Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi
Hemibiotrophic fungal plant pathogens represent a group of agronomically significant disease‐causing agents that grow first on living tissue and then cause host death in later, necrotrophic growth. Among these, Colletotrichum spp. are devastating pathogens of many crops. Identifying expanded classes...
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| Veröffentlicht in: | The New phytologist 2013-03, Vol.197 (4), p.1236-1249 |
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| creator | Gan, Pamela Ikeda, Kyoko Irieda, Hiroki Narusaka, Mari O'Connell, Richard J Narusaka, Yoshihiro Takano, Yoshitaka Kubo, Yasuyuki Shirasu, Ken |
| description | Hemibiotrophic fungal plant pathogens represent a group of agronomically significant disease‐causing agents that grow first on living tissue and then cause host death in later, necrotrophic growth. Among these, Colletotrichum spp. are devastating pathogens of many crops. Identifying expanded classes of genes in the genomes of phytopathogenic Colletotrichum, especially those associated with specific stages of hemibiotrophy, can provide insights on how these pathogens infect a large number of hosts. The genomes of Colletotrichum orbiculare, which infects cucurbits and Nicotiana benthamiana, and C. gloeosporioides, which infects a wide range of crops, were sequenced and analyzed, focusing on features with potential roles in pathogenicity. Regulation of C. orbiculare gene expression was investigated during infection of N. benthamiana using a custom microarray. Genes expanded in both genomes compared to other fungi included sequences encoding small, secreted proteins (SSPs), secondary metabolite synthesis genes, proteases and carbohydrate‐degrading enzymes. Many SSP and secondary metabolite synthesis genes were upregulated during initial stages of host colonization, whereas the necrotrophic stage of growth is characterized by upregulation of sequences encoding degradative enzymes. Hemibiotrophy in C. orbiculare is characterized by distinct stage‐specific gene expression profiles of expanded classes of potential pathogenicity genes. |
| doi_str_mv | 10.1111/nph.12085 |
| format | Article |
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Among these, Colletotrichum spp. are devastating pathogens of many crops. Identifying expanded classes of genes in the genomes of phytopathogenic Colletotrichum, especially those associated with specific stages of hemibiotrophy, can provide insights on how these pathogens infect a large number of hosts. The genomes of Colletotrichum orbiculare, which infects cucurbits and Nicotiana benthamiana, and C. gloeosporioides, which infects a wide range of crops, were sequenced and analyzed, focusing on features with potential roles in pathogenicity. Regulation of C. orbiculare gene expression was investigated during infection of N. benthamiana using a custom microarray. Genes expanded in both genomes compared to other fungi included sequences encoding small, secreted proteins (SSPs), secondary metabolite synthesis genes, proteases and carbohydrate‐degrading enzymes. Many SSP and secondary metabolite synthesis genes were upregulated during initial stages of host colonization, whereas the necrotrophic stage of growth is characterized by upregulation of sequences encoding degradative enzymes. Hemibiotrophy in C. orbiculare is characterized by distinct stage‐specific gene expression profiles of expanded classes of potential pathogenicity genes.</description><identifier>ISSN: 0028-646X</identifier><identifier>EISSN: 1469-8137</identifier><identifier>DOI: 10.1111/nph.12085</identifier><identifier>PMID: 23252678</identifier><language>eng</language><publisher>England: William Wesley and Son</publisher><subject>Base Composition ; Carbohydrates ; cell wall‐degrading enzymes ; Colletotrichum ; Colletotrichum - genetics ; Colletotrichum - physiology ; Colletotrichum orbiculare ; Colonization ; Crops ; Cucurbitaceae ; Cucurbitaceae - microbiology ; death ; DNA microarrays ; DNA, Fungal ; effectors ; Enzymes ; Fungi ; Gene expression ; Gene Expression Profiling ; gene expression regulation ; Genes ; Genes, Fungal ; genome ; Genome, Fungal ; Genomes ; Genomics ; hemibiotrophy ; hosts ; Hyphae ; Infections ; Metabolites ; microarray technology ; Nicotiana - microbiology ; Nicotiana benthamiana ; Pathogenicity ; Pathogens ; Plant Diseases - microbiology ; plant pathogenic fungi ; plant pathogenomics ; Plants ; protease ; proteinases ; proteins ; secondary metabolite ; Sequence Analysis, DNA ; Synthesis ; Tissues ; Transcriptome ; transcriptomics</subject><ispartof>The New phytologist, 2013-03, Vol.197 (4), p.1236-1249</ispartof><rights>2013 New Phytologist Trust</rights><rights>2012 The Authors New Phytologist © 2012 New Phytologist Trust</rights><rights>2012 The Authors New Phytologist © 2012 New Phytologist Trust.