Global transcriptome analyses reveal the molecular signatures in the early response of potato (Solanum tuberosum L.) to Phytophthora infestans, Ralstonia solanacearum, and Potato virus Y infection.
Identifieur interne : 000174 ( Main/Exploration ); précédent : 000173; suivant : 000175Global transcriptome analyses reveal the molecular signatures in the early response of potato (Solanum tuberosum L.) to Phytophthora infestans, Ralstonia solanacearum, and Potato virus Y infection.
Auteurs : Weilin Cao [République populaire de Chine] ; Liming Gan [République populaire de Chine] ; Kaijie Shang [République populaire de Chine] ; Chenchen Wang [République populaire de Chine] ; Yunzhi Song [République populaire de Chine] ; Hongmei Liu [République populaire de Chine] ; Shumei Zhou [République populaire de Chine] ; Changxiang Zhu [République populaire de Chine]Source :
- Planta [ 1432-2048 ] ; 2020.
Abstract
MAIN CONCLUSION
Specific and common genes including transcription factors, resistance genes and pathways were significantly induced in potato by Phytophthora infestans, Ralstonia solanacearum, and Potato virus Y infection. The three major pathogens, namely, Phytophthora infestans, Ralstonia solanacearum, and Potato virus Y, can cause late blight, bacterial wilt, and necrotic ringspot, respectively, and thus severely reduce the yield and quality of potatoes (Solanum tuberosum L.). This study was the first to systematically analyze the relationship between transcriptome alterations in potato infected by these pathogens at the early stages. A total of 75,500 unigenes were identified, and 44,008 were annotated into 5 databases, namely, non-redundant (NR), Swiss-Prot protein, clusters of orthologous groups for eukaryotic complete genomes (KOG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A total of 6945 resistance genes and 11,878 transcription factors (TFs) were identified from all transcriptome data. Differential expression analysis revealed that 13,032 (9490 specifics), 9877 (6423 specifics), and 6661 (4144 specifics) differentially expressed genes (DEGs) were generated from comparisons of the P. infestans/control (Pi vs. Pi-CK), R. solanacearum/control (Rs vs. Rs-CK), and PVY/control (PVY vs. PVY-CK) treatments, respectively. The specific DEGs from the 3 comparisons were assigned to 13 common pathways, such as biosynthesis of amino acids, plant hormone signal transduction, carbon metabolism, and starch and sucrose metabolism. Weighted Gene Co-Expression Network Analysis (WGCNA) identified many hub unigenes, of which several unigenes were reported to regulate plant immune responses, such as FLAGELLIN-SENSITIVE 2 and chitinases. The present study provide crucial systems-level insights into the relationship between transcriptome changes in potato infected with the three pathogens. Moreover, this study presents a theoretical basis for breeding broad-spectrum and specific pathogen-resistant cultivars.
DOI: 10.1007/s00425-020-03471-6
PubMed: 32955625
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W" first="Weilin" last="Cao">Weilin Cao</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong</wicri:regionArea><wicri:noRegion>Shandong</wicri:noRegion></affiliation></author><author><name sortKey="Gan, Liming" sort="Gan, Liming" uniqKey="Gan L" first="Liming" last="Gan">Liming Gan</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong</wicri:regionArea><wicri:noRegion>Shandong</wicri:noRegion></affiliation></author><author><name sortKey="Shang, Kaijie" sort="Shang, Kaijie" uniqKey="Shang K" first="Kaijie" last="Shang">Kaijie Shang</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong</wicri:regionArea><wicri:noRegion>Shandong</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Chenchen" sort="Wang, Chenchen" uniqKey="Wang C" first="Chenchen" last="Wang">Chenchen Wang</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China.</nlm:affiliation><country 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wicri:level="1"><nlm:affiliation>State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong</wicri:regionArea><wicri:noRegion>Shandong</wicri:noRegion></affiliation></author><author><name sortKey="Zhou, Shumei" sort="Zhou, Shumei" uniqKey="Zhou S" first="Shumei" last="Zhou">Shumei Zhou</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 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xml:lang="en"><p><b>MAIN CONCLUSION</b></p><p>Specific and common genes including transcription factors, resistance genes and pathways were significantly induced in potato by Phytophthora infestans, Ralstonia solanacearum, and Potato virus Y infection. The three major pathogens, namely, Phytophthora infestans, Ralstonia solanacearum, and Potato virus Y, can cause late blight, bacterial wilt, and necrotic ringspot, respectively, and thus severely reduce the yield and quality of potatoes (Solanum tuberosum L.). This study was the first to systematically analyze the relationship between transcriptome alterations in potato infected by these pathogens at the early stages. A total of 75,500 unigenes were identified, and 44,008 were annotated into 5 databases, namely, non-redundant (NR), Swiss-Prot protein, clusters of orthologous groups for eukaryotic complete genomes (KOG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A total of 6945 resistance genes and 11,878 transcription factors (TFs) were identified from all transcriptome data. Differential expression analysis revealed that 13,032 (9490 specifics), 9877 (6423 specifics), and 6661 (4144 specifics) differentially expressed genes (DEGs) were generated from comparisons of the P. infestans/control (Pi vs. Pi-CK), R. solanacearum/control (Rs vs. Rs-CK), and PVY/control (PVY vs. PVY-CK) treatments, respectively. The specific DEGs from the 3 comparisons were assigned to 13 common pathways, such as biosynthesis of amino acids, plant hormone signal transduction, carbon metabolism, and starch and sucrose metabolism. Weighted Gene Co-Expression Network Analysis (WGCNA) identified many hub unigenes, of which several unigenes were reported to regulate plant immune responses, such as FLAGELLIN-SENSITIVE 2 and chitinases. The present study provide crucial systems-level insights into the relationship between transcriptome changes in potato infected with the three pathogens. Moreover, this study presents a theoretical basis for breeding broad-spectrum and specific pathogen-resistant cultivars.</p></div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">32955625</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>22</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1432-2048</ISSN><JournalIssue CitedMedium="Internet"><Volume>252</Volume><Issue>4</Issue><PubDate><Year>2020</Year><Month>Sep</Month><Day>21</Day></PubDate></JournalIssue><Title>Planta</Title><ISOAbbreviation>Planta</ISOAbbreviation></Journal><ArticleTitle>Global transcriptome analyses reveal the molecular signatures in the early response of potato (Solanum tuberosum L.) to Phytophthora infestans, Ralstonia solanacearum, and Potato virus Y infection.</ArticleTitle><Pagination><MedlinePgn>57</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00425-020-03471-6</ELocationID><Abstract><AbstractText Label="MAIN CONCLUSION" NlmCategory="UNASSIGNED">Specific and common genes including transcription factors, resistance genes and pathways were significantly induced in potato by Phytophthora infestans, Ralstonia solanacearum, and Potato virus Y infection. The three major pathogens, namely, Phytophthora infestans, Ralstonia solanacearum, and Potato virus Y, can cause late blight, bacterial wilt, and necrotic ringspot, respectively, and thus severely reduce the yield and quality of potatoes (Solanum tuberosum L.). This study was the first to systematically analyze the relationship between transcriptome alterations in potato infected by these pathogens at the early stages. A total of 75,500 unigenes were identified, and 44,008 were annotated into 5 databases, namely, non-redundant (NR), Swiss-Prot protein, clusters of orthologous groups for eukaryotic complete genomes (KOG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A total of 6945 resistance genes and 11,878 transcription factors (TFs) were identified from all transcriptome data. Differential expression analysis revealed that 13,032 (9490 specifics), 9877 (6423 specifics), and 6661 (4144 specifics) differentially expressed genes (DEGs) were generated from comparisons of the P. infestans/control (Pi vs. Pi-CK), R. solanacearum/control (Rs vs. Rs-CK), and PVY/control (PVY vs. PVY-CK) treatments, respectively. The specific DEGs from the 3 comparisons were assigned to 13 common pathways, such as biosynthesis of amino acids, plant hormone signal transduction, carbon metabolism, and starch and sucrose metabolism. Weighted Gene Co-Expression Network Analysis (WGCNA) identified many hub unigenes, of which several unigenes were reported to regulate plant immune responses, such as FLAGELLIN-SENSITIVE 2 and chitinases. The present study provide crucial systems-level insights into the relationship between transcriptome changes in potato infected with the three pathogens. Moreover, this study presents a theoretical basis for breeding broad-spectrum and specific pathogen-resistant cultivars.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cao</LastName><ForeName>Weilin</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gan</LastName><ForeName>Liming</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shang</LastName><ForeName>Kaijie</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Chenchen</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Song</LastName><ForeName>Yunzhi</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Hongmei</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhou</LastName><ForeName>Shumei</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Changxiang</ForeName><Initials>C</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-5640-6312</Identifier><AffiliationInfo><Affiliation>State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China. zhchx@sdau.edu.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>31720103912</GrantID><Agency>National Natural Science Foundation of China</Agency><Country></Country></Grant><Grant><GrantID>SYL2017XTTD11</GrantID><Agency>Shandong"Double Tops" Program</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>09</Month><Day>21</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Planta</MedlineTA><NlmUniqueID>1250576</NlmUniqueID><ISSNLinking>0032-0935</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Phytophthora infestans</Keyword><Keyword MajorTopicYN="N">Potato</Keyword><Keyword MajorTopicYN="N">Potato virus Y</Keyword><Keyword MajorTopicYN="N">Ralstonia solanacearum</Keyword><Keyword MajorTopicYN="N">Resistance gene</Keyword><Keyword MajorTopicYN="N">Transcription factor</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>05</Month><Day>27</Day></PubMedPubDate><PubMedPubDate 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