Biases underlying species detection using fluorescent amplified-fragment length polymorphisms yielded from roots.
Identifieur interne : 001E78 ( Main/Exploration ); précédent : 001E77; suivant : 001E79Biases underlying species detection using fluorescent amplified-fragment length polymorphisms yielded from roots.
Auteurs : Justine Karst ; Pak Chow ; Simon M. Landh UsserSource :
- Plant methods [ 1746-4811 ] ; 2015.
Abstract
BACKGROUND
Roots of different plant species are typically morphologically indistinguishable. Of the DNA-based techniques, fluorescent amplified-fragment length polymorphisms (FAFLPs) are considered reliable, high throughput, inexpensive methods to identify roots from mixed species samples. False-negatives, however, are not uncommon and their underlying causes are poorly understood. We investigated several sources of potential biases originating in DNA extraction and amplification. Specifically, we examined the effects of sample storage, tissue, and species on DNA yield and purity, and the effects of DNA concentration and fragment size on amplification of three non-coding chloroplast regions (trnT-trnL intergenic spacer, trnL intron, and trnL-trnF intergenic spacer).
RESULTS
We found that sample condition, tissue and species all affected DNA yield. A single freeze-thaw reduces DNA yield, DNA yield is less for roots than shoots, and species vary in the amount of DNA yielded from extractions. The effects of template DNA concentration, species identity, and their interaction on amplicon yield differed across the three chloroplast regions tested. We found that the effect of species identity on amplicon production was generally more pronounced than that of DNA concentration. Though these factors influenced DNA yield, they likely do not have a pronounced effect on detection success of fragments and only underscore the restriction on the use of FAFLPs for measuring species presence rather than their abundance. However, for two of the regions tested-the trnT-trnL intergenic spacer and the trnL intron-size-based fragment competition occurred and the likelihood of detection was higher for smaller than larger fragments. This result reveals a methodological bias when using FAFLPs.
CONCLUSIONS
To avoid potential bias with the use of FAFLPs, we recommend users check for the disproportionate absence of species detected belowground versus aboveground as a function of fragment size, and explore other regions, aside from the trnT-trnL intergenic spacer and trnL intron, for amplification.
DOI: 10.1186/s13007-015-0079-1
PubMed: 26113872
PubMed Central: PMC4480983
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Biases underlying species detection using fluorescent amplified-fragment length polymorphisms yielded from roots.</title><author><name sortKey="Karst, Justine" sort="Karst, Justine" uniqKey="Karst J" first="Justine" last="Karst">Justine Karst</name><affiliation><nlm:affiliation>Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, AB T6G 2E3 Canada.</nlm:affiliation><wicri:noCountry code="subField">AB T6G 2E3 Canada</wicri:noCountry></affiliation></author><author><name sortKey="Chow, Pak" sort="Chow, Pak" uniqKey="Chow P" first="Pak" last="Chow">Pak Chow</name><affiliation><nlm:affiliation>Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, AB T6G 2E3 Canada.</nlm:affiliation><wicri:noCountry code="subField">AB T6G 2E3 Canada</wicri:noCountry></affiliation></author><author><name sortKey="Landh Usser, Simon M" sort="Landh Usser, Simon M" uniqKey="Landh Usser S" first="Simon M" last="Landh Usser">Simon M. Landh Usser</name><affiliation><nlm:affiliation>Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, AB T6G 2E3 Canada.</nlm:affiliation><wicri:noCountry code="subField">AB T6G 2E3 Canada</wicri:noCountry></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:26113872</idno><idno type="pmid">26113872</idno><idno type="doi">10.1186/s13007-015-0079-1</idno><idno type="pmc">PMC4480983</idno><idno type="wicri:Area/Main/Corpus">001C40</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">001C40</idno><idno type="wicri:Area/Main/Curation">001C40</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">001C40</idno><idno type="wicri:Area/Main/Exploration">001C40</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Biases underlying species detection using fluorescent amplified-fragment length polymorphisms yielded from roots.</title><author><name sortKey="Karst, Justine" sort="Karst, Justine" uniqKey="Karst J" first="Justine" last="Karst">Justine Karst</name><affiliation><nlm:affiliation>Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, AB T6G 2E3 Canada.</nlm:affiliation><wicri:noCountry code="subField">AB T6G 2E3 Canada</wicri:noCountry></affiliation></author><author><name sortKey="Chow, Pak" sort="Chow, Pak" uniqKey="Chow P" first="Pak" last="Chow">Pak Chow</name><affiliation><nlm:affiliation>Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, AB T6G 2E3 Canada.</nlm:affiliation><wicri:noCountry code="subField">AB T6G 2E3 Canada</wicri:noCountry></affiliation></author><author><name sortKey="Landh Usser, Simon M" sort="Landh Usser, Simon M" uniqKey="Landh Usser S" first="Simon M" last="Landh Usser">Simon M. Landh Usser</name><affiliation><nlm:affiliation>Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, AB T6G 2E3 Canada.