Transcriptomic analysis of the rice white tip nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae)
The rice white tip nematode Aphelenchoides besseyi, a devastating nematode whose genome has not been sequenced, is distributed widely throughout almost all the rice-growing regions of the world. The aims of the present study were to define the transcriptome of A. besseyi and to identify parasite-rel...
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description | The rice white tip nematode Aphelenchoides besseyi, a devastating nematode whose genome has not been sequenced, is distributed widely throughout almost all the rice-growing regions of the world. The aims of the present study were to define the transcriptome of A. besseyi and to identify parasite-related, mortality-related or host resistance-overcoming genes in this nematode.
Using Solexa/Illumina sequencing, we profiled the transcriptome of mixed-stage populations of A. besseyi. A total of 51,270 transcripts without gaps were produced based on high-quality clean reads. Of all the A. besseyi transcripts, 9,132 KEGG Orthology assignments were annotated. Carbohydrate-active enzymes of glycoside hydrolases (GHs), glycosyltransferases (GTs), carbohydrate esterases (CEs) and carbohydrate-binding modules (CBMs) were identified. The presence of the A. besseyi GH45 cellulase gene was verified by in situ hybridization. Given that 13 unique A. besseyi potential effector genes were identified from 41 candidate effector homologs, further studies of these homologs are merited. Finally, comparative analyses were conducted between A. besseyi contigs and Caenorhabditis elegans genes to look for orthologs of RNAi phenotypes, neuropeptides and peptidases.
The present results provide comprehensive insight into the genetic makeup of A. besseyi. Many of this species' genes are parasite related, nematode mortality-related or necessary to overcome host resistance. The generated transcriptome dataset of A. besseyi reported here lays the foundation for further studies of the molecular mechanisms related to parasitism and facilitates the development of new control strategies for this species. |
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Using Solexa/Illumina sequencing, we profiled the transcriptome of mixed-stage populations of A. besseyi. A total of 51,270 transcripts without gaps were produced based on high-quality clean reads. Of all the A. besseyi transcripts, 9,132 KEGG Orthology assignments were annotated. Carbohydrate-active enzymes of glycoside hydrolases (GHs), glycosyltransferases (GTs), carbohydrate esterases (CEs) and carbohydrate-binding modules (CBMs) were identified. The presence of the A. besseyi GH45 cellulase gene was verified by in situ hybridization. Given that 13 unique A. besseyi potential effector genes were identified from 41 candidate effector homologs, further studies of these homologs are merited. Finally, comparative analyses were conducted between A. besseyi contigs and Caenorhabditis elegans genes to look for orthologs of RNAi phenotypes, neuropeptides and peptidases.
The present results provide comprehensive insight into the genetic makeup of A. besseyi. Many of this species' genes are parasite related, nematode mortality-related or necessary to overcome host resistance. The generated transcriptome dataset of A. besseyi reported here lays the foundation for further studies of the molecular mechanisms related to parasitism and facilitates the development of new control strategies for this species.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0091591</identifier><identifier>PMID: 24637831</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Agricultural production ; Amino Acid Sequence ; Analysis ; Animals ; Aphelenchoides besseyi ; Barley ; Biology and Life Sciences ; Caenorhabditis elegans ; Carbohydrates ; Cell Wall - metabolism ; Cellulase ; Cellulase - chemistry ; Cellulase - genetics ; Computational Biology ; Databases, Nucleic Acid ; Esterases ; Gene expression ; Gene Expression Profiling ; Gene Regulatory Networks ; Gene sequencing ; Genes ; Genomes ; Genomics ; Glycoside hydrolase ; Health aspects ; Homology ; Hydrolases ; Medicine and Health Sciences ; Molecular modelling ; Molecular Sequence Data ; Mortality ; Nematoda - classification ; Nematoda - genetics ; Nematoda - metabolism ; Nematodes ; Neuropeptides ; Neuropeptides - genetics ; Neuropeptides - metabolism ; Orthology ; Oryza - parasitology ; Parasitism ; Peptidases ; Peptide Hydrolases - genetics ; Peptide Hydrolases - metabolism ; Phylogeny ; Proteins ; Quality ; Rice ; RNA Interference ; RNA, Messenger - genetics ; RNA-mediated interference ; Roundworms ; Sequence Alignment ; Transcriptome</subject><ispartof>PloS one, 2014-03, Vol.9 (3), p.e91591-e91591</ispartof><rights>COPYRIGHT 2014 Public Library of Science</rights><rights>2014 Wang 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. