RNA Sequencing Reveals That Both Abiotic and Biotic Stress-Responsive Genes are Induced during Expression of Steroidal Glycoalkaloid in Potato Tuber Subjected to Light Exposure
Steroidal glycoalkaloids (SGAs), which are widely produced by potato, even in other plants, are a class of potentially toxic compounds, but are beneficial to host resistance. However, changes of the other metabolic process along with SGA accumulation are still poorly understood and researched. Based...
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| Veröffentlicht in: | Genes 2019-11, Vol.10 (11), p.920 |
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| creator | Zhang, Weina Zuo, Cunwu Chen, Zhongjian Kang, Yichen Qin, Shuhao |
| description | Steroidal glycoalkaloids (SGAs), which are widely produced by potato, even in other
plants, are a class of potentially toxic compounds, but are beneficial to host resistance. However, changes of the other metabolic process along with SGA accumulation are still poorly understood and researched. Based on RNA sequencing (RNA-seq) and bioinformatics analysis, the global gene expression profiles of potato variety Helan 15 (Favorita) was investigated at four-time points during light exposure. The data was further verified by using quantitative Real-time PCR (qRT-PCR). When compared to the control group, 1288, 1592, 1737, and 1870 differentially expressed genes (DEGs) were detected at 6 h, 24 h, 48 h, and 8 d, respectively. The results of both RNAseq and qRT-PCR showed that SGA biosynthetic genes were up-regulated in the potato tuber under light exposure. Functional enrichment analysis revealed that genes related to PS light reaction and Protein degradation were significantly enriched in most time points of light exposure. Additionally, enriched Bins included Receptor kinases, Secondary metabolic process in flavonoids, Abiotic stress, and Biotic stress in the early stage of light exposure, but PS Calvin cycle, RNA regulation of transcription, and UDP glucosyl and glucoronyl transferases in the later stage. Most of the DEGs involved in PS light reaction and Abiotic stress were up-regulated at all four time points, whereas DEGs that participated in biotic stresses were mainly up-regulated at the later stage (48 h and 8 d).
-element prediction and co-expression assay were used to confirm the expressional correlation between genes that are responsible for SGA biosynthesis and disease resistance. In conclusion, the expressions of genes involved in PS light reaction, Abiotic stress, and Biotic stress were obviously aroused during the accumulation of SGAs induced by light exposure. Moreover, an increased defense response might contribute to the potato resistance to the infection by phytopathogenic microorganisms. |
| doi_str_mv | 10.3390/genes10110920 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_6896166</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2548393303</sourcerecordid><originalsourceid>FETCH-LOGICAL-c415t-e34ed1ededbb6c2b8558c987ce7d0c463f7202f1952959b1fac83956422b0ca33</originalsourceid><addsrcrecordid>eNpVkUtPGzEUhUdVK0CUJdvKUtfT-jGex6ZSQJAiRS1Kwtry407idLBT2xOVf9WfWI9CEXjja_vc7x75FMUlwV8Y6_DXDTiIBBOCO4rfFWcUN6ysKsrfv6pPi4sYdzivClOM-UlxykhDWlyRs-Lv8scMreD3CE5bt0FLOIAcIlpvZUJXPm3RTFmfrEbSGXR1LFcpQIzlEuLeu2gPgOaTESQDoDtnRg0GmTFMvJs_-0lrvUO-z40QvDVyQPPhSXs5_JJDPiPr0L1PMnm0HhUEtBrVDnTKmHy1sJttmkA-jgE-Fh_6bBAunvfz4uH2Zn39vVz8nN9dzxalrghPJbAKDAEDRqlaU9Vy3uqubTQ0BuuqZn1DMe1Jx2nHO0V6qVvW8bqiVGEtGTsvvh25-1E9gtHgUpCD2Af7KMOT8NKKty_ObsXGH0TddjWp6wz4_AwIPn9vTGLnx-CyZ0F5lYcxhqcx5VGlg48xQP8ygWAxZSzeZJz1n17belH_T5T9A2clpnM</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2548393303</pqid></control><display><type>article</type><title>RNA Sequencing Reveals That Both Abiotic and Biotic Stress-Responsive Genes are Induced during Expression of Steroidal Glycoalkaloid in Potato Tuber Subjected to Light Exposure</title><source>MEDLINE</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>PubMed Central Open Access</source><source>MDPI - Multidisciplinary Digital Publishing Institute</source><source>PubMed Central</source><creator>Zhang, Weina ; Zuo, Cunwu ; Chen, Zhongjian ; Kang, Yichen ; Qin, Shuhao</creator><creatorcontrib>Zhang, Weina ; Zuo, Cunwu ; Chen, Zhongjian ; Kang, Yichen ; Qin, Shuhao</creatorcontrib><description>Steroidal glycoalkaloids (SGAs), which are widely produced by potato, even in other
plants, are a class of potentially toxic compounds, but are beneficial to host resistance. However, changes of the other metabolic process along with SGA accumulation are still poorly understood and researched. Based on RNA sequencing (RNA-seq) and bioinformatics analysis, the global gene expression profiles of potato variety Helan 15 (Favorita) was investigated at four-time points during light exposure. The data was further verified by using quantitative Real-time PCR (qRT-PCR). When compared to the control group, 1288, 1592, 1737, and 1870 differentially expressed genes (DEGs) were detected at 6 h, 24 h, 48 h, and 8 d, respectively. The results of both RNAseq and qRT-PCR showed that SGA biosynthetic genes were up-regulated in the potato tuber under light exposure. Functional enrichment analysis revealed that genes related to PS light reaction and Protein degradation were significantly enriched in most time points of light exposure. Additionally, enriched Bins included Receptor kinases, Secondary metabolic process in flavonoids, Abiotic stress, and Biotic stress in the early stage of light exposure, but PS Calvin cycle, RNA regulation of transcription, and UDP glucosyl and glucoronyl transferases in the later stage. Most of the DEGs involved in PS light reaction and Abiotic stress were up-regulated at all four time points, whereas DEGs that participated in biotic stresses were mainly up-regulated at the later stage (48 h and 8 d).