</nlm:affiliation><wicri:noCountry code="subField">AB T6G 2E3 Canada</wicri:noCountry></affiliation></author></analytic><series><title level="j">Plant methods</title><idno type="ISSN">1746-4811</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Roots of different plant species are typically morphologically indistinguishable. Of the DNA-based techniques, fluorescent amplified-fragment length polymorphisms (FAFLPs) are considered reliable, high throughput, inexpensive methods to identify roots from mixed species samples. False-negatives, however, are not uncommon and their underlying causes are poorly understood. We investigated several sources of potential biases originating in DNA extraction and amplification. Specifically, we examined the effects of sample storage, tissue, and species on DNA yield and purity, and the effects of DNA concentration and fragment size on amplification of three non-coding chloroplast regions (trnT-trnL intergenic spacer, trnL intron, and trnL-trnF intergenic spacer).</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We found that sample condition, tissue and species all affected DNA yield. A single freeze-thaw reduces DNA yield, DNA yield is less for roots than shoots, and species vary in the amount of DNA yielded from extractions. The effects of template DNA concentration, species identity, and their interaction on amplicon yield differed across the three chloroplast regions tested. We found that the effect of species identity on amplicon production was generally more pronounced than that of DNA concentration. Though these factors influenced DNA yield, they likely do not have a pronounced effect on detection success of fragments and only underscore the restriction on the use of FAFLPs for measuring species presence rather than their abundance. However, for two of the regions tested-the trnT-trnL intergenic spacer and the trnL intron-size-based fragment competition occurred and the likelihood of detection was higher for smaller than larger fragments. This result reveals a methodological bias when using FAFLPs.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>To avoid potential bias with the use of FAFLPs, we recommend users check for the disproportionate absence of species detected belowground versus aboveground as a function of fragment size, and explore other regions, aside from the trnT-trnL intergenic spacer and trnL intron, for amplification.</p></div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">26113872</PMID><DateCompleted><Year>2015</Year><Month>06</Month><Day>26</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1746-4811</ISSN><JournalIssue CitedMedium="Print"><Volume>11</Volume><PubDate><Year>2015</Year></PubDate></JournalIssue><Title>Plant methods</Title><ISOAbbreviation>Plant Methods</ISOAbbreviation></Journal><ArticleTitle>Biases underlying species detection using fluorescent amplified-fragment length polymorphisms yielded from roots.</ArticleTitle><Pagination><MedlinePgn>36</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s13007-015-0079-1</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Roots of different plant species are typically morphologically indistinguishable. Of the DNA-based techniques, fluorescent amplified-fragment length polymorphisms (FAFLPs) are considered reliable, high throughput, inexpensive methods to identify roots from mixed species samples. False-negatives, however, are not uncommon and their underlying causes are poorly understood. We investigated several sources of potential biases originating in DNA extraction and amplification. Specifically, we examined the effects of sample storage, tissue, and species on DNA yield and purity, and the effects of DNA concentration and fragment size on amplification of three non-coding chloroplast regions (trnT-trnL intergenic spacer, trnL intron, and trnL-trnF intergenic spacer).</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We found that sample condition, tissue and species all affected DNA yield. A single freeze-thaw reduces DNA yield, DNA yield is less for roots than shoots, and species vary in the amount of DNA yielded from extractions. The effects of template DNA concentration, species identity, and their interaction on amplicon yield differed across the three chloroplast regions tested. We found that the effect of species identity on amplicon production was generally more pronounced than that of DNA concentration. Though these factors influenced DNA yield, they likely do not have a pronounced effect on detection success of fragments and only underscore the restriction on the use of FAFLPs for measuring species presence rather than their abundance. However, for two of the regions tested-the trnT-trnL intergenic spacer and the trnL intron-size-based fragment competition occurred and the likelihood of detection was higher for smaller than larger fragments. This result reveals a methodological bias when using FAFLPs.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">To avoid potential bias with the use of FAFLPs, we recommend users check for the disproportionate absence of species detected belowground versus aboveground as a function of fragment size, and explore other regions, aside from the trnT-trnL intergenic spacer and trnL intron, for amplification.