De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)
The bird cherry-oat aphid, Rhopalosiphum padi (L.), is one of the most abundant aphid pests of cereals and has a global distribution. Next-generation sequencing (NGS) is a rapid and efficient method for developing molecular markers. However, transcriptomic and genomic resources of R. padi have not b...
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| description | The bird cherry-oat aphid, Rhopalosiphum padi (L.), is one of the most abundant aphid pests of cereals and has a global distribution. Next-generation sequencing (NGS) is a rapid and efficient method for developing molecular markers. However, transcriptomic and genomic resources of R. padi have not been investigated. In this study, we used transcriptome information obtained by RNA-Seq to develop polymorphic microsatellites for investigating population genetics in this species. The transcriptome of R. padi was sequenced on an Illumina HiSeq 2000 platform. A total of 114.4 million raw reads with a GC content of 40.03% was generated. The raw reads were cleaned and assembled into 29,467 unigenes with an N50 length of 1,580 bp. Using several public databases, 82.47% of these unigenes were annotated. Of the annotated unigenes, 8,022 were assigned to COG pathways, 9,895 were assigned to GO pathways, and 14,586 were mapped to 257 KEGG pathways. A total of 7,936 potential microsatellites were identified in 5,564 unigenes, 60 of which were selected randomly and amplified using specific primer pairs. Fourteen loci were found to be polymorphic in the four R. padi populations. The transcriptomic data presented herein will facilitate gene discovery, gene analyses, and development of molecular markers for future studies of R. padi and other closely related aphid species. |
| doi_str_mv | 10.1371/journal.pone.0172513 |
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(Hemiptera: Aphididae)</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>Public Library of Science (PLoS)</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Duan, Xinle ; Wang, Kang ; Su, Sha ; Tian, Ruizheng ; Li, Yuting ; Chen, Maohua</creator><contributor>Hull, J. Joe</contributor><creatorcontrib>Duan, Xinle ; Wang, Kang ; Su, Sha ; Tian, Ruizheng ; Li, Yuting ; Chen, Maohua ; Hull, J. Joe</creatorcontrib><description>The bird cherry-oat aphid, Rhopalosiphum padi (L.), is one of the most abundant aphid pests of cereals and has a global distribution. Next-generation sequencing (NGS) is a rapid and efficient method for developing molecular markers. However, transcriptomic and genomic resources of R. padi have not been investigated. In this study, we used transcriptome information obtained by RNA-Seq to develop polymorphic microsatellites for investigating population genetics in this species. The transcriptome of R. padi was sequenced on an Illumina HiSeq 2000 platform. A total of 114.4 million raw reads with a GC content of 40.03% was generated. The raw reads were cleaned and assembled into 29,467 unigenes with an N50 length of 1,580 bp. Using several public databases, 82.47% of these unigenes were annotated. Of the annotated unigenes, 8,022 were assigned to COG pathways, 9,895 were assigned to GO pathways, and 14,586 were mapped to 257 KEGG pathways. A total of 7,936 potential microsatellites were identified in 5,564 unigenes, 60 of which were selected randomly and amplified using specific primer pairs. Fourteen loci were found to be polymorphic in the four R. padi populations. The transcriptomic data presented herein will facilitate gene discovery, gene analyses, and development of molecular markers for future studies of R. padi and other closely related aphid species.