Penicillium crustosum","Penicillium dipodomyicola","Penicillium expansum","Penicillium gladioli","Penicillium nordicum","Penicillium olsonii","Penicillium palitans","Penicillium salamii","Penicillium verrucosum","Penicillium viridicatum","Rhodotorula mucilaginosa","Torulopsis candida","Yarrowia alimentaria","Yarrowia bubula","Yarrowia lipolytica","Yarrowia porcina","Candida aaseri","Candida apicola","Kazachstania saulgeensis","Saccharomyces bayanus","Saccharomyces pastorianus","Saccharomyces uvarum","Saturnispora diversa","Schizosaccharomyces japonicus","Candida carpophila","Hyphopichia pseudoburtonii","Kazachstania barnettii","Kazachstania bozae","Kazachstania bulderi","Kazachstania exigua","Kazachstania humilis","Kazachstania servazzii","Pichia norvegensis","Penicillium camemberti var. camemberti","Penicillium nalgiovense","Penicillium solitum","Aspergillus fumigatus","Cyberlindnera jadinii","Geotrichum candidum","Lichtheimia corymbifera","Mucor circinelloides","Mucor fuscus","Mucor lanceolatus","Mucor racemosus","Penicillium antarcticum","Penicillium chrysogenum_CBS","Penicillium roqueforti","Trichosporon asahii","Yarrowia deformans","Candida zeylanoides","Candida metapsilosis","Candida vini","Cryptococcus neoformans","Cystobasidium slooffiae","Dekkera bruxellensis","Diutina rugosa","Hanseniaspora occidentalis","Hanseniaspora opuntiae","Hyphopichia burtonii","Meyerozyma caribbica","Mrakia frigida","Papiliotrema flavescens","Papiliotrema terrestris","Rhodotorula nothofagi","Schwanniomyces etchellsii","Starmerella bacillaris","Symmetrospora coprosmae","Trigonopsis vinaria","Candida glabrata","Kazachstania unispora","Kluyveromyces marxianus","Lodderomyces elongisporus","Meyerozyma guilliermondii","Millerozyma farinosa","Pichia fermentans","Pichia kudriavzevii","Pichia occidentalis","Rhodotorula mucilaginosa var. mucilaginosa","Debaryomyces hansenii","Aureobasidium pullulans","Candida intermedia","Clavispora lusitaniae","Zygosaccharomyces rouxii","Saccharomyces cerevisiae","Wickerhamomyces anomalus","Aciculoconidium aculeatum","Barnettozyma californica","Candida santamariae","Cyberlindnera mrakii","Diutina catenulata","Geotrichum klebahnii","Hanseniaspora valbyensis","Kluyveromyces dobzhanskii","Kluyveromyces lactis var. lactis","Kregervanrija fluxuum","Lachancea fermentati","Naganishia globosa","Nakazawaea holstii","Rhodotorula diobovata","Starmerella lactis-condensi","Candida tropicalis","Lachancea kluyveri","Starmerella stellata","Candida sake","Sporobolomyces roseus","Citeromyces matritensis","Cystobasidium minutum","Filobasidium magnum","Hanseniaspora guilliermondii","Hanseniaspora osmophila","Hanseniaspora uvarum","Hanseniaspora vineae","Lachancea thermotolerans","Metschnikowia 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class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Species<\/th>\n      <th>SSpecies<\/th>\n      <th>pident<\/th>\n      <th>pcov<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":10,"scrollX":true,"language":{"search":"Filter:"},"dom":"Bfrtip","buttons":["copy","csv","excel","pdf","print"],"columnDefs":[{"className":"dt-right","targets":[3,4]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
<p>71 hits have the same Species.</p>
</div>
</div>
<div id="analysis-by-phylum" class="section level1 tabset">
<h1 class="tabset">Analysis by Phylum</h1>
