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opencc-by-4.0Oct 2024View details →

TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing

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opencc-zeroJan 2024View details →

Linked collectors and determiners for: Zoologische Staatssammlung Muenchen - International Barcode of Life (iBOL) - Barcode of Life Project Specimen Data.

Natural history specimen data linked to collectors and determiners held within, "Zoologische Staatssammlung Muenchen - International Barcode of Life (iBOL) - Barcode of Life Project Specimen Data". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/f29ab192-5964-40ae-a397-fa48ffdf0661">https://bionomia.net/dataset/f29ab192-5964-40ae-a397-fa48ffdf0661</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/f29ab192-5964-40ae-a397-fa48ffdf0661">https://gbif.org/dataset/f29ab192-5964-40ae-a397-fa48ffdf0661</a>. Formatted as a Frictionless Data package.

opencc-zeroJan 2024View details →

Linked collectors and determiners for: Monophyly, review, six new species and DNA barcode of micropterous Afromontane Afropictinus (Heteroptera: Aradidae).

Natural history specimen data linked to collectors and determiners held within, "Monophyly, review, six new species and DNA barcode of micropterous Afromontane Afropictinus (Heteroptera: Aradidae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/eeff9760-db0d-4b4d-ac0f-2ec2b7c729cd">https://bionomia.net/dataset/eeff9760-db0d-4b4d-ac0f-2ec2b7c729cd</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/eeff9760-db0d-4b4d-ac0f-2ec2b7c729cd">https://gbif.org/dataset/eeff9760-db0d-4b4d-ac0f-2ec2b7c729cd</a>. Formatted as a Frictionless Data package.

opennotspecifiedOct 2024View details →

TABLE 2 in A twin of Polydora hoplura (Annelida: Spionidae) from the Arabian (Persian) Gulf, with review of primers used for barcoding of Spionidae

