{"corpus_id":2033419,"paper_sha":null,"doi":"10.1038/s41598-017-05377-y","arxiv_id":null,"pmid":28687784,"pmcid":"5501815","mag_id":2724197362,"dblp_id":null,"acl_id":null,"title":"Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genes","year":2017,"publication_date":"2017-07-07","venue":"Scientific Reports","journal":{"name":"Scientific Reports","pages":null,"volume":"7"},"journal_issn":null,"journal_title":null,"publication_types":["JournalArticle"],"pubmed_pub_types":["Journal Article","Research Support, Non-U.S. Gov't"],"s2_fields_of_study":["Biology","Medicine","Environmental Science"],"reference_count":75,"citation_count":53,"influential_citation_count":1,"is_open_access":true,"arxiv_categories":null,"arxiv_license":null,"arxiv_journal_ref":null,"mesh_headings":[{"d":"Actinidia","mj":false,"qs":[{"q":"genetics","mj":true,"ui":"Q000235"},{"q":"immunology","mj":false,"ui":"Q000276"},{"q":"microbiology","mj":false,"ui":"Q000382"}],"ui":"D029042"},{"d":"Cluster Analysis","mj":false,"ui":"D016000"},{"d":"Gene Expression Profiling","mj":false,"ui":"D020869"},{"d":"Gene Expression Regulation, Plant","mj":true,"ui":"D018506"},{"d":"Gene Regulatory Networks","mj":false,"ui":"D053263"},{"d":"Host Specificity","mj":false,"ui":"D058507"},{"d":"Plant Diseases","mj":false,"qs":[{"q":"genetics","mj":false,"ui":"Q000235"},{"q":"immunology","mj":false,"ui":"Q000276"},{"q":"microbiology","mj":false,"ui":"Q000382"}],"ui":"D010935"},{"d":"Plant Immunity","mj":false,"qs":[{"q":"genetics","mj":false,"ui":"Q000235"}],"ui":"D057865"},{"d":"Plant Proteins","mj":false,"qs":[{"q":"genetics","mj":true,"ui":"Q000235"},{"q":"immunology","mj":false,"ui":"Q000276"}],"ui":"D010940"},{"d":"Pseudomonas syringae","mj":false,"qs":[{"q":"pathogenicity","mj":true,"ui":"Q000472"},{"q":"physiology","mj":false,"ui":"Q000502"}],"ui":"D044224"},{"d":"RNA, Long Noncoding","mj":false,"qs":[{"q":"genetics","mj":true,"ui":"Q000235"},{"q":"immunology","mj":false,"ui":"Q000276"}],"ui":"D062085"},{"d":"RNA, Plant","mj":false,"qs":[{"q":"genetics","mj":false,"ui":"Q000235"},{"q":"immunology","mj":false,"ui":"Q000276"}],"ui":"D018749"},{"d":"Signal Transduction","mj":false,"ui":"D015398"},{"d":"Transcriptome","mj":true,"ui":"D059467"},{"d":"Exome Sequencing","mj":false,"ui":"D000073359"}],"chemicals":[{"n":"Plant Proteins","ui":"D010940","reg":"0"},{"n":"RNA, Long Noncoding","ui":"D062085","reg":"0"},{"n":"RNA, Plant","ui":"D018749","reg":"0"}],"comments_corrections":null,"source_flags":5,"s2_open_access_pdf_url":"https://www.nature.com/articles/s41598-017-05377-y.pdf","s2_open_access_landing_url":"https://www.semanticscholar.org/paper/22fe905859184516d6b15592540a1431ee387f36","s2_open_access_license":"CCBY","s2_open_access_status":"GOLD","pmc_open_access_pdf_url":null,"pmc_open_access_landing_url":null,"pmc_open_access_license":null,"pmc_open_access_status":null,"unpaywall_open_access_pdf_url":null,"unpaywall_open_access_landing_url":null,"unpaywall_open_access_license":null,"unpaywall_open_access_status":null,"abstract":"An outbreak of kiwifruit bacterial canker disease caused by Pseudomonas syringae pv. actinidiae (Psa) beginning in 2008 caused disaster to the kiwifruit industry. However the mechanisms of interaction between kiwifruit and Psa are unknown. Long noncoding RNAs (lncRNAs) are known to regulate many biological processes, but comprehensive repertoires of kiwifruit lncRNAs and their effects on the interaction between kiwifruit and Psa are unknown. Here, based on in-depth transcriptomic analysis of four kiwifruit materials at three stages of infection with Psa, we identified 14,845 transcripts from 12,280 loci as putative lncRNAs. Hierarchical clustering analysis of differentially-expressed transcripts reveals