<p><strong>Ascomycota are less present in databanks than Basidiomycota, except for D1D2 (less clear).</strong></p>
<div id="its1-1" class="section level2">
<h2>ITS1</h2>
<pre class="r"><code>a &lt;- full_join(t_its1,ggd,by=&quot;Strain&quot;) %&gt;% filter(marker == &quot;ITS1&quot;)
p &lt;- ggplot(a, aes(x=pident, y=pcov, color=Phylum)) + geom_point(size = 3, alpha = 0.3)
p + stat_ellipse()</code></pre>
<p><img src="references_files/figure-html/unnamed-chunk-9-1.png" width="1008" /></p>
</div>
<div id="its2-1" class="section level2">
<h2>ITS2</h2>
<pre class="r"><code>a &lt;- full_join(t_its2,ggd,by=&quot;Strain&quot;) %&gt;% filter(marker == &quot;ITS2&quot;)
p &lt;- ggplot(a, aes(x=pident, y=pcov, color=Phylum)) + geom_point(size = 3, alpha = 0.3)
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p + stat_ellipse()</code></pre>
<p><img src="references_files/figure-html/unnamed-chunk-10-1.png" width="1008" /></p>
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</div>
<div id="d1d2-1" class="section level2">
<h2>D1D2</h2>
<pre class="r"><code>a &lt;- full_join(t_d1d2,ggd,by=&quot;Strain&quot;) %&gt;% filter(marker == &quot;D1D2&quot;)
p &lt;- ggplot(a, aes(x=pident, y=pcov, color=Phylum)) + geom_point(size = 3, alpha = 0.3)
p + stat_ellipse()</code></pre>
<p><img src="references_files/figure-html/unnamed-chunk-11-1.png" width="1008" /></p>
</div>
<div id="rpb2-1" class="section level2">
<h2>RPB2</h2>
<pre class="r"><code>a &lt;- full_join(t_rpb2,ggd,by=&quot;Strain&quot;) %&gt;% filter(marker == &quot;RPB2&quot;)
p &lt;- ggplot(a, aes(x=pident, y=pcov, color=Phylum)) + geom_point(size = 3, alpha = 0.3)
p + stat_ellipse()</code></pre>
<p><img src="references_files/figure-html/unnamed-chunk-12-1.png" width="1008" /></p>
</div>
</div>
<div id="can-nt-be-more-precise-than-unite-for-its" class="section level1 tabset">
<h1 class="tabset">Can nt be more precise than UNITE for ITS?</h1>
<div id="its1-2" class="section level2">
<h2>ITS1</h2>
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<pre class="r"><code>its1_unite &lt;- read.delim(&quot;REFERENCES/ALL_ITS1.blast_vs_UNITE&quot;, sep=&quot;\t&quot;, header=F)
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colnames(its1_unite) &lt;- c(&quot;Strain&quot;, &quot;sseqid&quot;, &quot;pident&quot;, &quot;length&quot;, &quot;mismatch&quot;, &quot;gapopen&quot;, &quot;qstart&quot;, &quot;qend&quot;, &quot;sstart&quot;, &quot;send&quot;, &quot;evalue&quot;, &quot;bitscore&quot;, &quot;qlen&quot;,&quot;taxonomy&quot;)
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t_its1_unite &lt;- its1_unite %&gt;% as_tibble() %&gt;% mutate(pcov = length/qlen) %&gt;% mutate(marker = &quot;ITS1&quot;, db = &quot;UNITE&quot;)

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its1_nt &lt;- read.delim(&quot;REFERENCES/ALL_ITS1.blast_vs_NT&quot;, sep=&quot;\t&quot;, header=F)
colnames(its1_nt) &lt;- c(&quot;Strain&quot;, &quot;sseqid&quot;, &quot;pident&quot;, &quot;length&quot;, &quot;mismatch&quot;, &quot;gapopen&quot;, &quot;qstart&quot;, &quot;qend&quot;, &quot;sstart&quot;, &quot;send&quot;, &quot;evalue&quot;, &quot;bitscore&quot;, &quot;qlen&quot;,&quot;taxonomy&quot;)
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t_its1_nt &lt;- its1_nt %&gt;% as_tibble() %&gt;% mutate(pcov = length/qlen) %&gt;% mutate(marker = &quot;ITS1&quot;, db = &quot;NT&quot;)

t &lt;- bind_rows(t_its1_unite, t_its1_nt)
p &lt;- ggplot(t, aes(x=pident, y=pcov, color=db)) + geom_point(size = 3, alpha = 0.3)