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2014 Wang et al 2014 Wang et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c688t-f941a4798eb248865eafedeca0a08c6e40f4810541c63229cfcec9972eb5d33e3</citedby><cites>FETCH-LOGICAL-c688t-f941a4798eb248865eafedeca0a08c6e40f4810541c63229cfcec9972eb5d33e3</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/PMC3956754/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3956754/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,728,781,785,865,886,2103,2929,23870,27928,27929,53795,53797</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24637831$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Bonaventure, Gustavo</contributor><creatorcontrib>Wang, Feng</creatorcontrib><creatorcontrib>Li, Danlei</creatorcontrib><creatorcontrib>Wang, Zhiying</creatorcontrib><creatorcontrib>Dong, Airong</creatorcontrib><creatorcontrib>Liu, Lihong</creatorcontrib><creatorcontrib>Wang, Buyong</creatorcontrib><creatorcontrib>Chen, Qiaoli</creatorcontrib><creatorcontrib>Liu, Xiaohan</creatorcontrib><title>Transcriptomic analysis of the rice white tip nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae)</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The rice white tip nematode Aphelenchoides besseyi, a devastating nematode whose genome has not been sequenced, is distributed widely throughout almost all the rice-growing regions of the world. The aims of the present study were to define the transcriptome of A. besseyi and to identify parasite-related, mortality-related or host resistance-overcoming genes in this nematode.
Using Solexa/Illumina sequencing, we profiled the transcriptome of mixed-stage populations of A. besseyi. A total of 51,270 transcripts without gaps were produced based on high-quality clean reads. Of all the A. besseyi transcripts, 9,132 KEGG Orthology assignments were annotated. Carbohydrate-active enzymes of glycoside hydrolases (GHs), glycosyltransferases (GTs), carbohydrate esterases (CEs) and carbohydrate-binding modules (CBMs) were identified. The presence of the A. besseyi GH45 cellulase gene was verified by in situ hybridization. Given that 13 unique A. besseyi potential effector genes were identified from 41 candidate effector homologs, further studies of these homologs are merited. Finally, comparative analyses were conducted between A. besseyi contigs and Caenorhabditis elegans genes to look for orthologs of RNAi phenotypes, neuropeptides and peptidases.
The present results provide comprehensive insight into the genetic makeup of A. besseyi. Many of this species' genes are parasite related, nematode mortality-related or necessary to overcome host resistance. The generated transcriptome dataset of A. besseyi reported here lays the foundation for further studies of the molecular mechanisms related to parasitism and facilitates the development of new control strategies for this species.</description><subject>Agricultural production</subject><subject>Amino Acid Sequence</subject><subject>Analysis</subject><subject>Animals</subject><subject>Aphelenchoides besseyi</subject><subject>Barley</subject><subject>Biology and Life Sciences</subject><subject>Caenorhabditis elegans</subject><subject>Carbohydrates</subject><subject>Cell Wall - metabolism</subject><subject>Cellulase</subject><subject>Cellulase - chemistry</subject><subject>Cellulase - genetics</subject><subject>Computational Biology</subject><subject>Databases, Nucleic Acid</subject><subject>Esterases</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Regulatory Networks</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Glycoside hydrolase</subject><subject>Health aspects</subject><subject>Homology</subject><subject>Hydrolases</subject><subject>Medicine and Health Sciences</subject><subject>Molecular modelling</subject><subject>Molecular Sequence Data</subject><subject>Mortality</subject><subject>Nematoda - classification</subject><subject>Nematoda - genetics</subject><subject>Nematoda - metabolism</subject><subject>Nematodes</subject><subject>Neuropeptides</subject><subject>Neuropeptides - genetics</subject><subject>Neuropeptides - metabolism</subject><subject>Orthology</subject><subject>Oryza - parasitology</subject><subject>Parasitism</subject><subject>Peptidases</subject><subject>Peptide Hydrolases - genetics</subject><subject>Peptide Hydrolases - metabolism</subject><subject>Phylogeny</subject><subject>Proteins</subject><subject>Quality</subject><subject>Rice</subject><subject>RNA Interference</subject><subject>RNA, Messenger - genetics</subject><subject>RNA-mediated interference</subject><subject>Roundworms</subject><subject>Sequence Alignment</subject><subject>Transcriptome</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</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>eNqNk22L1DAQx4so3oN-A9GCcNyBuyZNmqa-EJbDh4XDAz19G7LpZJu1bWqSqvvtzbq9Yyv3QvIiYfKb_2QmM0nyDKM5JgV-vbGD62Qz720Hc4RKnJf4QXKMS5LNWIbIw4PzUXLi_QahnHDGHidHGWWk4AQfJ99vnOy8cqYPtjUqlVFy641PrU5DDakzCtJftQmQBtOnHbQy2ApepYu-hgY6VVtTgU9X4D1sTXr-aU_INxPCVBIuniSPtGw8PB330-Tr-3c3lx9nV9cflpeLq5linIeZLimWtCg5rDLKOctBaqhASSQRVwwo0pRjlFOsGMmyUmkFqiyLDFZ5RQiQ0-TFXrdvrBdjnbzAOeKIlxlDkVjuicrKjeidaaXbCiuN-Guwbi2kC0Y1IDKlCWNshTRWtIoxlARNCFKEgdKURq23Y7Rh1UKloAtONhPR6U1narG2PwUpc1bkO4HzUcDZHwP4IFrjFTSN7MAO-3ezoshZFtGX_6D3ZzdSaxkTMJ22Ma7aiYoFLXjBMKI7rfk9VFwVxEaITaVNtE8cLiYOkQnwO6zl4L1Yfvn8_-z1tyl7dsDWIJtQe9sMwdjOT0G6B5Wz3jvQd0XGSOxm4rYaYjcTYpyJ6Pb88IPunG6HgPwBDBwIFw</recordid><startdate>20140317</startdate><enddate>20140317</enddate><creator>Wang, Feng</creator><creator>Li, Danlei</creator><creator>Wang, Zhiying</creator><creator>Dong, Airong</creator><creator>Liu, Lihong</creator><creator>Wang, Buyong</creator><creator>Chen, Qiaoli</creator><creator>Liu, Xiaohan</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>IOV</scope><scope>ISR</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>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>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20140317</creationdate><title>Transcriptomic analysis of the rice white tip nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae)</title><author>Wang, Feng ; Li, Danlei ; Wang, Zhiying ; Dong, Airong ; Liu, Lihong ; Wang, Buyong ; Chen, Qiaoli ; Liu, Xiaohan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c688t-f941a4798eb248865eafedeca0a08c6e40f4810541c63229cfcec9972eb5d33e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Agricultural production</topic><topic>Amino Acid Sequence</topic><topic>Analysis</topic><topic>Animals</topic><topic>Aphelenchoides besseyi</topic><topic>Barley</topic><topic>Biology and Life Sciences</topic><topic>Caenorhabditis elegans</topic><topic>Carbohydrates</topic><topic>Cell Wall - metabolism</topic><topic>Cellulase</topic><topic>Cellulase - chemistry</topic><topic>Cellulase - genetics</topic><topic>Computational Biology</topic><topic>Databases, Nucleic Acid</topic><topic>Esterases</topic><topic>Gene expression</topic><topic>Gene Expression Profiling</topic><topic>Gene Regulatory Networks</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Glycoside hydrolase</topic><topic>Health aspects</topic><topic>Homology</topic><topic>Hydrolases</topic><topic>Medicine and Health Sciences</topic><topic>Molecular modelling</topic><topic>Molecular Sequence Data</topic><topic>Mortality</topic><topic>Nematoda - classification</topic><topic>Nematoda - genetics</topic><topic>Nematoda - metabolism</topic><topic>Nematodes</topic><topic>Neuropeptides</topic><topic>Neuropeptides - genetics</topic><topic>Neuropeptides - metabolism</topic><topic>Orthology</topic><topic>Oryza - parasitology</topic><topic>Parasitism</topic><topic>Peptidases</topic><topic>Peptide Hydrolases - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wang, Feng</au><au>Li, Danlei</au><au>Wang, Zhiying</au><au>Dong, Airong</au><au>Liu, Lihong</au><au>Wang, Buyong</au><au>Chen, Qiaoli</au><au>Liu, Xiaohan</au><au>Bonaventure, Gustavo</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Transcriptomic analysis of the rice white tip nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae)</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2014-03-17</date><risdate>2014</risdate><volume>9</volume><issue>3</issue><spage>e91591</spage><epage>e91591</epage><pages>e91591-e91591</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The rice white tip nematode Aphelenchoides besseyi, a devastating nematode whose genome has not been sequenced, is distributed widely throughout almost all the rice-growing regions of the world. The aims of the present study were to define the transcriptome of A. besseyi and to identify parasite-related, mortality-related or host resistance-overcoming genes in this nematode.
