Genomic profiling of virulence in the soybean cyst nematode using single-nematode sequencing.
Identifieur interne : 000146 ( Main/Exploration ); précédent : 000145; suivant : 000147Genomic profiling of virulence in the soybean cyst nematode using single-nematode sequencing.
Auteurs : Dave T. Ste-Croix [Canada] ; Anne-Frédérique Gendron St-Marseille [Canada, Oman] ; Etienne Lord [Canada] ; Richard R. Belanger [Canada] ; Jacques Brodeur [Canada] ; Benjamin Mimee [Canada]Source :
- Phytopathology [ 0031-949X ] ; 2020.
Abstract
Soybean cyst nematode (SCN) is one of the most important diseases in soybean. Currently, the main management strategy relies on planting resistant cultivars. However, the overuse of a single resistance source has led to the selection of virulent SCN populations, although the mechanisms by which the nematode overcomes the resistance genes remain unknown. In this study, we used a nematode-adapted single-cell RNA-seq approach to identify SCN genes potentially involved in resistance breakdown in Peking and PI 88788 parental soybean lines. We established for the first time the full transcriptome of single SCN individuals allowing us to identify a list of putative virulence genes against both major SCN resistance sources. Our analysis identified 48 differentially expressed putative effectors (secreted proteins required for infection) alongside 40 effectors showing evidence of novel structural variants, and 11 effector genes containing phenotype-specific sequence polymorphisms. Additionally, a differential expression analysis revealed an interesting phenomenon of co-expressed gene regions with some containing putative effectors. The selection of virulent SCN individuals on Peking resulted in a profoundly altered transcriptome, especially for genes known to be involved in parasitism. Several sequence polymorphisms were also specific to these virulent nematodes and could potentially play a role in the acquisition of nematode virulence. On the other hand, the transcriptome of virulent individuals on PI 88788 was very similar to avirulent ones with the exception of a few genes, which suggest a distinct virulence strategy to Peking.
DOI: 10.1094/PHYTO-08-20-0348-FI
PubMed: 33100145
Affiliations:
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Ste-Croix</name><affiliation wicri:level="1"><nlm:affiliation>Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jean-sur-Richelieu, Quebec, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jean-sur-Richelieu, Quebec</wicri:regionArea><wicri:noRegion>Quebec</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Laval University Faculty of Agricultural and Food Sciences, 98676, Laval, Quebec, Canada; dave.thibouthotste-croix@canada.ca.</nlm:affiliation><country wicri:rule="url">Canada</country><wicri:regionArea>Laval University Faculty of Agricultural and Food Sciences, 98676, Laval, Quebec</wicri:regionArea><wicri:noRegion>Quebec</wicri:noRegion></affiliation></author><author><name sortKey="Gendron St Marseille, Anne Frederique" sort="Gendron St Marseille, Anne Frederique" uniqKey="Gendron St Marseille A" first="Anne-Frédérique" last="Gendron St-Marseille">Anne-Frédérique Gendron St-Marseille</name><affiliation wicri:level="1"><nlm:affiliation>Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jean-sur-Richelieu, Quebec, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jean-sur-Richelieu, Quebec</wicri:regionArea><wicri:noRegion>Quebec</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Université de Montréal Faculté des Arts et des Sciences, 141639, Institut de recherche en biologie végétale , Montreal, Quebec, Canada; anne-frederique.gendron@outlook.com.</nlm:affiliation><country wicri:rule="url">Oman</country><wicri:regionArea>Université de Montréal Faculté des Arts et des Sciences, 141639, Institut de recherche en biologie végétale , Montreal, Quebec</wicri:regionArea><wicri:noRegion>Quebec</wicri:noRegion></affiliation></author><author><name sortKey="Lord, Etienne" sort="Lord, Etienne" uniqKey="Lord E" first="Etienne" last="Lord">Etienne Lord</name><affiliation wicri:level="1"><nlm:affiliation>Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jean-sur-Richelieu, Quebec, Canada; etienne.lord@canada.ca.</nlm:affiliation><country wicri:rule="url">Canada</country><wicri:regionArea>Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jean-sur-Richelieu, Quebec</wicri:regionArea><wicri:noRegion>Quebec</wicri:noRegion></affiliation></author><author><name sortKey="Belanger, Richard R" sort="Belanger, Richard R" uniqKey="Belanger R" first="Richard R" last="Belanger">Richard R. Belanger</name><affiliation wicri:level="1"><nlm:affiliation>Laval University Faculty of Agricultural and Food Sciences, 98676, 2425 rue de l'Agriculture, Laval, Quebec, Canada, G1V0A6; richard.belanger@fsaa.ulaval.ca.