p + stat_ellipse()</code></pre>
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<p><img src="references_files/figure-html/unnamed-chunk-13-1.png" width="1008" /></p>
<pre class="r"><code>infos &lt;- full_join(t_its1_nt,ggd,by=&quot;Strain&quot;) %&gt;% filter(marker == &quot;ITS1&quot;) %&gt;% mutate(pcov = length/qlen) %&gt;% mutate(pident = pident/100)%&gt;% mutate(marker = &quot;ITS1&quot;) %&gt;%  mutate(SSpecies = sub(&quot;^(\\S*\\s+\\S+).*&quot;, &quot;\\1&quot;, taxonomy)) %&gt;% select(Species, SSpecies, pident, pcov)
 
infos %&gt;% datatable()</code></pre>
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vineae","Lachancea thermotolerans","Lachancea thermotolerans","Lachancea thermotolerans","Lachancea thermotolerans","Metschnikowia pulcherrima","Metschnikowia reukaufii","Naganishia albida","Papiliotrema laurentii","Pichia kluyveri","Pichia terricola","Rhodotorula babjevae","Saccharomycodes ludwigii","Zygotorulaspora florentina","Candida parapsilosis","Candida parapsilosis","Torulaspora delbrueckii","Pichia membranifaciens"],["Aspergillus sp.","Aspergillus elegans","Cladosporium allicinum","Cladosporium cladosporioides","Uncultured fungus","Aspergillus proliferans","Uncultured fungus","Aspergillus lentulus","Penicillium aurantiogriseum","Penicillium brevicompactum","Uncultured fungus","Penicillium chermesinum","Penicillium camemberti","Penicillium commune","Uncultured fungus","Penicillium sp.","Penicillium polonicum","Penicillium sublectaticum","Penicillium allii","Digitaria exilis","Digitaria exilis","Digitaria exilis","Penicillium commune","Uncultured fungus","Penicillium verrucosum","Penicillium neoechinulatum","Rhodotorula mucilaginosa","[Candida] saitoana","Yarrowia alimentaria","Yarrowia bubula","Yarrowia lipolytica","Yarrowia porcina","[Candida] aaseri","Starmerella apicola","Kazachstania saulgeensis","Saccharomyces bayanus","Saccharomyces pastorianus","Saccharomyces uvarum","Saturnispora diversa","Schizosaccharomyces japonicus","Meyerozyma caribbica","Hyphopichia pseudoburtonii","Hyphopichia pseudoburtonii","Kazachstania barnettii","Kazachstania sp.","Kazachstania bulderi","Kazachstania exigua","Kazachstania humilis","Kazachstania servazzii","Pichia norvegensis","Penicillium commune","Penicillium vinaceum","Penicillium simplicissimum","Aspergillus fumigatus","Cyberlindnera jadinii","Dipodascaceae sp.","Uncultured compost","Mucoraceae sp.","Mucor fuscus","Mucor lanceolatus","Mucor racemosus","Penicillium attenuatum","Penicillium camemberti","Uncultured fungus","Uncultured fungus","Uncultured fungus","[Candida] zeylanoides","Wickerhamiella azyma","Candida metapsilosis","Candida tropicalis","Aspergillus flavus","Aspergillus flavus","Uncultured fungus","Uncultured fungus","Diutina rugosa","Uncultured fungus","Hanseniaspora opuntiae","Hyphopichia burtonii","Meyerozyma carpophila","Mrakia frigida","Papiliotrema flavescens","Cryptococcus sp.","Uncultured fungus","Schwanniomyces etchellsii","Aureobasidium pullulans","Uncultured fungus","Trigonopsis vinaria","[Candida] glabrata","Kazachstania unispora","Kluyveromyces marxianus","Uncultured fungus","Meyerozyma guilliermondii","Meyerozyma guilliermondii","Millerozyma farinosa","Pichia fermentans","Pichia kudriavzevii","Saccharomycetales sp.","Rhodotorula mucilaginosa","Debaryomyces subglobosus","Aureobasidium leucospermi","[Candida] intermedia","Clavispora