Genome-wide identification and expression analysis of the Brassica oleracea L. chitin-binding genes and response to pathogens infections
Abstract Chitinase, a category of pathogenesis-related proteins, is believed to play an important role in defending against external stress in plants. However, a comprehensive analysis of the chitin-binding gene family has not been reported to date in cabbage (Brassica oleracea L.), especially regar...
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| Veröffentlicht in: | Planta 2021-04, Vol.253 (4), p.1-14, Article 80 |
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| creator | Zhu, Mingzhao Lu, Shujin Zhuang, Mu Zhang, Yangyong Lv, Honghao Ji, Jialei Hou, Xilin Fang, Zhiyuan Wang, Yong Yang, Limei |
| description | Abstract Chitinase, a category of pathogenesis-related proteins, is believed to play an important role in defending against external stress in plants. However, a comprehensive analysis of the chitin-binding gene family has not been reported to date in cabbage (Brassica oleracea L.), especially regarding the roles that chitinases play in response to various diseases. In this study, a total of 20 chitinase genes were identified using a genome-wide search method. Phylogenetic analysis was employed to classify these genes into two groups. The genes were distributed unevenly across six chromosomes in cabbage, and all of them contained few introns (≤ 2). The results of collinear analysis showed that the cabbage genome contained 1–5 copies of each chitinase gene (excluding Bol035470) identified in Arabidopsis. The heatmap of the chitinase gene family showed that these genes were expressed in various tissues and organs. Two genes (Bol023322 and Bol041024) were relatively highly expressed in all of the investigated tissues under normal conditions, exhibiting the expression characteristics of housekeeping genes. In addition, under four different stresses, namely, Fusarium wilt, powdery mildew, black spot and downy mildew, we detected 9, 5, 8 and 8 genes with different expression levels in different treatments, respectively. Our results may help to elucidate the roles played by chitinases in the responses of host plants to various diseases. |
| doi_str_mv | 10.1007/s00425-021-03596-2 |
| format | Article |
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However, a comprehensive analysis of the chitin-binding gene family has not been reported to date in cabbage (Brassica oleracea L.), especially regarding the roles that chitinases play in response to various diseases. In this study, a total of 20 chitinase genes were identified using a genome-wide search method. Phylogenetic analysis was employed to classify these genes into two groups. The genes were distributed unevenly across six chromosomes in cabbage, and all of them contained few introns (≤ 2). The results of collinear analysis showed that the cabbage genome contained 1–5 copies of each chitinase gene (excluding Bol035470) identified in Arabidopsis. The heatmap of the chitinase gene family showed that these genes were expressed in various tissues and organs. Two genes (Bol023322 and Bol041024) were relatively highly expressed in all of the investigated tissues under normal conditions, exhibiting the expression characteristics of housekeeping genes. In addition, under four different stresses, namely, Fusarium wilt, powdery mildew, black spot and downy mildew, we detected 9, 5, 8 and 8 genes with different expression levels in different treatments, respectively. Our results may help to elucidate the roles played by chitinases in the responses of host plants to various diseases.</description><identifier>ISSN: 0032-0935</identifier><identifier>EISSN: 1432-2048</identifier><identifier>DOI: 10.1007/s00425-021-03596-2</identifier><identifier>PMID: 33742226</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Science + Business Media</publisher><subject>Agriculture ; Airborne microorganisms ; Binding ; Biomedical and Life Sciences ; Black spot ; Brassica ; Brassica - genetics ; Brassica - microbiology ; Brassica oleracea ; Chitin ; Chitin - metabolism ; Chitinase ; Chitinases - genetics ; Chromosomes ; Downy mildew ; Ecology ; Forestry ; Fusarium ; Gene expression ; Gene Expression Regulation, Plant ; Genes ; Genome, Plant ; Genomes ; Host plants ; Introns ; Life Sciences ; Organs ; Original ; ORIGINAL ARTICLE ; Pathogenesis ; Pathogenesis-related proteins ; Phylogeny ; Plant Immunity ; Plant Proteins - genetics ; Plant Sciences ; Powdery mildew ; Wilt</subject><ispartof>Planta, 2021-04, Vol.253 (4), p.1-14, Article 80</ispartof><rights>The Author(s) 2021</rights><rights>The Author(s) 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c496t-a643adb42ac647bd017920fe8a56279794286997cc810450eb6bab16df7fb0dc3</citedby><cites>FETCH-LOGICAL-c496t-a643adb42ac647bd017920fe8a56279794286997cc810450eb6bab16df7fb0dc3</cites><orcidid>0000-0002-0890-5854</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00425-021-03596-2$$EPDF$$P50$$Gspringer$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00425-021-03596-2$$EHTML$$P50$$Gspringer$$Hfree_for_read</linktohtml><link.rule.ids>230,314,776,780,881,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33742226$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhu, Mingzhao</creatorcontrib><creatorcontrib>Lu, Shujin</creatorcontrib><creatorcontrib>Zhuang, Mu</creatorcontrib><creatorcontrib>Zhang, Yangyong</creatorcontrib><creatorcontrib>Lv, Honghao</creatorcontrib><creatorcontrib>Ji, Jialei</creatorcontrib><creatorcontrib>Hou, Xilin</creatorcontrib><creatorcontrib>Fang, Zhiyuan</creatorcontrib><creatorcontrib>Wang, Yong</creatorcontrib><creatorcontrib>Yang, Limei</creatorcontrib><title>Genome-wide identification and expression analysis of the Brassica oleracea L. chitin-binding genes and response to pathogens