that both protein-coding and lncRNA transcripts are expressed species-specifically. Comparing differentially-expressed transcripts from different species, variations in pattern-triggered immunity (PTI) were the main causes of species-specific responses to infection by Psa. Using weighted gene co-expression network analysis, we identified species-specific expressed key lncRNAs which were closely related to plant immune response and signal transduction. Our results illustrate that different kiwifruit species employ multiple different plant immunity layers to fight against Psa infection, which causes distinct responses. We also discovered that lncRNAs might affect kiwifruit responses to Psa infection, indicating that both protein-coding regions and noncoding regions can affect kiwifruit response to Psa infection.","claims":[{"public_id":"cl_6d690f42a7847e23d27cee6ef59c1e1d","status":"active","text":"Different kiwifruit species employ multiple plant immunity layers to fight against Pseudomonas syringae pv. actinidiae infection, producing distinct responses.","confidence":0.86,"contributors":[{"id":136,"public_id":"3c2apqe3ut","public_label":"Anonymous (3c2apqe3ut)","roles":["extraction"],"url":"https://sah.borca.ai/u/3c2apqe3ut"},{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["review"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale 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transcriptomic analysis of four kiwifruit materials at three stages of infection with Pseudomonas syringae pv. actinidiae identified 14,845 transcripts from 12,280 loci as putative long noncoding RNAs.","confidence":0.96,"contributors":[{"id":136,"public_id":"3c2apqe3ut","public_label":"Anonymous (3c2apqe3ut)","roles":["extraction"],"url":"https://sah.borca.ai/u/3c2apqe3ut"},{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["review"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"}],"url":"https://sah.borca.ai/claims/cl_bdd16afe9cf97e7ce7ea8cb88d7ba0a6"},{"public_id":"cl_6c7ff3815be2a91c5a3625dcd6acca47","status":"active","text":"Variations in pattern-triggered immunity were identified as the main causes of species-specific responses to infection by Pseudomonas syringae pv. actinidiae.","confidence":0.9,"contributors":[{"id":136,"public_id":"3c2apqe3ut","public_label":"Anonymous (3c2apqe3ut)","roles":["extraction"],"url":"https://sah.borca.ai/u/3c2apqe3ut"},{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["review"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"}],"url":"https://sah.borca.ai/claims/cl_6c7ff3815be2a91c5a3625dcd6acca47"},{"public_id":"cl_811a85c389281c3a3a543db527cbc614","status":"active","text":"Weighted gene co-expression network analysis identified species-specific expressed key long noncoding RNAs closely related to plant immune response and signal transduction.","confidence":0.91,"contributors":[{"id":136,"public_id":"3c2apqe3ut","public_label":"Anonymous (3c2apqe3ut)","roles":["extraction"],"url":"https://sah.borca.ai/u/3c2apqe3ut"},{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["review"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"}],"url":"https://sah.borca.ai/claims/cl_811a85c389281c3a3a543db527cbc614"}],"concepts":[{"public_id":"co_19b930dbdd40c2a3be262bd1ce746c01","status":"active","name":"in-depth transcriptomic analysis","description":"A sequencing-based analysis of transcript expression across kiwifruit materials and infection stages.","types":["method"],"aliases":[],"contributors":[{"id":136,"public_id":"3c2apqe3ut","public_label":"Anonymous (3c2apqe3ut)","roles":["extraction"],"url":"https://sah.borca.ai/u/3c2apqe3ut"},{"id":2,"public_id":"4715169a40","public_label":"AK 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