lusitaniae","Zygosaccharomyces rouxii","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Saccharomyces cerevisiae","Wickerhamomyces anomalus","Uncultured fungus","Uncultured fungus","[Candida] santamariae","Cyberlindnera saturnus","Diutina catenulata","Geotrichum sp.","Hanseniaspora valbyensis","Kluyveromyces dobzhanskii","Kluyveromyces lactis","Kregervanrija fluxuum","Lachancea fermentati","Lachancea waltii","Uncultured fungus","Nakazawaea ernobii","Uncultured fungus","Starmerella lactis-condensi","Candida tropicalis","Candida tropicalis","Candida tropicalis","Lachancea kluyveri","Starmerella stellata","Uncultured fungus","Rhodotorula glutinis","Uncultured fungus","Citeromyces matritensis","Cystobasidium minutum","Uncultured fungus","Hanseniaspora guilliermondii","Hanseniaspora osmophila","Uncultured fungus","Hanseniaspora vineae","Lachancea thermotolerans","Lachancea thermotolerans","Lachancea thermotolerans","Lachancea thermotolerans","Metschnikowia pulcherrima","Metschnikowia sp.","Naganishia albida","Uncultured Cryptococcus","Uncultured fungus","Pichia terricola","Uncultured fungus","Saccharomycodes ludwigii","Zygotorulaspora florentina","Candida metapsilosis","Candida metapsilosis","Uncultured fungus","Bactrocera tryoni"],[1,1,1,1,1,1,1,1,1,1,1,1,0.99602,1,1,1,1,1,1,1,0.88538,0.88538,1,1,1,1,1,1,1,1,1,0.99219,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.98819,1,1,1,1,1,1,1,1,1,0.99648,0.99648,1,1,1,0.99612,1,1,1,1,0.99375,1,1,1,1,1,1,1,0.9888,1,1,1,0.9958,1,1,1,0.98897,1,1,1,1,1,1,1,1,1,1,1,1,0.98773,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.99099,1,0.9918,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.97902,1,0.99471,1,1,1,1,1,1,0.88285,1,1],[1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1.02016129032258,1.02016129032258,1,1,1,1,1,0.973180076628352,0.977272727272727,0.894736842105263,1,0.948148148148148,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.888888888888889,1,1,1,0.218274111675127,1,1,1,1.00847457627119,1,1,1,1,1,1,1,0.985507246376812,1,1,1,1,1,1,1,0.583732057416268,0.110047846889952,1,1,1,1,1,1,1,0.897959183673469,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1.00225733634312,1,0.592233009708738,1,1,1,1,1,1,1,1,1,1,0.993265993265993,1,1,1,1,1,1,1,1,1,1,1,1,0.994082840236686,1,1,0.997267759562842,1,1,0.988200589970501,1,1,1,0.397306397306397,1,0.979452054794521,1,1,1,1,1,1,0.991769547325103,0.486373165618449,0.50104821802935,1,1]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Species<\/th>\n      <th>SSpecies<\/th>\n      <th>pident<\/th>\n      <th>pcov<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":10,"scrollX":true,"language":{"search":"Filter:"},"dom":"Bfrtip","buttons":["copy","csv","excel","pdf","print"],"columnDefs":[{"className":"dt-right","targets":[3,4]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
<p>72 hits have the same Species.</p>
</div>
<div id="its2-2" class="section level2">
<h2>ITS2</h2>
<pre class="r"><code>its2_unite &lt;- read.delim(&quot;REFERENCES/ALL_ITS2.blast_vs_UNITE&quot;, sep=&quot;\t&quot;, header=F)
colnames(its2_unite) &lt;- c(&quot;Strain&quot;, &quot;sseqid&quot;, &quot;pident&quot;, &quot;length&quot;, &quot;mismatch&quot;, &quot;gapopen&quot;, &quot;qstart&quot;, &quot;qend&quot;, &quot;sstart&quot;, &quot;send&quot;, &quot;evalue&quot;, &quot;bitscore&quot;, &quot;qlen&quot;,&quot;taxonomy&quot;)