</nlm:affiliation><country wicri:rule="url">Canada</country><wicri:regionArea>Laval University Faculty of Agricultural and Food Sciences, 98676, 2425 rue de l'Agriculture, Laval, Quebec, Canada</wicri:regionArea><wicri:noRegion>Canada</wicri:noRegion></affiliation></author><author><name sortKey="Brodeur, Jacques" sort="Brodeur, Jacques" uniqKey="Brodeur J" first="Jacques" last="Brodeur">Jacques Brodeur</name><affiliation wicri:level="1"><nlm:affiliation>Université de Montréal Faculté des Arts et des Sciences, 141639, Institut de recherche en biologie végétale , Montreal, Quebec, Canada; jacques.brodeur@umontreal.ca.</nlm:affiliation><country wicri:rule="url">Canada</country><wicri:regionArea>Université de Montréal Faculté des Arts et des Sciences, 141639, Institut de recherche en biologie végétale , Montreal, Quebec</wicri:regionArea><wicri:noRegion>Quebec</wicri:noRegion></affiliation></author><author><name sortKey="Mimee, Benjamin" sort="Mimee, Benjamin" uniqKey="Mimee B" first="Benjamin" last="Mimee">Benjamin Mimee</name><affiliation wicri:level="1"><nlm:affiliation>Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, 430 boul. Gouin, Saint-Jean-sur-Richelieu, Quebec, Canada, J3B 3E6; benjamin.mimee@canada.ca.</nlm:affiliation><country wicri:rule="url">Canada</country><wicri:regionArea>Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, 430 boul. Gouin, Saint-Jean-sur-Richelieu, Quebec, Canada</wicri:regionArea><wicri:noRegion>Canada</wicri:noRegion></affiliation></author></analytic><series><title level="j">Phytopathology</title><idno type="ISSN">0031-949X</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Soybean cyst nematode (SCN) is one of the most important diseases in soybean. Currently, the main management strategy relies on planting resistant cultivars. However, the overuse of a single resistance source has led to the selection of virulent SCN populations, although the mechanisms by which the nematode overcomes the resistance genes remain unknown. In this study, we used a nematode-adapted single-cell RNA-seq approach to identify SCN genes potentially involved in resistance breakdown in Peking and PI 88788 parental soybean lines. We established for the first time the full transcriptome of single SCN individuals allowing us to identify a list of putative virulence genes against both major SCN resistance sources. Our analysis identified 48 differentially expressed putative effectors (secreted proteins required for infection) alongside 40 effectors showing evidence of novel structural variants, and 11 effector genes containing phenotype-specific sequence polymorphisms. Additionally, a differential expression analysis revealed an interesting phenomenon of co-expressed gene regions with some containing putative effectors. The selection of virulent SCN individuals on Peking resulted in a profoundly altered transcriptome, especially for genes known to be involved in parasitism. Several sequence polymorphisms were also specific to these virulent nematodes and could potentially play a role in the acquisition of nematode virulence. On the other hand, the transcriptome of virulent individuals on PI 88788 was very similar to avirulent ones with the exception of a few genes, which suggest a distinct virulence strategy to Peking.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">33100145</PMID><DateRevised><Year>2020</Year><Month>10</Month><Day>26</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0031-949X</ISSN><JournalIssue CitedMedium="Print"><PubDate><Year>2020</Year><Month>Oct</Month><Day>25</Day></PubDate></JournalIssue><Title>Phytopathology</Title><ISOAbbreviation>Phytopathology</ISOAbbreviation></Journal><ArticleTitle>Genomic profiling of virulence in the soybean cyst nematode using single-nematode sequencing.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1094/PHYTO-08-20-0348-FI</ELocationID><Abstract><AbstractText>Soybean cyst nematode (SCN) is one of the most important diseases in soybean. Currently, the main management strategy relies on planting resistant cultivars. However, the overuse of a single resistance source has led to the selection of virulent SCN populations, although the mechanisms by which the nematode overcomes the resistance genes remain unknown. In this study, we used a nematode-adapted single-cell RNA-seq approach to identify SCN genes potentially involved in resistance breakdown in Peking and PI 88788 parental soybean lines. We established for the first time the full transcriptome of single SCN individuals allowing us to identify a list of putative virulence genes against both major SCN resistance sources. Our analysis identified 48 differentially expressed putative effectors (secreted proteins required for infection) alongside 40 effectors showing evidence of novel structural