infections</title><title>Planta</title><addtitle>Planta</addtitle><addtitle>Planta</addtitle><description>Abstract Chitinase, a category of pathogenesis-related proteins, is believed to play an important role in defending against external stress in plants. However, a comprehensive analysis of the chitin-binding gene family has not been reported to date in cabbage (Brassica oleracea L.), especially regarding the roles that chitinases play in response to various diseases. In this study, a total of 20 chitinase genes were identified using a genome-wide search method. Phylogenetic analysis was employed to classify these genes into two groups. The genes were distributed unevenly across six chromosomes in cabbage, and all of them contained few introns (≤ 2). The results of collinear analysis showed that the cabbage genome contained 1–5 copies of each chitinase gene (excluding Bol035470) identified in Arabidopsis. The heatmap of the chitinase gene family showed that these genes were expressed in various tissues and organs. Two genes (Bol023322 and Bol041024) were relatively highly expressed in all of the investigated tissues under normal conditions, exhibiting the expression characteristics of housekeeping genes. In addition, under four different stresses, namely, Fusarium wilt, powdery mildew, black spot and downy mildew, we detected 9, 5, 8 and 8 genes with different expression levels in different treatments, respectively. Our results may help to elucidate the roles played by chitinases in the responses of host plants to various diseases.</description><subject>Agriculture</subject><subject>Airborne microorganisms</subject><subject>Binding</subject><subject>Biomedical and Life Sciences</subject><subject>Black spot</subject><subject>Brassica</subject><subject>Brassica - genetics</subject><subject>Brassica - microbiology</subject><subject>Brassica oleracea</subject><subject>Chitin</subject><subject>Chitin - metabolism</subject><subject>Chitinase</subject><subject>Chitinases - genetics</subject><subject>Chromosomes</subject><subject>Downy mildew</subject><subject>Ecology</subject><subject>Forestry</subject><subject>Fusarium</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Plant</subject><subject>Genes</subject><subject>Genome, Plant</subject><subject>Genomes</subject><subject>Host plants</subject><subject>Introns</subject><subject>Life Sciences</subject><subject>Organs</subject><subject>Original</subject><subject>ORIGINAL ARTICLE</subject><subject>Pathogenesis</subject><subject>Pathogenesis-related proteins</subject><subject>Phylogeny</subject><subject>Plant Immunity</subject><subject>Plant Proteins - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Planta</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhu, Mingzhao</au><au>Lu, Shujin</au><au>Zhuang, Mu</au><au>Zhang, Yangyong</au><au>Lv, Honghao</au><au>Ji, Jialei</au><au>Hou, Xilin</au><au>Fang, Zhiyuan</au><au>Wang, Yong</au><au>Yang, Limei</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-wide identification and expression analysis of the Brassica oleracea L. chitin-binding genes and response to pathogens infections</atitle><jtitle>Planta</jtitle><stitle>Planta</stitle><addtitle>Planta</addtitle><date>2021-04-01</date><risdate>2021</risdate><volume>253</volume><issue>4</issue><spage>1</spage><epage>14</epage><pages>1-14</pages><artnum>80</artnum><issn>0032-0935</issn><eissn>1432-2048</eissn><abstract>Abstract Chitinase, a category of pathogenesis-related proteins, is believed to play an important role in defending against external stress in plants. However, a comprehensive analysis of the chitin-binding gene family has not been reported to date in cabbage (Brassica oleracea L.), especially regarding the roles that chitinases play in response to various diseases. In this study, a total of 20 chitinase genes were identified using a genome-wide search method. Phylogenetic analysis was employed to classify these genes into two groups. The genes were distributed unevenly across six chromosomes in cabbage, and all of them contained few introns (≤ 2). The results of collinear analysis showed that the cabbage genome contained 1–5 copies of each chitinase gene (excluding Bol035470) identified in Arabidopsis. The heatmap of the chitinase gene family showed that these genes were expressed in various tissues and organs. Two genes (Bol023322 and Bol041024) were relatively highly expressed in all of the investigated tissues under normal conditions, exhibiting the expression characteristics of housekeeping genes. In addition, under four different stresses, namely, Fusarium wilt, powdery mildew, black spot and downy mildew, we detected 9, 5, 8 and 8 genes with different expression levels in different treatments, respectively. Our results may help to elucidate the roles played by chitinases in the responses of host plants to various diseases.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Science + Business Media</pub><pmid>33742226</pmid><doi>10.1007/s00425-021-03596-2</doi><tpages>14</tpages><orcidid>https://orcid.org/0000-0002-0890-5854</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Agriculture Airborne microorganisms Binding Biomedical and Life Sciences Black spot Brassica Brassica - genetics Brassica - microbiology Brassica oleracea Chitin Chitin - metabolism Chitinase Chitinases - genetics Chromosomes Downy mildew Ecology Forestry Fusarium Gene expression Gene Expression Regulation, Plant Genes Genome, Plant Genomes Host plants Introns Life Sciences Organs Original ORIGINAL ARTICLE Pathogenesis Pathogenesis-related proteins Phylogeny Plant Immunity Plant Proteins - genetics Plant Sciences Powdery mildew Wilt |
| title | Genome-wide identification and expression analysis of the Brassica oleracea L. chitin-binding genes and response to pathogens infections |
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