TABLE 2. Uncorrected pairwise average genetic distances (p, in %) between population clades of COI, 16S, 18S, 28S and Histone 3 gene sequences of Polydora species.<table><tbody><tr><th>Group*</th><th>Species</th><th>Country</th><th>N</th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th></tr></tbody><tbody><tr><th>COI</th><td></td><td></td><td></td><td>1</td><td>2</td><td>3</td><td>5</td><td>6</td><td>9</td><td></td><td></td><td></td></tr><tr><th>1</th><td>P. brevipalpa</td><td>Russia</td><td>3</td><td>0.65</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>2</th><td>P. hoplura</td><td>Brazil</td><td>3</td><td>17.58</td><td>0.00</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>3</th><td>P. hoplura</td><td>France</td><td>2</td><td>17.75</td><td>1.54</td><td>0.62</td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>5</th><td>P. hoplura</td><td>South Korea</td><td>1</td><td>17.81</td><td>5.82</td><td>6.22</td><td>−</td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>6</th><td>P. hoplura</td><td>USA, California</td><td>1</td><td>17.81</td><td>5.82</td><td>6.22</td><td>0.00</td><td>−</td><td></td><td></td><td></td><td></td></tr><tr><th>9</th><td>P. mohammadi</td><td>Kuwait</td><td>10</td><td>19.10</td><td>12.26</td><td>12.51</td><td>11.77 11.77</td><td>1.48</td><td></td><td></td><td></td></tr><tr><th>16S</th><td></td><td></td><td></td><td>1</td><td>2</td><td>3</td><td>4</td><td>5</td><td>6</td><td>7</td><td>8</td><td>9</td></tr><tr><th>1</th><td>P. brevipalpa</td><td>Russia</td><td>3</td><td>0.00</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>2</th><td>P. hoplura</td><td>Brazil</td><td>5</td><td>10.16</td><td>0.00</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>3</th><td>P. hoplura</td><td>France</td><td>7</td><td>10.51</td><td>0.35</td><td>0.12</td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>4</th><td>P. hoplura</td><td>France/Italy</td><td>11</td><td>10.38</td><td>0.22</td><td>0.19</td><td>0.22</td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>5</th><td>P. hoplura</td><td>South Korea</td><td>16</td><td>9.98</td><td>2.67</td><td>3.02</td><td>2.89</td><td>0.21</td><td></td><td></td><td></td><td></td></tr><tr><th>6</th><td>P. hoplura</td><td>USA, California</td><td>4</td><td>10.06</td><td>2.03</td><td>2.38</td><td>2.25</td><td>0.81</td><td>1.49</td><td></td><td></td><td></td></tr><tr><th>7</th><td>P. lingshuiensis</td><td>China</td><td>5</td><td>12.60</td><td>8.54</td><td>8.19</td><td>8.31</td><td>9.42</td><td>9.23</td><td>0.33</td><td></td><td></td></tr><tr><th>8</th><td>P. lingulicola</td><td>Japan</td><td>7</td><td>12.60</td><td>13.01</td><td>13.01</td><td>13.01 14.46 14.13</td><td>14.39</td><td>0.00</td><td></td></tr><tr><th>9</th><td>P. mohammadi</td><td>Kuwait</td><td>10</td><td>10.37</td><td>4.76</td><td>5.10</td><td>4.98</td><td>4.98</td><td>4.96</td><td>10.04</td><td>14.31</td><td>0.53</td></tr><tr><th>18S</th><td></td><td></td><td></td><td>1</td><td>2</td><td>3</td><td>4</td><td>5</td><td>6</td><td>7</td><td>8</td><td>9</td></tr><tr><th>1</th><td>P. brevipalpa</td><td>Russia</td><td>3</td><td>0.00</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>2</th><td>P. hoplura</td><td>Brazil</td><td>5</td><td>1.08</td><td>0.00</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>3</th><td>P. hoplura</td><td>France</td><td>5</td><td>1.08</td><td>0.00</td><td>0.00</td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>4</th><td>P. hoplura</td><td>France/Italy</td><td>4</td><td>1.08</td><td>0.00</td><td>0.00</td><td>0.00</td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>5</th><td>P. hoplura</td><td>South