variants, and 11 effector genes containing phenotype-specific sequence polymorphisms. Additionally, a differential expression analysis revealed an interesting phenomenon of co-expressed gene regions with some containing putative effectors. The selection of virulent SCN individuals on Peking resulted in a profoundly altered transcriptome, especially for genes known to be involved in parasitism. Several sequence polymorphisms were also specific to these virulent nematodes and could potentially play a role in the acquisition of nematode virulence. On the other hand, the transcriptome of virulent individuals on PI 88788 was very similar to avirulent ones with the exception of a few genes, which suggest a distinct virulence strategy to Peking.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ste-Croix</LastName><ForeName>Dave T</ForeName><Initials>DT</Initials><AffiliationInfo><Affiliation>Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jean-sur-Richelieu, Quebec, Canada.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Laval University Faculty of Agricultural and Food Sciences, 98676, Laval, Quebec, Canada; dave.thibouthotste-croix@canada.ca.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gendron St-Marseille</LastName><ForeName>Anne-Frédérique</ForeName><Initials>AF</Initials><AffiliationInfo><Affiliation>Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jean-sur-Richelieu, Quebec, Canada.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Université de Montréal Faculté des Arts et des Sciences, 141639, Institut de recherche en biologie végétale , Montreal, Quebec, Canada; anne-frederique.gendron@outlook.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lord</LastName><ForeName>Etienne</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jean-sur-Richelieu, Quebec, Canada; etienne.lord@canada.ca.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Belanger</LastName><ForeName>Richard R</ForeName><Initials>RR</Initials><AffiliationInfo><Affiliation>Laval University Faculty of Agricultural and Food Sciences, 98676, 2425 rue de l'Agriculture, Laval, Quebec, Canada, G1V0A6; richard.belanger@fsaa.ulaval.ca.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Brodeur</LastName><ForeName>Jacques</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Université de Montréal Faculté des Arts et des Sciences, 141639, Institut de recherche en biologie végétale , Montreal, Quebec, Canada; jacques.brodeur@umontreal.ca.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mimee</LastName><ForeName>Benjamin</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, 430 boul. Gouin, Saint-Jean-sur-Richelieu, Quebec, Canada, J3B 3E6; benjamin.mimee@canada.ca.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>10</Month><Day>25</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Phytopathology</MedlineTA><NlmUniqueID>9427222</NlmUniqueID><ISSNLinking>0031-949X</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Disease Resistance</Keyword><Keyword MajorTopicYN="N">Evolution</Keyword><Keyword MajorTopicYN="N">Genomics</Keyword><Keyword MajorTopicYN="N">Host Parasite Interactions</Keyword><Keyword MajorTopicYN="N">Nematodes</Keyword><Keyword MajorTopicYN="N">Pathogen Effectors</Keyword><Keyword MajorTopicYN="N">Population Biology</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>10</Month><Day>26</Day><Hour>5</Hour><Minute>17</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>10</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>10</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">33100145</ArticleId><ArticleId IdType="doi">10.1094/PHYTO-08-20-0348-FI</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Canada</li><li>Oman</li></country></list><tree><country name="Canada"><noRegion><name sortKey="Ste Croix, Dave T" sort="Ste Croix, Dave T" uniqKey="Ste Croix D" first="Dave T" last="Ste-Croix">Dave T. Ste-Croix</name></noRegion><name sortKey="Belanger, Richard R" sort="Belanger, Richard R" uniqKey="Belanger R" first="Richard R" last="Belanger">Richard R. Belanger</name><name sortKey="Brodeur, Jacques" sort="Brodeur, Jacques" uniqKey="Brodeur J" first="Jacques" last="Brodeur">Jacques Brodeur</name><name sortKey="Gendron St Marseille, Anne Frederique" sort="Gendron St Marseille, Anne Frederique" uniqKey="Gendron St Marseille A" first="Anne-Frédérique" last="Gendron St-Marseille">Anne-Frédérique Gendron St-Marseille</name><name sortKey="Lord, Etienne" sort="Lord, Etienne" uniqKey="Lord E" first="Etienne" last="Lord">Etienne Lord</name><name sortKey="Mimee, Benjamin" sort="Mimee, Benjamin" uniqKey="Mimee B" first="Benjamin" last="Mimee">Benjamin Mimee</name><name sortKey="Ste Croix, Dave T" sort="Ste Croix, Dave T" uniqKey="Ste Croix D" first="Dave T" last="Ste-Croix">Dave T. 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