t_its2_unite &lt;- its2_unite %&gt;% as_tibble() %&gt;% mutate(pcov = length/qlen) %&gt;% mutate(marker = &quot;ITS2&quot;, db = &quot;UNITE&quot;)

its2_nt &lt;- read.delim(&quot;REFERENCES/ALL_ITS2.blast_vs_NT&quot;, sep=&quot;\t&quot;, header=F)
colnames(its2_nt) &lt;- c(&quot;Strain&quot;, &quot;sseqid&quot;, &quot;pident&quot;, &quot;length&quot;, &quot;mismatch&quot;, &quot;gapopen&quot;, &quot;qstart&quot;, &quot;qend&quot;, &quot;sstart&quot;, &quot;send&quot;, &quot;evalue&quot;, &quot;bitscore&quot;, &quot;qlen&quot;,&quot;taxonomy&quot;)
t_its2_nt &lt;- its2_nt %&gt;% as_tibble() %&gt;% mutate(pcov = length/qlen) %&gt;% mutate(marker = &quot;ITS2&quot;, db = &quot;NT&quot;)

t &lt;- bind_rows(t_its2_unite, t_its2_nt)
p &lt;- ggplot(t, aes(x=pident, y=pcov, color=db)) + geom_point(size = 3, alpha = 0.3)
p + stat_ellipse()</code></pre>
<p><img src="references_files/figure-html/unnamed-chunk-14-1.png" width="1008" /></p>
<pre class="r"><code>infos &lt;- full_join(t_its2_nt,ggd,by=&quot;Strain&quot;) %&gt;% filter(marker == &quot;ITS2&quot;) %&gt;% mutate(pcov = length/qlen) %&gt;% mutate(pident = pident/100)%&gt;% mutate(marker = &quot;ITS2&quot;) %&gt;%  mutate(SSpecies = sub(&quot;^(\\S*\\s+\\S+).*&quot;, &quot;\\1&quot;, taxonomy)) %&gt;% select(Species, SSpecies, pident, pcov)
infos %&gt;% datatable() </code></pre>
<div id="htmlwidget-ba0d477eba07c0a41a12" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-ba0d477eba07c0a41a12">{"x":{"filter":"none","data":[["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","23","24","25","26","27","28","29","30","31","32","33","34","35","36","37","38","39","40","41","42","43","44","45","46","47","48","49","50","51","52","53","54","55","56","57","58","59","60","61","62","63","64","65","66","67","68","69","70","71","72","73","74","75","76","77","78","79","80","81","82","83","84","85","86","87","88","89","90","91","92","93","94","95","96","97","98","99","100","101","102","103","104","105","106","107","108","109","110","111","112","113","114","115","116","117","118","119","120","121","122","123","124","125","126","127","128","129","130","131","132","133","134","135","136","137","138","139","140","141","142","143","144"],["Aspergillus candidus","Aspergillus ochraceus","Cladosporium allicinum","Cladosporium cladosporioides","Cladosporium sphaerospermum","Eurotium amstelodami","Guehomyces pullulans","Neosartorya fischeri","Penicillium aurantiogriseum","Penicillium bialowiezense","Penicillium brevicompactum","Penicillium chermesinum","Penicillium chrysogenum_F7M11","Penicillium commune","Penicillium crustosum","Penicillium dipodomyicola","Penicillium expansum","Penicillium gladioli","Penicillium nordicum","Penicillium olsonii","Penicillium palitans","Penicillium salamii","Penicillium verrucosum","Penicillium viridicatum","Rhodotorula mucilaginosa","Torulopsis candida","Yarrowia alimentaria","Yarrowia bubula","Yarrowia lipolytica","Yarrowia porcina","Candida aaseri","Candida apicola","Kazachstania saulgeensis","Saccharomyces bayanus","Saccharomyces pastorianus","Saccharomyces uvarum","Saturnispora diversa","Schizosaccharomyces japonicus","Candida carpophila","Hyphopichia pseudoburtonii","Hyphopichia pseudoburtonii","Kazachstania barnettii","Kazachstania bozae","Kazachstania bulderi","Kazachstania exigua","Kazachstania humilis","Kazachstania servazzii","Pichia norvegensis","Penicillium camemberti