</rights><rights>Copyright © 2013 New Phytologist Trust</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4775-40450cca31afc72e3728eb439d752262234d1ceb28e6ecfbb4022b10e1f3fed53</citedby><cites>FETCH-LOGICAL-c4775-40450cca31afc72e3728eb439d752262234d1ceb28e6ecfbb4022b10e1f3fed53</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/newphytologist.197.4.1236$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/newphytologist.197.4.1236$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,776,780,799,1411,1427,27903,27904,45553,45554,46387,46811,57995,58228</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23252678$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Gan, Pamela</creatorcontrib><creatorcontrib>Ikeda, Kyoko</creatorcontrib><creatorcontrib>Irieda, Hiroki</creatorcontrib><creatorcontrib>Narusaka, Mari</creatorcontrib><creatorcontrib>O'Connell, Richard J</creatorcontrib><creatorcontrib>Narusaka, Yoshihiro</creatorcontrib><creatorcontrib>Takano, Yoshitaka</creatorcontrib><creatorcontrib>Kubo, Yasuyuki</creatorcontrib><creatorcontrib>Shirasu, Ken</creatorcontrib><title>Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi</title><title>The New phytologist</title><addtitle>New Phytol</addtitle><description>Hemibiotrophic fungal plant pathogens represent a group of agronomically significant disease‐causing agents that grow first on living tissue and then cause host death in later, necrotrophic growth. Among these, Colletotrichum spp. are devastating pathogens of many crops. Identifying expanded classes of genes in the genomes of phytopathogenic Colletotrichum, especially those associated with specific stages of hemibiotrophy, can provide insights on how these pathogens infect a large number of hosts. The genomes of Colletotrichum orbiculare, which infects cucurbits and Nicotiana benthamiana, and C. gloeosporioides, which infects a wide range of crops, were sequenced and analyzed, focusing on features with potential roles in pathogenicity. Regulation of C. orbiculare gene expression was investigated during infection of N. benthamiana using a custom microarray. Genes expanded in both genomes compared to other fungi included sequences encoding small, secreted proteins (SSPs), secondary metabolite synthesis genes, proteases and carbohydrate‐degrading enzymes. Many SSP and secondary metabolite synthesis genes were upregulated during initial stages of host colonization, whereas the necrotrophic stage of growth is characterized by upregulation of sequences encoding degradative enzymes. Hemibiotrophy in C. orbiculare is characterized by distinct stage‐specific gene expression profiles of expanded classes of potential pathogenicity genes.</description><subject>Base Composition</subject><subject>Carbohydrates</subject><subject>cell wall‐degrading enzymes</subject><subject>Colletotrichum</subject><subject>Colletotrichum - genetics</subject><subject>Colletotrichum - physiology</subject><subject>Colletotrichum orbiculare</subject><subject>Colonization</subject><subject>Crops</subject><subject>Cucurbitaceae</subject><subject>Cucurbitaceae - microbiology</subject><subject>death</subject><subject>DNA microarrays</subject><subject>DNA, Fungal</subject><subject>effectors</subject><subject>Enzymes</subject><subject>Fungi</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>gene expression regulation</subject><subject>Genes</subject><subject>Genes, Fungal</subject><subject>genome</subject><subject>Genome, Fungal</subject><subject>Genomes</subject><subject>Genomics</subject><subject>hemibiotrophy</subject><subject>hosts</subject><subject>Hyphae</subject><subject>Infections</subject><subject>Metabolites</subject><subject>microarray technology</subject><subject>Nicotiana - microbiology</subject><subject>Nicotiana benthamiana</subject><subject>Pathogenicity</subject><subject>Pathogens</subject><subject>Plant