Korea</td><td>12</td><td>1.07</td><td>0.02</td><td>0.02</td><td>0.02</td><td>0.03</td><td></td><td></td><td></td><td></td></tr><tr><th>6</th><td>P. hoplura</td><td>USA, California</td><td>3</td><td>1.08</td><td>0.00</td><td>0.00</td><td>0.00</td><td>0.02</td><td>0.00</td><td></td><td></td><td></td></tr><tr><th>7</th><td>P. lingshuiensis</td><td>China</td><td>5</td><td>1.85</td><td>1.40</td><td>1.40</td><td>1.40</td><td>1.42</td><td>1.40</td><td>0.00</td><td></td><td></td></tr><tr><th>8</th><td>P. lingulicola</td><td>Japan</td><td>7</td><td>1.21</td><td>0.89</td><td>0.89</td><td>0.89</td><td>0.91</td><td>0.89</td><td>1.59</td><td>0.00</td><td></td></tr><tr><th>9</th><td>P. mohammadi</td><td>Kuwait</td><td>4</td><td>1.02</td><td>0.06</td><td>0.06</td><td>0.06</td><td>0.08</td><td>0.06</td><td>1.47</td><td>0.96</td><td>0.00</td></tr><tr><th>28S</th><td></td><td></td><td></td><td>1</td><td>2</td><td>3</td><td>4</td><td>5</td><td>6</td><td>7</td><td>8</td><td>9</td></tr><tr><th>1</th><td>P. brevipalpa</td><td>Russia</td><td>3</td><td>0.00</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>2</th><td>P. hoplura</td><td>Brazil</td><td>5</td><td>2.63</td><td>0.00</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>3</th><td>P. hoplura</td><td>France</td><td>7</td><td>2.63</td><td>0.00</td><td>0.00</td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>4</th><td>P. hoplura</td><td>France/Italy</td><td>11</td><td>2.63</td><td>0.00</td><td>0.00</td><td>0.00</td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>5</th><td>P. hoplura</td><td>South Korea</td><td>15</td><td>2.66</td><td>0.03</td><td>0.03</td><td>0.03</td><td>0.06</td><td></td><td></td><td></td><td></td></tr><tr><th>6</th><td>P. hoplura</td><td>USA, California</td><td>3</td><td>2.63</td><td>0.00</td><td>0.00</td><td>0.00</td><td>0.03</td><td>0.00</td><td></td><td></td><td></td></tr><tr><th>7</th><td>P. lingshuiensis</td><td>China</td><td>5</td><td>3.51</td><td>0.88</td><td>0.88</td><td>0.88</td><td>0.91</td><td>0.88</td><td>0.00</td><td></td><td></td></tr><tr><th>8</th><td>P. lingulicola</td><td>Japan</td><td>7</td><td>3.51</td><td>1.75</td><td>1.75</td><td>1.75</td><td>1.78</td><td>1.75</td><td>2.63</td><td>0.00</td><td></td></tr><tr><th>9</th><td>P. mohammadi</td><td>Kuwait</td><td>7</td><td>2.63</td><td>0.00</td><td>0.00</td><td>0.00</td><td>0.03</td><td>0.00</td><td>0.88</td><td>1.75</td><td>0.00</td></tr><tr><th>H3</th><td></td><td></td><td></td><td>1</td><td>2</td><td>3</td><td>4</td><td>5</td><td>6</td><td>9</td><td></td><td></td></tr><tr><th>1</th><td>P. brevipalpa</td><td>Russia</td><td>3</td><td>0.00</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>2</th><td>P. hoplura</td><td>Brazil</td><td>4</td><td>12.16</td><td>0.00</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>3</th><td>P. hoplura</td><td>France</td><td>5</td><td>11.89</td><td>0.27</td><td>0.14</td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>4</th><td>P. hoplura</td><td>France/Italy</td><td>6</td><td>11.82</td><td>0.34</td><td>0.07</td><td>0.00</td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>5</th><td>P. hoplura</td><td>South Korea</td><td>11</td><td>11.89</td><td>0.34</td><td>0.21</td><td>0.18</td><td>0.32</td><td></td><td></td><td></td><td></td></tr><tr><th>6</th><td>P. hoplura</td><td>USA, California</td><td>4</td><td>11.82</td><td>0.34</td><td>0.07</td><td>0.00</td><td>0.18</td><td>0.00</td><td></td><td></td><td></td></tr><tr><th>9</th><td>P. mohammadi</td><td>Kuwait</td><td>3</td><td>12.39</td><td>1.46</td><td>1.73</td><td>1.80</td><td>1.80</td><td>1.80</td><td>0.23</td><td></td><td></td></tr></tbody></table>