Using Solexa/Illumina sequencing, we profiled the transcriptome of mixed-stage populations of A. besseyi. A total of 51,270 transcripts without gaps were produced based on high-quality clean reads. Of all the A. besseyi transcripts, 9,132 KEGG Orthology assignments were annotated. Carbohydrate-active enzymes of glycoside hydrolases (GHs), glycosyltransferases (GTs), carbohydrate esterases (CEs) and carbohydrate-binding modules (CBMs) were identified. The presence of the A. besseyi GH45 cellulase gene was verified by in situ hybridization. Given that 13 unique A. besseyi potential effector genes were identified from 41 candidate effector homologs, further studies of these homologs are merited. Finally, comparative analyses were conducted between A. besseyi contigs and Caenorhabditis elegans genes to look for orthologs of RNAi phenotypes, neuropeptides and peptidases.
The present results provide comprehensive insight into the genetic makeup of A. besseyi. Many of this species' genes are parasite related, nematode mortality-related or necessary to overcome host resistance. The generated transcriptome dataset of A. besseyi reported here lays the foundation for further studies of the molecular mechanisms related to parasitism and facilitates the development of new control strategies for this species.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>24637831</pmid><doi>10.1371/journal.pone.0091591</doi><tpages>e91591</tpages><oa>free_for_read</oa></addata></record> |
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source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
subjects | Agricultural production Amino Acid Sequence Analysis Animals Aphelenchoides besseyi Barley Biology and Life Sciences Caenorhabditis elegans Carbohydrates Cell Wall - metabolism Cellulase Cellulase - chemistry Cellulase - genetics Computational Biology Databases, Nucleic Acid Esterases Gene expression Gene Expression Profiling Gene Regulatory Networks Gene sequencing Genes Genomes Genomics Glycoside hydrolase Health aspects Homology Hydrolases Medicine and Health Sciences Molecular modelling Molecular Sequence Data Mortality Nematoda - classification Nematoda - genetics Nematoda - metabolism Nematodes Neuropeptides Neuropeptides - genetics Neuropeptides - metabolism Orthology Oryza - parasitology Parasitism Peptidases Peptide Hydrolases - genetics Peptide Hydrolases - metabolism Phylogeny Proteins Quality Rice RNA Interference RNA, Messenger - genetics RNA-mediated interference Roundworms Sequence Alignment Transcriptome |
title | Transcriptomic analysis of the rice white tip nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae) |
url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-17T05%3A30%3A54IST&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=Transcriptomic%20analysis%20of%20the%20rice%20white%20tip%20nematode,%20Aphelenchoides%20besseyi%20(Nematoda:%20Aphelenchoididae)&rft.jtitle=PloS%20one&rft.au=Wang,%20Feng&rft.date=2014-03-17&rft.volume=9&rft.issue=3&rft.spage=e91591&rft.epage=e91591&rft.pages=e91591-e91591&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0091591&rft_dat=%3Cgale_plos_%3EA478761042%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=1508089260&rft_id=info:pmid/24637831&rft_galeid=A478761042&rft_doaj_id=oai_doaj_org_article_2cf3666b0f1c4d2ebcaef330c36ecf44&rfr_iscdi=true |