Microsatellites for the marsh fritillary butterfly: de novo transcriptome sequencing, and a comparison with amplified fragment length polymorphism (AFLP) markers
Until recently the isolation of microsatellite markers from Lepidoptera has proved troublesome, expensive and time-consuming. Following on from a previous study of Edith's checkerspot butterfly, Euphydryas editha, we developed novel microsatellite markers for the vulnerable marsh fritillary but...
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| creator | Smee, Melanie R Pauchet, Yannick Wilkinson, Paul Wee, Brian Singer, Michael C ffrench-Constant, Richard H Hodgson, David J Mikheyev, Alexander S |
| description | Until recently the isolation of microsatellite markers from Lepidoptera has proved troublesome, expensive and time-consuming. Following on from a previous study of Edith's checkerspot butterfly, Euphydryas editha, we developed novel microsatellite markers for the vulnerable marsh fritillary butterfly, E. aurinia. Our goal was to optimize the process in order to reduce both time and cost relative to prevailing techniques. This was accomplished by using a combination of previously developed techniques: in silico mining of a de novo assembled transcriptome sequence, and genotyping the microsatellites found there using an economic method of fluorescently labelling primers.
In total, we screened nine polymorphic microsatellite markers, two of which were previously published, and seven that were isolated de novo. These markers were able to amplify across geographically isolated populations throughout Continental Europe and the UK. Significant deviations from Hardy-Weinberg equilibrium were evident in some populations, most likely due to the presence of null alleles. However, we used an F(st) outlier approach to show that these markers are likely selectively neutral. Furthermore, using a set of 128 individuals from 11 populations, we demonstrate consistency in population differentiation estimates with previously developed amplified fragment length polymorphism (AFLP) markers (r = 0.68, p |
| doi_str_mv | 10.1371/journal.pone.0054721 |
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In total, we screened nine polymorphic microsatellite markers, two of which were previously published, and seven that were isolated de novo. These markers were able to amplify across geographically isolated populations throughout Continental Europe and the UK. Significant deviations from Hardy-Weinberg equilibrium were evident in some populations, most likely due to the presence of null alleles. However, we used an F(st) outlier approach to show that these markers are likely selectively neutral. Furthermore, using a set of 128 individuals from 11 populations, we demonstrate consistency in population differentiation estimates with previously developed amplified fragment length polymorphism (AFLP) markers (r = 0.68, p<0.001).
Rapid development of microsatellite markers for difficult taxa such as Lepidoptera, and concordant results with other putatively neutral molecular markers, demonstrate the potential of de novo transcriptional sequencing for future studies of population structure and gene flow that are desperately needed for declining species across fragmented landscapes.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0054721</identifier><identifier>PMID: 23349956</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Amplification ; Amplified fragment length polymorphism ; Amplified Fragment Length Polymorphism Analysis ; Analysis ; Animals ; Automation ; Bioinformatics ; Biology ; Biometrics ; Butterflies & moths ; Butterflies - genetics ; Deoxyribonucleic acid ; DNA ; Ecology ; Euphydryas ; Evolution ; Fluorescence ; Fragmentation ; Gene Flow ; Gene sequencing ; Genetic aspects ; Genetic markers ; Genetic Variation ; Genetics, Population ; Genomes ; Genotype ; Genotyping ; High-Throughput Nucleotide Sequencing ; Labeling ; Labelling ; Lepidoptera ; Linux ; Markers ; Methods ; Microsatellite Repeats - genetics ; Microsatellites ; Molecular biology ; Polymorphism ; Population decline ; Population differentiation ; Population genetics ; Population structure ; Population studies ; Populations ; Primers ; Studies ; Taxa ; Transcription ; Transcription (Genetics) ; Transcriptome - genetics</subject><ispartof>PloS one, 2013-01, Vol.8 (1), p.e54721-e54721</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Smee et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2013 Smee et al 2013 Smee et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c593t-6703164a3e8bcce158f3ec0a25d69e8b73a64210a83ab750992bc08b7f6412943</citedby><cites>FETCH-LOGICAL-c593t-6703164a3e8bcce158f3ec0a25d69e8b73a64210a83ab750992bc08b7f6412943</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549983/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549983/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,725,778,782,862,883,2098,2917,23849,27907,27908,53774,53776,79351,79352</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23349956$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Breuker, Casper</contributor><creatorcontrib>Smee, Melanie R</creatorcontrib><creatorcontrib>Pauchet, Yannick</creatorcontrib><creatorcontrib>Wilkinson, Paul</creatorcontrib><creatorcontrib>Wee, Brian</creatorcontrib><creatorcontrib>Singer, Michael C</creatorcontrib><creatorcontrib>ffrench-Constant, Richard H</creatorcontrib><creatorcontrib>Hodgson, David J</creatorcontrib><creatorcontrib>Mikheyev, Alexander S</creatorcontrib><title>Microsatellites for the marsh fritillary butterfly: de novo transcriptome sequencing, and a comparison with amplified fragment length polymorphism (AFLP) markers</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Until recently the isolation of microsatellite markers from Lepidoptera has proved troublesome, expensive and time-consuming. Following on from a previous study of Edith's checkerspot butterfly, Euphydryas editha, we developed novel microsatellite markers for the vulnerable marsh fritillary butterfly, E. aurinia. Our goal was to optimize the process in order to reduce both time and cost relative to prevailing techniques. This was accomplished by using a combination of previously developed techniques: in silico mining of a de novo assembled transcriptome sequence, and genotyping the microsatellites found there using an economic method of fluorescently labelling primers.