opennotspecifiedOct 2024View details →

TABLE 1 in A twin of Polydora hoplura (Annelida: Spionidae) from the Arabian (Persian) Gulf, with review of primers used for barcoding of Spionidae

TABLE 1. Taxa, sampling location data, museum registration numbers of voucher specimens and GenBank accession numbers of sequences used in the analysis.<table><tbody><tr><th>Group* VIR ID Species</th><th>Museum</th><th>Locality</th><th>GenBank accession number**, *** COI 16S 18S</th><th>28S</th><th>Histone 3</th></tr></tbody><tbody><tr><th>1</th><td>18049</td><td>P. brevipalpa</td><td>MIMB 28135</td><td>Russia, Primorye, Sea of Japan, Vostok Bay</td><td>PP441928−30</td><td>OM418504−06</td><td>OM418464−66</td><td>OM418398−00</td><td>OM416709−11</td></tr><tr><th>2</th><td>19332</td><td>P. hoplura</td><td>Genbank</td><td>Brazil, São Paulo, São Sebastião, Ilhabela</td><td>PP441932−34</td><td>OM418534−36</td><td>OM418479−81</td><td>OM418427−29</td><td>OM416725−27</td></tr><tr><th>2</th><td>19334</td><td>P. hoplura</td><td>MIMB 28149</td><td>Brazil, São Paulo, São Sebastião, Ilhabela</td><td></td><td>OM418537,38</td><td>OM418482,83</td><td>OM418430,31</td><td>OM416728</td></tr><tr><th>3</th><td>18609</td><td>P. hoplura</td><td>MIMB 33031</td><td>France, Aquitaine, Bay of Biscay, Arcachon</td><td></td><td>OM418516−18</td><td>OM418471−73</td><td>OM418409−11</td><td>OM416716−18</td></tr><tr><th>3</th><td>20233</td><td>P. hoplura</td><td>MIMB 33064</td><td>France, Aquitaine, Bay of Biscay, Legallais</td><td>PP441937,38</td><td>OM418547,48</td><td>OM418489,90</td><td>OM418439,40</td><td>OM416734,35</td></tr><tr><th>3</th><td>18596</td><td>P. hoplura</td><td>MIMB 33030</td><td>France, Brittany, La Manche, Roscoff</td><td></td><td>OM418514−15</td><td></td><td>OM418407−08</td><td></td></tr><tr><th>4</th><td>18634</td><td>P. hoplura</td><td>MIMB 33033</td><td>France, Languedoc−Roussillon, Gulf of Lion, Leucate</td><td></td><td>OM418519−23</td><td>OM418474,75</td><td>OM418412−16</td><td>OM416719−21</td></tr><tr><th>4</th><td>18672</td><td>P. hoplura</td><td>MIMB 33029</td><td>Italy, Apulia, Ionian Sea, Taranto</td><td></td><td>OM418527−32</td><td></td><td>OM418420−25</td><td></td></tr><tr><th>4</th><td>18660</td><td>P. hoplura</td><td>MIMB 28148</td><td>Italy, Tyrrhenian Sea, Campania, Ischia</td><td></td><td>OM418524−26</td><td>OM418476,77</td><td>OM418417−19</td><td>OM416722,23</td></tr><tr><th>4</th><td>20313</td><td>P. hoplura</td><td>SMF 24359</td><td>Italy, Tyrrhenian Sea, Campania, Ischia</td><td></td><td>OM418553</td><td></td><td>OM418445</td><td>OM416736</td></tr><tr><th>5</th><td>18019</td><td>P. hoplura</td><td>MIMB 33035</td><td>South Korea, East Sea, Bogyl</td><td></td><td>OM418496−99</td><td>OM418457−59</td><td>OM418390−93</td><td>OM416703−05</td></tr><tr><th>5</th><td>20000</td><td>P. hoplura</td><td>MIMB 33056</td><td>South Korea, East Sea, Geoje Is.</td><td>PP441936</td><td>OM418546</td><td>OM418488</td><td>OM418438</td><td>OM416733</td></tr><tr><th>5</th><td>18246</td><td>P. hoplura</td><td>MIMB 33041</td><td>South Korea, East Sea, Geoje Is.