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y" EqualContrib="Y"><LastName>Karst</LastName><ForeName>Justine</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, AB T6G 2E3 Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y" EqualContrib="Y"><LastName>Chow</LastName><ForeName>Pak</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, AB T6G 2E3 Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Landhäusser</LastName><ForeName>Simon M</ForeName><Initials>SM</Initials><AffiliationInfo><Affiliation>Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, AB T6G 2E3 Canada.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>06</Month><Day>26</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Plant Methods</MedlineTA><NlmUniqueID>101245798</NlmUniqueID><ISSNLinking>1746-4811</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">AFLP</Keyword><Keyword MajorTopicYN="N">Bromus inermis Leyss.</Keyword><Keyword MajorTopicYN="N">Community</Keyword><Keyword MajorTopicYN="N">False-negatives</Keyword><Keyword MajorTopicYN="N">Mixed template</Keyword><Keyword MajorTopicYN="N">Populus tremuloides Michx.</Keyword><Keyword MajorTopicYN="N">belowground diversity</Keyword><Keyword MajorTopicYN="N">trnL intron</Keyword><Keyword MajorTopicYN="N">trnL-trnF intergenic spacer</Keyword><Keyword MajorTopicYN="N">trnT-trnL intergenic spacer</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>04</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>06</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>6</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>6</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>6</Month><Day>27</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26113872</ArticleId><ArticleId IdType="doi">10.1186/s13007-015-0079-1</ArticleId><ArticleId IdType="pii">79</ArticleId><ArticleId IdType="pmc">PMC4480983</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Mol Ecol. 2011 Mar;20(6):1289-302</Citation><ArticleIdList><ArticleId IdType="pubmed">21255172</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Biotechnol. 2014 Jan 30;14:10</Citation><ArticleIdList><ArticleId IdType="pubmed">24479830</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol Resour. 2008 Sep;8(5):947-53</Citation><ArticleIdList><ArticleId IdType="pubmed">21585938</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 1995 Nov 11;23(21):4407-14</Citation><ArticleIdList><ArticleId IdType="pubmed">7501463</ArticleId></ArticleIdList></Reference><Reference><Citation>Ecology. 2010 Nov;91(11):3201-9</Citation><ArticleIdList><ArticleId IdType="pubmed">21141181</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Plant Sci. 2014 Nov 01;2(11):null</Citation><ArticleIdList><ArticleId IdType="pubmed">25383267</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2003 Aug 15;31(16):e99</Citation><ArticleIdList><ArticleId IdType="pubmed">12907751</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Methods. 2014 Jun 27;10:21</Citation><ArticleIdList><ArticleId IdType="pubmed">25053969</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol Resour. 2011 Jan;11(1):185-95</Citation><ArticleIdList><ArticleId IdType="pubmed">21429121</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol. 2012 Aug;21(15):3647-55</Citation><ArticleIdList><ArticleId IdType="pubmed">22507540</ArticleId></ArticleIdList></Reference><Reference><Citation>J Microbiol Methods. 2010 Aug;82(2):124-30</Citation><ArticleIdList><ArticleId IdType="pubmed">20470836</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Mol Biol. 1991 Nov;17(5):1105-9</Citation><ArticleIdList><ArticleId IdType="pubmed">1932684</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 1996 Feb;62(2):625-30</Citation><ArticleIdList><ArticleId IdType="pubmed">8593063</ArticleId></ArticleIdList></Reference><Reference><Citation>Am J Bot. 2005 Jan;92(1):142-66</Citation><ArticleIdList><ArticleId IdType="pubmed">21652394</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol. 2012 Apr;21(8):2004-16</Citation><ArticleIdList><ArticleId IdType="pubmed">22168247</ArticleId></ArticleIdList></Reference><Reference><Citation>Environ Microbiol. 2000 Feb;2(1):39-50</Citation><ArticleIdList><ArticleId IdType="pubmed">11243261</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Microbiol Biotechnol. 2010 Feb;85(5):1251-8</Citation><ArticleIdList><ArticleId IdType="pubmed">19911178</ArticleId></ArticleIdList></Reference><Reference><Citation>Am J Bot. 2007 Mar;94(3):275-88</Citation><ArticleIdList><ArticleId IdType="pubmed">21636401</ArticleId></ArticleIdList></Reference><Reference><Citation>Trends Ecol Evol. 1999 Oct;14(10):389-394</Citation><ArticleIdList><ArticleId IdType="pubmed">10481200</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list></list><tree><noCountry><name sortKey="Chow, Pak" sort="Chow, Pak" uniqKey="Chow P" first="Pak" last="Chow">Pak Chow</name><name sortKey="Karst, Justine" sort="Karst, Justine" uniqKey="Karst J" first="Justine" last="Karst">Justine Karst</name><name sortKey="Landh Usser, Simon M" sort="Landh Usser, Simon M" uniqKey="Landh Usser S" first="Simon M" last="Landh Usser">Simon M. Landh Usser</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PoplarV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001E78 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 001E78 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= PoplarV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:26113872
|texte= Biases underlying species detection using fluorescent amplified-fragment length polymorphisms yielded from roots.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:26113872" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PoplarV1
| This area was generated with Dilib version V0.6.37. |  |