var. camemberti","Penicillium nalgiovense","Penicillium solitum","Aspergillus fumigatus","Cyberlindnera jadinii","Geotrichum candidum","Lichtheimia corymbifera","Mucor circinelloides","Mucor fuscus","Mucor lanceolatus","Mucor racemosus","Penicillium antarcticum","Penicillium chrysogenum_CBS","Penicillium roqueforti","Trichosporon asahii","Yarrowia deformans","Candida zeylanoides","Candida azyma","Candida metapsilosis","Candida vini","Cryptococcus neoformans","Cystobasidium slooffiae","Dekkera bruxellensis","Dekkera bruxellensis","Diutina rugosa","Hanseniaspora occidentalis","Hanseniaspora opuntiae","Hyphopichia burtonii","Meyerozyma caribbica","Mrakia frigida","Papiliotrema flavescens","Papiliotrema terrestris","Rhodotorula nothofagi","Schwanniomyces etchellsii","Starmerella bacillaris","Symmetrospora coprosmae","Trigonopsis vinaria","Candida glabrata","Kazachstania unispora","Kluyveromyces marxianus","Lodderomyces elongisporus","Meyerozyma guilliermondii","Millerozyma farinosa","Pichia fermentans","Pichia kudriavzevii","Pichia occidentalis","Rhodotorula mucilaginosa var. mucilaginosa","Debaryomyces hansenii","Aureobasidium pullulans","Candida intermedia","Clavispora lusitaniae","Zygosaccharomyces rouxii","Saccharomyces cerevisiae","Wickerhamomyces anomalus","Aciculoconidium aculeatum","Barnettozyma californica","Candida santamariae","Cyberlindnera mrakii","Diutina catenulata","Geotrichum klebahnii","Hanseniaspora valbyensis","Kluyveromyces dobzhanskii","Kluyveromyces lactis var. lactis","Kregervanrija fluxuum","Lachancea fermentati","Lachancea waltii","Naganishia globosa","Nakazawaea holstii","Rhodotorula diobovata","Starmerella lactis-condensi","Candida tropicalis","Lachancea kluyveri","Starmerella stellata","Candida sake","Rhodotorula glutinis","Sporobolomyces roseus","Citeromyces matritensis","Cystobasidium minutum","Filobasidium magnum","Hanseniaspora guilliermondii","Hanseniaspora osmophila","Hanseniaspora uvarum","Hanseniaspora vineae","Lachancea thermotolerans","Metschnikowia pulcherrima","Metschnikowia reukaufii","Naganishia albida","Papiliotrema laurentii","Pichia kluyveri","Pichia terricola","Rhodotorula babjevae","Saccharomycodes ludwigii","Zygotorulaspora florentina","Candida parapsilosis","Torulaspora delbrueckii","Pichia membranifaciens"],["Aspergillus tritici","Aspergillus elegans","Cladosporium sp.","Cladosporium sp.","Cladosporium sphaerospermum","Aspergillus ruber","Uncultured fungus","Aspergillus fischeri","Penicillium bialowiezense","Penicillium bialowiezense","Penicillium brevicompactum","Penicillium sp.","Penicillium olsonii","Penicillium sp.","Penicillium expansum","Penicillium camemberti","Penicillium sp.","Penicillium gladioli","Penicillium sp.","Didymella pinodella","Penicillium sp.","Penicillium olsonii","Penicillium sp.","Penicillium sp.","Rhodotorula mucilaginosa","[Candida] saitoana","Yarrowia alimentaria","Yarrowia bubula","Yarrowia lipolytica","Yarrowia porcina","[Candida] aaseri","Starmerella apicola","Kazachstania saulgeensis","Saccharomyces bayanus","Saccharomyces pastorianus","Saccharomyces bayanus","Saturnispora diversa","Schizosaccharomyces japonicus","Meyerozyma smithsonii","Hyphopichia pseudoburtonii","Hyphopichia pseudoburtonii","Uncultured eukaryote","Kazachstania sp.","Kazachstania bulderi","Kazachstania exigua","Kazachstania humilis","Kazachstania servazzii","Pichia norvegensis","Penicillium camemberti","Penicillium