</td><td></td><td>OM418507−09</td><td></td><td>OM418401,02</td><td></td></tr><tr><th>5</th><td>18032</td><td>P. hoplura</td><td>MIMB 33036</td><td>South Korea, East Sea, Keumil</td><td></td><td>OM418500−03</td><td>OM418460−63</td><td>OM418394−97</td><td>OM416706−08</td></tr><tr><th>5</th><td>18283</td><td>P. hoplura</td><td>MIMB 33038</td><td>South Korea, East Sea, Seohwa</td><td></td><td>OM418511−13</td><td>OM418468−70</td><td>OM418404−06</td><td>OM416713−15</td></tr><tr><th>5</th><td>18277</td><td>P. hoplura</td><td>MIMB 33040</td><td>South Korea, East Sea, Yeosu</td><td></td><td>OM418510</td><td>OM418467</td><td>OM418403</td><td>OM416712</td></tr><tr><th>6</th><td>20710</td><td>P. hoplura</td><td>MIMB 39108</td><td>USA, California, Los Angeles</td><td></td><td>OM418554,55</td><td>OM418491</td><td>OM418446</td><td>OM416737,38</td></tr><tr><th>6</th><td>20715</td><td>P. hoplura</td><td>MIMB 39109</td><td>USA, California, Los Angeles</td><td>PP441941</td><td>OM418556,57</td><td>OM418492,93</td><td>OM418447,48</td><td>OM416739,40</td></tr><tr><th>7</th><td>23931</td><td>P.</td><td>Genbank</td><td>China, Hainan, Hainan Is., Xincun Bay</td><td></td><td>KF562230,32</td><td>KF562236,37</td><td>KF562243,46</td><td></td></tr><tr><th></th><td></td><td>lingshuiensis</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>7</th><td>23932</td><td>P.</td><td>Genbank</td><td>China, Hainan, Hainan Is., Xincun Bay</td><td></td><td>KF562229,31,33</td><td>KF562238−40</td><td>KF562244,45,47</td><td></td></tr><tr><th></th><td></td><td>lingshuiensis</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>8</th><td>24908</td><td>P. lingulicola</td><td>Genbank</td><td>Japan, Kumamoto, Kyushu Is., Ariake Sea</td><td></td><td>LC500924−30</td><td>LC500909−15</td><td>LC500916−22</td><td></td></tr><tr><th>9</th><td>18814</td><td>P. mohammadi</td><td>MIMB 33067</td><td>Kuwait, Arabian Gulf, Al-Judailiat</td><td>PP441931</td><td>OM418533</td><td>OM418478</td><td>OM418426</td><td>OM416724</td></tr><tr><th>9</th><td>19861</td><td>P. mohammadi</td><td>MIMB 33068</td><td>Kuwait, Arabian Gulf, Auhah Is.</td><td>PP441935</td><td>OM418545</td><td>OM418487</td><td>OM418437</td><td>OM416732</td></tr><tr><th>9</th><td>20309</td><td>P. mohammadi</td><td>MIMB 42694</td><td>Kuwait, Arabian Gulf, Ras Ajuza</td><td>PP441939,40</td><td>OM418549−52</td><td></td><td>OM418441−44</td><td></td></tr><tr><th>9</th><td>24102</td><td>P. mohammadi</td><td>MIMB 42696</td><td>Kuwait, Arabian Gulf, Failaka Is.</td><td>PP441942-45</td><td>PP444465,66</td><td></td><td></td><td></td></tr><tr><th>9</th><td>25282</td><td>P. mohammadi</td><td>MIMB 42697</td><td>Kuwait, Arabian Gulf, Failaka Is.</td><td>PP441946</td><td>OM418559</td><td>OM418495</td><td>OM418449</td><td>OM416741</td></tr><tr><th>9</th><td>25283</td><td>P. mohammadi</td><td>MIMB 42698</td><td>Kuwait, Arabian Gulf, Failaka Is.</td><td>PP441947</td><td>OM418558</td><td>OM418494</td><td></td><td></td></tr></tbody></table>