In total, we screened nine polymorphic microsatellite markers, two of which were previously published, and seven that were isolated de novo. These markers were able to amplify across geographically isolated populations throughout Continental Europe and the UK. Significant deviations from Hardy-Weinberg equilibrium were evident in some populations, most likely due to the presence of null alleles. However, we used an F(st) outlier approach to show that these markers are likely selectively neutral. Furthermore, using a set of 128 individuals from 11 populations, we demonstrate consistency in population differentiation estimates with previously developed amplified fragment length polymorphism (AFLP) markers (r = 0.68, p<0.001).
Rapid development of microsatellite markers for difficult taxa such as Lepidoptera, and concordant results with other putatively neutral molecular markers, demonstrate the potential of de novo transcriptional sequencing for future studies of population structure and gene flow that are desperately needed for declining species across fragmented landscapes.</description><subject>Amplification</subject><subject>Amplified fragment length polymorphism</subject><subject>Amplified Fragment Length Polymorphism Analysis</subject><subject>Analysis</subject><subject>Animals</subject><subject>Automation</subject><subject>Bioinformatics</subject><subject>Biology</subject><subject>Biometrics</subject><subject>Butterflies & moths</subject><subject>Butterflies - genetics</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Ecology</subject><subject>Euphydryas</subject><subject>Evolution</subject><subject>Fluorescence</subject><subject>Fragmentation</subject><subject>Gene Flow</subject><subject>Gene sequencing</subject><subject>Genetic aspects</subject><subject>Genetic markers</subject><subject>Genetic Variation</subject><subject>Genetics, Population</subject><subject>Genomes</subject><subject>Genotype</subject><subject>Genotyping</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Labeling</subject><subject>Labelling</subject><subject>Lepidoptera</subject><subject>Linux</subject><subject>Markers</subject><subject>Methods</subject><subject>Microsatellite Repeats - genetics</subject><subject>Microsatellites</subject><subject>Molecular biology</subject><subject>Polymorphism</subject><subject>Population decline</subject><subject>Population differentiation</subject><subject>Population genetics</subject><subject>Population structure</subject><subject>Population studies</subject><subject>Populations</subject><subject>Primers</subject><subject>Studies</subject><subject>Taxa</subject><subject>Transcription</subject><subject>Transcription (Genetics)</subject><subject>Transcriptome - genetics</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNptUttu1DAQjRCIlsIfILDES5HYxbfceEBaVRQqLYIHeLYmjpP14tjB9hbt5_CnON206qLKD7Zmzpw5Mz5Z9pLgJWEleb91O2_BLEdn1RLjnJeUPMpOSc3ooqCYPb73PsmehbBNIFYVxdPshDLG6zovTrO_X7X0LkBUxuioAuqcR3Gj0AA-bFDnddTGgN-jZhej8p3Zf0CtQtZdOxQ92CC9HqMbFArq905ZqW3_DoFtESDphhG8Ds6iPzpuEAyj0Z1WbeKFflA2IqNsnzKjM_vB-XGjw4DOV5fr728nBb-UD8-zJx2YoF7M91n28_LTj4svi_W3z1cXq_VC5jWLi6LEjBQcmKoaKRXJq44piYHmbVGnWMmg4JRgqBg0ZY7rmjYSp3hXcEJrzs6y1wfe0bgg5u0GQRgtq6KmlCTE1QHROtiK0eukcC8caHETcL4X4KOWRomcty2UDaV52XFVF02VlHHMgJV5xW-4Ps7dds2gWpl24cEckR5nrN6I3l0Llqefq1giOJ8JvEt7D1EMOsj0i2CV2yXdtKKY0xxPvd78B314uhnVQxpA286lvnIiFSteVqSivJpQywdQ6bRq0DJZsdMpflTADwWTzYJX3d2MBIvJyLdixGRkMRs5lb26v5-7olvnsn9Ws_KK</recordid><startdate>20130121</startdate><enddate>20130121</enddate><creator>Smee, Melanie R</creator><creator>Pauchet, Yannick</creator><creator>Wilkinson, Paul</creator><creator>Wee, Brian</creator><creator>Singer, Michael C</creator><creator>ffrench-Constant, Richard H</creator><creator>Hodgson, David J</creator><creator>Mikheyev, Alexander S</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20130121</creationdate><title>Microsatellites for the marsh fritillary butterfly: de novo transcriptome sequencing, and a comparison with amplified fragment length polymorphism (AFLP) markers</title><author>Smee, Melanie R ; Pauchet, Yannick ; Wilkinson, Paul ; Wee, Brian ; Singer, Michael C ; ffrench-Constant, Richard H ; Hodgson, David J ; Mikheyev, Alexander