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0172513</identifier><identifier>PMID: 28212394</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Animals ; Aphididae ; Aphids - genetics ; Barley ; Biology ; Biology and Life Sciences ; Cereals ; Climate change ; Cloning ; Deoxyribonucleic acid ; DNA ; DNA methylation ; DNA Primers ; Female ; Gene expression ; Gene Expression Profiling - methods ; Genetic diversity ; Genetic markers ; Genetics ; Genetics, Population ; Genomes ; Genomics ; Hemiptera ; High-Throughput Nucleotide Sequencing ; Insect pests ; Insects ; Laboratories ; Markers ; Microsatellite Repeats ; Microsatellites ; Microsatellites (Genetics) ; Mitochondrial DNA ; Molecular Sequence Annotation ; Pests ; Population genetics ; Population studies ; Reproducibility of Results ; Research and Analysis Methods ; Rhopalosiphum padi ; Ribonucleic acid ; RNA ; RNA sequencing ; Studies ; Triticum ; Wheat</subject><ispartof>PloS one, 2017-02, Vol.12 (2), p.e0172513-e0172513</ispartof><rights>COPYRIGHT 2017 Public Library of Science</rights><rights>2017 Duan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://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. 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Joe</contributor><creatorcontrib>Duan, Xinle</creatorcontrib><creatorcontrib>Wang, Kang</creatorcontrib><creatorcontrib>Su, Sha</creatorcontrib><creatorcontrib>Tian, Ruizheng</creatorcontrib><creatorcontrib>Li, Yuting</creatorcontrib><creatorcontrib>Chen, Maohua</creatorcontrib><title>De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The bird cherry-oat aphid, Rhopalosiphum padi (L.), is one of the most abundant aphid pests of cereals and has a global distribution. Next-generation sequencing (NGS) is a rapid and efficient method for developing molecular markers. However, transcriptomic and genomic resources of R. padi have not been investigated. 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The transcriptomic data presented herein will facilitate gene discovery, gene analyses, and development of molecular markers for future studies of R. padi and other closely related aphid species.</description><subject>Animals</subject><subject>Aphididae</subject><subject>Aphids - genetics</subject><subject>Barley</subject><subject>Biology</subject><subject>Biology and Life Sciences</subject><subject>Cereals</subject><subject>Climate change</subject><subject>Cloning</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA methylation</subject><subject>DNA Primers</subject><subject>Female</subject><subject>Gene expression</subject><subject>Gene Expression Profiling - methods</subject><subject>Genetic diversity</subject><subject>Genetic markers</subject><subject>Genetics</subject><subject>Genetics, Population</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Hemiptera</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Insect pests</subject><subject>Insects</subject><subject>Laboratories</subject><subject>Markers</subject><subject>Microsatellite Repeats</subject><subject>Microsatellites</subject><subject>Microsatellites (Genetics)</subject><subject>Mitochondrial DNA</subject><subject>Molecular Sequence Annotation</subject><subject>Pests</subject><subject>Population genetics</subject><subject>Population studies</subject><subject>Reproducibility of Results</subject><subject>Research and Analysis Methods</subject><subject>Rhopalosiphum padi</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA sequencing</subject><subject>Studies</subject><subject>Triticum</subject><subject>Wheat</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</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>eNqNk9tu1DAQhiMEolB4AwSWkFArsYsPseNwgVSVQytVqlQOt5bXmey6JHGwnYq-Ek_JLN1WXdSLyhe27G_-TP6ZKYoXjM6ZqNi78zDFwXbzMQwwp6zikokHxRNWCz5TnIqHt847xdOUzimVQiv1uNjhmjMu6vJJ8ecjkCFcBJKjHZKLfsyhB2JR-TL5hIeG9N7FkGyGrvMZSG_jT4ikgQvowtjDkEkbIhnDOHU2-zCQJQyQvSMpT80lCS2xJEH0YUrEDwlcJiOk_JacrcJou5D8uJp6MtrGk72T-T7ZO4IeE4Fo35ODceUb31jYf1Y8am2X4Plm3y2-f_707fBodnL65fjw4GTmqprlGShBW66plLxtG8FKXcrKCq5KpWllKXOUgcRXkG4hRcUdaKilKCvBacNrsVu8utIdMTWzsTkZphVSXFVr4viKaII9N2P0aMmlCdabfxchLo2NaEAHRmoHQjpbqoaWNRMLZW3VsHIBVmE5BGp92HxtWvTQOLQz2m5LdPtl8CuzDBdGCiZFrVFgbyMQw68JfTW9Tw5rZQdAxzHvimumS0Xvgaq6VpJKhejr_9C7jdhQS4v_6oc2YIpuLWoOSs2kVhXaulvM76BwNVhmh-3berzfCtjfCkAmw--8tFNK5vjr2f3Z0x_b7Jtb7Apsl1cpdNO6adM2WF6B68ZPEdqbejBq1tN37YZZT5_ZTB-Gvbxdy5ug63ETfwH_VyrY</recordid><startdate>20170217</startdate><enddate>20170217</enddate><creator>Duan, 