sp.","Penicillium simplicissimum","Aspergillus fumigatus","Cyberlindnera jadinii","Geotrichum candidum","Lichtheimia corymbifera","Mucor sp.","Mucor fuscus","Mucor fuscus","Mucor racemosus","Penicillium atrovenetum","Penicillium griseoroseum","Penicillium roqueforti","Trichosporon asahii","Yarrowia deformans","[Candida] zeylanoides","Wickerhamiella azyma","Candida metapsilosis","Kregervanrija fluxuum","Cryptococcus neoformans","Cystobasidium slooffiae","Brettanomyces bruxellensis","Brettanomyces bruxellensis","Diutina rugosa","Hanseniaspora occidentalis","Fungal sp.","Hyphopichia burtonii","Meyerozyma smithsonii","Mrakia frigida","Papiliotrema flavescens","Papiliotrema terrestris","Curvibasidium pallidicorallinum","Schwanniomyces etchellsii","Starmerella bacillaris","Uncultured fungus","Trigonopsis vinaria","[Candida] glabrata","Kazachstania unispora","Kluyveromyces marxianus","Lodderomyces elongisporus","Meyerozyma guilliermondii","Millerozyma farinosa","Pichia fermentans","Pichia kudriavzevii","Pichia kudriavzevii","Rhodotorula mucilaginosa","Debaryomyces hansenii","Aureobasidium namibiae","[Candida] intermedia","Clavispora lusitaniae","Zygosaccharomyces rouxii","Saccharomyces cerevisiae","Wickerhamomyces anomalus","Uncultured fungus","Barnettozyma californica","[Candida] aaseri","Cyberlindnera mrakii","Diutina catenulata","Geotrichum klebahnii","Hanseniaspora valbyensis","Kluyveromyces dobzhanskii","Kluyveromyces lactis","Kregervanrija fluxuum","Lachancea fermentati","Lachancea waltii","Uncultured fungus","Uncultured fungus","Rhodotorula diobovata","Starmerella lactis-condensi","Candida tropicalis","Lachancea kluyveri","Starmerella stellata","Uncultured fungus","Rhodotorula glutinis","Sporobolomyces roseus","Citeromyces matritensis","Cystobasidium minutum","Filobasidium magnum","Hanseniaspora opuntiae","Hanseniaspora osmophila","Hanseniaspora uvarum","Hanseniaspora vineae","Lachancea thermotolerans","Metschnikowia ziziphicola","Metschnikowia reukaufii","Uncultured fungus","Papiliotrema laurentii","Pichia kluyveri","Pichia terricola","Rhodotorula babjevae","Saccharomycodes ludwigii","Zygotorulaspora florentina","Candida parapsilosis","Uncultured fungus","Pichia membranifaciens"],[1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.97821,1,1,1,1,1,1,1,1,1,0.99692,1,1,1,0.99687,0.99688,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.99728,1,1,1,1,1,1,1,1,1,1,0.99677,1,1,1,1,1,1,1,1,0.99621,1,1,1,1,1,1,1,1,0.9918,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.9876,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1],[1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.983333333333333,0.962216624685139,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.806122448979592,0.193877551020408,1,1,1,1,1,1,1,1,1,1,1,1,0.990415335463259,1,1,1,1,1,1,1,1,1.00380228136882,1,1,1,1,1,1,1,1,0.592233009708738,1,1,1,1,1,1,1,1,1,1,0.980281690140845,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Species<\/th>\n      <th>SSpecies<\/th>\n      <th>pident<\/th>\n      <th>pcov<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":10,"scrollX":true,"language":{"search":"Filter:"},"dom":"Bfrtip","buttons":["copy","csv","excel","pdf","print"],"columnDefs":[{"className":"dt-right","targets":[3,4]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
<p>88 hits have the same Species.</p>
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