S</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c593t-6703164a3e8bcce158f3ec0a25d69e8b73a64210a83ab750992bc08b7f6412943</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Amplification</topic><topic>Amplified fragment length polymorphism</topic><topic>Amplified Fragment Length Polymorphism Analysis</topic><topic>Analysis</topic><topic>Animals</topic><topic>Automation</topic><topic>Bioinformatics</topic><topic>Biology</topic><topic>Biometrics</topic><topic>Butterflies & moths</topic><topic>Butterflies - 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Following on from a previous study of Edith's checkerspot butterfly, Euphydryas editha, we developed novel microsatellite markers for the vulnerable marsh fritillary butterfly, E. aurinia. Our goal was to optimize the process in order to reduce both time and cost relative to prevailing techniques. This was accomplished by using a combination of previously developed techniques: in silico mining of a de novo assembled transcriptome sequence, and genotyping the microsatellites found there using an economic method of fluorescently labelling primers.
In total, we screened nine polymorphic microsatellite markers, two of which were previously published, and seven that were isolated de novo. These markers were able to amplify across geographically isolated populations throughout Continental Europe and the UK. Significant deviations from Hardy-Weinberg equilibrium were evident in some populations, most likely due to the presence of null alleles. However, we used an F(st) outlier approach to show that these markers are likely selectively neutral. Furthermore, using a set of 128 individuals from 11 populations, we demonstrate consistency in population differentiation estimates with previously developed amplified fragment length polymorphism (AFLP) markers (r = 0.68, p<0.001).
Rapid development of microsatellite markers for difficult taxa such as Lepidoptera, and concordant results with other putatively neutral molecular markers, demonstrate the potential of de novo transcriptional sequencing for future studies of population structure and gene flow that are desperately needed for declining species across fragmented landscapes.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>23349956</pmid><doi>10.1371/journal.pone.0054721</doi><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
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| issn | 1932-6203 1932-6203 |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Public Library of Science (PLoS); PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Amplification Amplified fragment length polymorphism Amplified Fragment Length Polymorphism Analysis Analysis Animals Automation Bioinformatics Biology Biometrics Butterflies & moths Butterflies - genetics Deoxyribonucleic acid DNA Ecology Euphydryas Evolution Fluorescence Fragmentation Gene Flow Gene sequencing Genetic aspects Genetic markers Genetic Variation Genetics, Population Genomes Genotype Genotyping High-Throughput Nucleotide Sequencing Labeling Labelling Lepidoptera Linux Markers Methods Microsatellite Repeats - genetics Microsatellites Molecular biology Polymorphism Population decline Population differentiation Population genetics Population structure Population studies Populations Primers Studies Taxa Transcription Transcription (Genetics) Transcriptome - genetics |
| title | Microsatellites for the marsh fritillary butterfly: de novo transcriptome sequencing, and a comparison with amplified fragment length polymorphism (AFLP) markers |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-16T07%3A15%3A02IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Microsatellites%20for%20the%20marsh%20fritillary%20butterfly:%20de%20novo%20transcriptome%20sequencing,%20and%20a%20comparison%20with%20amplified%20fragment%20length%20polymorphism%20(AFLP)%20markers&rft.jtitle=PloS%20one&rft.au=Smee,%20Melanie%20R&rft.date=2013-01-21&rft.volume=8&rft.issue=1&rft.spage=e54721&rft.epage=e54721&rft.pages=e54721-e54721&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0054721&rft_dat=%3Cgale_plos_%3EA478182481%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1327869221&rft_id=info:pmid/23349956&rft_galeid=A478182481&rft_doaj_id=oai_doaj_org_article_54dda7b2257f4e96b84a3403a3758421&rfr_iscdi=true |