opencc-zeroDec 2015View details →

Data from: Promise and challenge of DNA barcoding in Venus slipper (Paphiopedilum)

Orchidaceae are one of the largest families of flowering plants, with over 27,000 species described and all orchids are listed in CITES. Moreover, the seedlings of orchid species from the same genus are similar. The objective of DNA barcoding is rapid, accurate, and automated species identification, which may be used to identify illegally traded endangered species from vegetative specimens of Paphiopedilum (Venus slipper), a flagship group for plant conservation with high ornamental and commercial values. Here, we selected eight chloroplast barcodes and nrITS to evaluate their suitability in Venus slippers. The results indicate that all tested barcodes had no barcoding gap and the core plant barcodes showed low resolution for the identification of Venus slippers (18.86%). Of the single-locus barcodes, nrITS is the most efficient for the species identification of the genus (52.27%), whereas matK + atpF-atpH is the most efficient multi-locus combination (28.97%). Therefore, we recommend the combination of matK + atpF-atpH + ITS as a barcode for Venus slippers. Furthermore, there is an upper limit of resolution of the candidate barcodes, and only half of the taxa with multiple samples were identified successfully. The low efficiency of these candidate barcodes in Venus slippers may be caused by relatively recent speciation, the upper limit of the barcodes, and/or the sampling density. Although the discriminatory power is relatively low, DNA barcoding may be a promising tool to identify species involved in illegal trade, which has broad applications and is valuable for orchid conservation.

opencc-zeroDec 2015View details →

Data from: Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species

Today most population genomic studies of nonmodel organisms either sequence a subset of the genome deeply in each individual or sequence pools of unlabelled individuals. With a step-by-step workflow, we illustrate how low-coverage whole-genome sequencing of hundreds of individually barcoded samples is now a practical alternative strategy for obtaining genomewide data on a population scale. We used a highly efficient protocol to generate high-quality libraries for ~6.5 USD from each of 876 Atlantic silversides (a teleost fish with a genome size ~730 Mb) that we sequenced to 1–4× genome coverage. In the absence of a reference genome, we developed a bioinformatic pipeline for mapping the genomic reads to a de novo assembled reference transcriptome. This provides an 'in silico' method for exome capture that avoids the complexities and expenses of using wet chemistry for target isolation. Using novel tools for analysis of low-coverage data, we extracted population allele frequencies, individual genotype likelihoods and polymorphism data for 2 504 335 SNPs across the exome for the 876 fish. To illustrate the use of the resulting data, we present a preliminary analysis of geographical patterns in the exome data and a comparison of complete mitochondrial genome sequences for each individual (constructed from the low-coverage data) that show population colonization patterns along the US east coast. With a total cost per sample of less than 50 USD (including sequencing) and ability to prepare 96 libraries in only 5 h, our approach adds a viable new option to the population genomics toolbox.

opencc-zeroDec 2014View details →

Data from: Accelerating plant DNA barcode reference library construction using herbarium specimens: improved experimental techniques

A well-covered reference library is crucial for successful identification of species by DNA barcoding. The biggest difficulty in building such a reference library is the lack of materials of organisms. Herbarium collections are potentially an enormous resource of materials. In this study, we demonstrate that it is likely to build such reference libraries using the reconstructed (self-primed PCR amplified) DNA from the herbarium specimens. We used 179 rosaceous specimens to test the effects of DNA reconstruction, 420 randomly sampled specimens to estimate the usable percentage and another 223 specimens of true cherries (Cerasus, Rosaceae) to test the coverage of usable specimens to the species. The barcode rbcLb (the central four-sevenths of rbcL gene) and matK was each amplified in two halves and sequenced on Roche GS 454 FLX+. DNA from the herbarium specimens was typically shorter than 300 bp. DNA reconstruction enabled amplification fragments of 400–500 bp without bringing or inducing any sequence errors. About one-third of specimens in the national herbarium of China (PE) were proven usable after DNA reconstruction. The specimens in PE cover all Chinese true cherry species and 91.5% of vascular species listed in Flora of China. It is very possible to build well-covered reference libraries for DNA barcoding of vascular species in China. As exemplified in this study, DNA reconstruction and DNA-labelled next-generation sequencing can accelerate the construction of local reference libraries. By putting the local reference libraries together, a global library for DNA barcoding becomes closer to reality.

opencc-zeroDec 2016View details →

Data from: Genetic barcoding of dark-spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies

Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.

opennotspecifiedApr 2006View details →

FIGURE 12 in DNA barcodes: Evaluating the potential of COI to diffentiate closely related species of Elachista (Lepidoptera: Gelechioidea: Elachistidae) from Australia