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novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) 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Joe</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2017-02-17</date><risdate>2017</risdate><volume>12</volume><issue>2</issue><spage>e0172513</spage><epage>e0172513</epage><pages>e0172513-e0172513</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The bird cherry-oat aphid, Rhopalosiphum padi (L.), is one of the most abundant aphid pests of cereals and has a global distribution. Next-generation sequencing (NGS) is a rapid and efficient method for developing molecular markers. However, transcriptomic and genomic resources of R. padi have not been investigated. In this study, we used transcriptome information obtained by RNA-Seq to develop polymorphic microsatellites for investigating population genetics in this species. The transcriptome of R. padi was sequenced on an Illumina HiSeq 2000 platform. A total of 114.4 million raw reads with a GC content of 40.03% was generated. The raw reads were cleaned and assembled into 29,467 unigenes with an N50 length of 1,580 bp. Using several public databases, 82.47% of these unigenes were annotated. Of the annotated unigenes, 8,022 were assigned to COG pathways, 9,895 were assigned to GO pathways, and 14,586 were mapped to 257 KEGG pathways. A total of 7,936 potential microsatellites were identified in 5,564 unigenes, 60 of which were selected randomly and amplified using specific primer pairs. Fourteen loci were found to be polymorphic in the four R. padi populations. The transcriptomic data presented herein will facilitate gene discovery, gene analyses, and development of molecular markers for future studies of R. padi and other closely related aphid species.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>28212394</pmid><doi>10.1371/journal.pone.0172513</doi><tpages>e0172513</tpages><orcidid>https://orcid.org/0000-0001-8599-2771</orcidid><oa>free_for_read</oa></addata></record> |
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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 | Animals Aphididae Aphids - genetics Barley Biology Biology and Life Sciences Cereals Climate change Cloning Deoxyribonucleic acid DNA DNA methylation DNA Primers Female Gene expression Gene Expression Profiling - methods Genetic diversity Genetic markers Genetics Genetics, Population Genomes Genomics Hemiptera High-Throughput Nucleotide Sequencing Insect pests Insects Laboratories Markers Microsatellite Repeats Microsatellites Microsatellites (Genetics) Mitochondrial DNA Molecular Sequence Annotation Pests Population genetics Population studies Reproducibility of Results Research and Analysis Methods Rhopalosiphum padi Ribonucleic acid RNA RNA sequencing Studies Triticum Wheat |
| title | De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae) |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-19T01%3A51%3A32IST&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=De%20novo%20transcriptome%20analysis%20and%20microsatellite%20marker%20development%20for%20population%20genetic%20study%20of%20a%20serious%20insect%20pest,%20Rhopalosiphum%20padi%20(L.)%20(Hemiptera:%20Aphididae)&rft.jtitle=PloS%20one&rft.au=Duan,%20Xinle&rft.date=2017-02-17&rft.volume=12&rft.issue=2&rft.spage=e0172513&rft.epage=e0172513&rft.pages=e0172513-e0172513&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0172513&rft_dat=%3Cgale_plos_%3EA481586747%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=1869532679&rft_id=info:pmid/28212394&rft_galeid=A481586747&rft_doaj_id=oai_doaj_org_article_58ce35ca46d04913b6aa7d14bea60533&rfr_iscdi=true |