Diseases - microbiology</subject><subject>plant pathogenic fungi</subject><subject>plant pathogenomics</subject><subject>Plants</subject><subject>protease</subject><subject>proteinases</subject><subject>proteins</subject><subject>secondary metabolite</subject><subject>Sequence Analysis, DNA</subject><subject>Synthesis</subject><subject>Tissues</subject><subject>Transcriptome</subject><subject>transcriptomics</subject><issn>0028-646X</issn><issn>1469-8137</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkktv1DAUhSMEotPCgj8AltiURaZ-5rGsRkCRKkCCSuwsx7lOPEriYDut5t_jkmkXSIA3V7r3O8fWPc6yVwRvSToX09xvCcWVeJJtCC_qvCKsfJptMKZVXvDix0l2GsIeY1yLgj7PTiijghZltcnGnRtn5VW0t4A6mNxoNVJTi6JXU9DezvHYUsMhQEAebkENKPaAehhtY130bu4TEqLqAIXemoicQTs3DBDT1Op-GZFZps6-yJ4ZNQR4eaxn2c2H9993V_n1l4-fdpfXueZlKXKOucBaK0aU0SUFVtIKGs7qthSUFpQy3hINTeoWoE3TcExpQzAQwwy0gp1l56vv7N3PBUKUow0ahkFN4JYgCSNpEYLh-v8orTit7u9N6Ns_0L1bfFpMkFQQxirMK_EvinBGGak5wYl6t1LauxA8GDl7Oyp_kATL-1BlClX-DjWxr4-OSzNC-0g-pJiAixW4swMc_u4kP3-9erDcrop9iM4_Kia4m_tDdIPrbHo4qUvJk5QVSfBmFRjlpOq8DfLmG8VEpE9FqrrG7BduTcU_</recordid><startdate>201303</startdate><enddate>201303</enddate><creator>Gan, Pamela</creator><creator>Ikeda, Kyoko</creator><creator>Irieda, Hiroki</creator><creator>Narusaka, Mari</creator><creator>O'Connell, Richard J</creator><creator>Narusaka, Yoshihiro</creator><creator>Takano, Yoshitaka</creator><creator>Kubo, Yasuyuki</creator><creator>Shirasu, Ken</creator><general>William Wesley and Son</general><general>New Phytologist Trust</general><general>Wiley Subscription Services, Inc</general><scope>FBQ</scope><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>7QO</scope><scope>7SN</scope><scope>8FD</scope><scope>C1K</scope><scope>F1W</scope><scope>FR3</scope><scope>H95</scope><scope>L.G</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>201303</creationdate><title>Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi</title><author>Gan, Pamela ; 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Among these, Colletotrichum spp. are devastating pathogens of many crops. Identifying expanded classes of genes in the genomes of phytopathogenic Colletotrichum, especially those associated with specific stages of hemibiotrophy, can provide insights on how these pathogens infect a large number of hosts. The genomes of Colletotrichum orbiculare, which infects cucurbits and Nicotiana benthamiana, and C. gloeosporioides, which infects a wide range of crops, were sequenced and analyzed, focusing on features with potential roles in pathogenicity. Regulation of C. orbiculare gene expression was investigated during infection of N. benthamiana using a custom microarray. Genes expanded in both genomes compared to other fungi included sequences encoding small, secreted proteins (SSPs), secondary metabolite synthesis genes, proteases and carbohydrate‐degrading enzymes. Many SSP and secondary metabolite synthesis genes were upregulated during initial stages of host colonization, whereas the necrotrophic stage of growth is characterized by upregulation of sequences encoding degradative enzymes. Hemibiotrophy in C. orbiculare is characterized by distinct stage‐specific gene expression profiles of expanded classes of potential pathogenicity genes.</abstract><cop>England</cop><pub>William Wesley and Son</pub><pmid>23252678</pmid><doi>10.1111/nph.12085</doi><tpages>14</tpages></addata></record> |
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| subjects | Base Composition Carbohydrates cell wall‐degrading enzymes Colletotrichum Colletotrichum - genetics Colletotrichum - physiology Colletotrichum orbiculare Colonization Crops Cucurbitaceae Cucurbitaceae - microbiology death DNA microarrays DNA, Fungal effectors Enzymes Fungi Gene expression Gene Expression Profiling gene expression regulation Genes Genes, Fungal genome Genome, Fungal Genomes Genomics hemibiotrophy hosts Hyphae Infections Metabolites microarray technology Nicotiana - microbiology Nicotiana benthamiana Pathogenicity Pathogens Plant Diseases - microbiology plant pathogenic fungi plant pathogenomics Plants protease proteinases proteins secondary metabolite Sequence Analysis, DNA Synthesis Tissues Transcriptome transcriptomics |
| title | Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi |
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