FIGURE 12. Larval mines of the taxa of the Elachista zigzagger complex. A: A1; B: A2; C: B2.

opennotspecifiedApr 2006View details →

FIGURE 9 in DNA barcodes: Evaluating the potential of COI to diffentiate closely related species of Elachista (Lepidoptera: Gelechioidea: Elachistidae) from Australia

FIGURE 9. Female genitalia of the taxa of the Elachista zigzagger complex. A: B1; B: B2; C: B3.

opennotspecifiedJun 2013View details →

FIGURE 3. Rhododendron baihuaense. A, Habitat. B, Leaves. C, Flowers. D in A new species of Rhododendron (Ericaceae) from the Gaoligong Mountains, Yunnan, China, supported by morphological and DNA barcoding data

FIGURE 3. Rhododendron baihuaense. A, Habitat. B, Leaves. C, Flowers. D, Fruits.

opennotspecifiedDec 2013View details →

FIGURE 1 in Pinellia hunanensis (Araceae), a new species supported by morphometric analysis and DNA barcoding

FIGURE 1. Sketch map of East Asia, indicating distribution of Pinellia.

Figure 2 from: Oliveira D, Chaves C, Pinto J, Paupério J, Fonseca N, Beja P, Ferreira S (2021) DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida). ZooKeys 1054: 67-84. https://doi.org/10.3897/zookeys.1054.64608

Figure 2 Neighbour-joining tree of all obtained DNA sequences for Portuguese Neuroptera and Raphidioptera. Neighbour-joining tree constructed in PAUP* 4.0a167. Non-highlighted terminal branches represent the two outgroup sequences.

Figure 3 from: Oliveira D, Chaves C, Pinto J, Paupério J, Fonseca N, Beja P, Ferreira S (2021) DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida). ZooKeys 1054: 67-84. https://doi.org/10.3897/zookeys.1054.64608

Figure 3 Neighbour-joining tree of Chrysopidae DNA barcode sequences. Neighbour-joining tree constructed in PAUP* 4.0a167 and contrasted with the results from the ABGD analysis and BIN attribution. Bootstrap values under 90% omitted.

Figure 1 from: Oliveira D, Chaves C, Pinto J, Paupério J, Fonseca N, Beja P, Ferreira S (2021) DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida). ZooKeys 1054: 67-84. https://doi.org/10.3897/zookeys.1054.64608

Figure 1 Map of continental Portugal with sampling locations A sampling locations of the 8 captured specimens of Raphidioptera (N = 8) B sampling locations of the 235 captured specimens of Neuroptera (N = 67).

opencc-zeroAug 2021View details →

Supplementary material 2 from: Oliveira D, Chaves C, Pinto J, Paupério J, Fonseca N, Beja P, Ferreira S (2021) DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida). ZooKeys 1054: 67-84. https://doi.org/10.3897/zookeys.1054.64608

Genetic distances

opencc-zeroAug 2021View details →

Supplementary material 1 from: Oliveira D, Chaves C, Pinto J, Paupério J, Fonseca N, Beja P, Ferreira S (2021) DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida). ZooKeys 1054: 67-84. https://doi.org/10.3897/zookeys.1054.64608

Summary table of all used sequences and specimens, with country of origin

Figure 4 from: Oliveira D, Chaves C, Pinto J, Paupério J, Fonseca N, Beja P, Ferreira S (2021) DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida). ZooKeys 1054: 67-84. https://doi.org/10.3897/zookeys.1054.64608

Figure 4 Neighbour-joining tree of Hemerobiidae DNA barcode sequences. Neighbour-joining tree constructed in PAUP* 4.0a167 and contrasted with the results from the ABGD analysis and BIN attribution. Bootstrap values under 90% omitted. Subtrees were collapsed for the monophyletic morphologically identified species. Triangle size for each species is proportional to the intraspecific distance.