-element prediction and co-expression assay were used to confirm the expressional correlation between genes that are responsible for SGA biosynthesis and disease resistance. In conclusion, the expressions of genes involved in PS light reaction, Abiotic stress, and Biotic stress were obviously aroused during the accumulation of SGAs induced by light exposure. Moreover, an increased defense response might contribute to the potato resistance to the infection by phytopathogenic microorganisms.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes10110920</identifier><identifier>PMID: 31718041</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Biodegradation ; Bioinformatics ; Biosynthesis ; Calvin cycle ; Cultivars ; Disease resistance ; Disease Resistance - genetics ; Flavonoids ; Gene expression ; Gene Expression Regulation, Plant - radiation effects ; Gene regulation ; Genomes ; Light ; Plant diseases ; Plant resistance ; Plant Tubers - genetics ; Plant Tubers - metabolism ; Plant Tubers - radiation effects ; Potatoes ; Ribonucleic acid ; RNA ; RNA-Seq ; Secondary Metabolism - genetics ; Software ; Solanine - analogs & derivatives ; Solanine - metabolism ; Solanum tuberosum - physiology ; Stress, Physiological - genetics ; Transcription ; Transcriptome - radiation effects ; Whole Exome Sequencing</subject><ispartof>Genes, 2019-11, Vol.10 (11), p.920</ispartof><rights>2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2019 by the authors. 2019</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c415t-e34ed1ededbb6c2b8558c987ce7d0c463f7202f1952959b1fac83956422b0ca33</citedby><cites>FETCH-LOGICAL-c415t-e34ed1ededbb6c2b8558c987ce7d0c463f7202f1952959b1fac83956422b0ca33</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6896166/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6896166/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27922,27923,53789,53791</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31718041$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhang, Weina</creatorcontrib><creatorcontrib>Zuo, Cunwu</creatorcontrib><creatorcontrib>Chen, Zhongjian</creatorcontrib><creatorcontrib>Kang, Yichen</creatorcontrib><creatorcontrib>Qin, Shuhao</creatorcontrib><title>RNA Sequencing Reveals That Both Abiotic and Biotic Stress-Responsive Genes are Induced during Expression of Steroidal Glycoalkaloid in Potato Tuber Subjected to Light Exposure</title><title>Genes</title><addtitle>Genes (Basel)</addtitle><description>Steroidal glycoalkaloids (SGAs), which are widely produced by potato, even in other
plants, are a class of potentially toxic compounds, but are beneficial to host resistance. However, changes of the other metabolic process along with SGA accumulation are still poorly understood and researched. Based on RNA sequencing (RNA-seq) and bioinformatics analysis, the global gene expression profiles of potato variety Helan 15 (Favorita) was investigated at four-time points during light exposure. The data was further verified by using quantitative Real-time PCR (qRT-PCR). When compared to the control group, 1288, 1592, 1737, and 1870 differentially expressed genes (DEGs) were detected at 6 h, 24 h, 48 h, and 8 d, respectively. The results of both RNAseq and qRT-PCR showed that SGA biosynthetic genes were up-regulated in the potato tuber under light exposure. Functional enrichment analysis revealed that genes related to PS light reaction and Protein degradation were significantly enriched in most time points of light exposure. Additionally, enriched Bins included Receptor kinases, Secondary metabolic process in flavonoids, Abiotic stress, and Biotic stress in the early stage of light exposure, but PS Calvin cycle, RNA regulation of transcription, and UDP glucosyl and glucoronyl transferases in the later stage. Most of the DEGs involved in PS light reaction and Abiotic stress were up-regulated at all four time points, whereas DEGs that participated in biotic stresses were mainly up-regulated at the later stage (48 h and 8 d).
-element prediction and co-expression assay were used to confirm the expressional correlation between genes that are responsible for SGA biosynthesis and disease resistance. In conclusion, the expressions of genes involved in PS light reaction, Abiotic stress, and Biotic stress were obviously aroused during the accumulation of SGAs induced by light exposure. Moreover, an increased defense response might contribute to the potato resistance to the infection by phytopathogenic microorganisms.</description><subject>Biodegradation</subject><subject>Bioinformatics</subject><subject>Biosynthesis</subject><subject>Calvin cycle</subject><subject>Cultivars</subject><subject>Disease resistance</subject><subject>Disease Resistance - genetics</subject><subject>Flavonoids</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Plant - radiation effects</subject><subject>Gene regulation</subject><subject>Genomes</subject><subject>Light</subject><subject>Plant diseases</subject><subject>Plant resistance</subject><subject>Plant Tubers - genetics</subject><subject>Plant Tubers - metabolism</subject><subject>Plant Tubers - radiation effects</subject><subject>Potatoes</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA-Seq</subject><subject>Secondary Metabolism - genetics</subject><subject>Software</subject><subject>Solanine - analogs & derivatives</subject><subject>Solanine - metabolism</subject><subject>Solanum tuberosum - physiology</subject><subject>Stress, Physiological - genetics</subject><subject>Transcription</subject><subject>Transcriptome - radiation effects</subject><subject>Whole Exome Sequencing</subject><issn>2073-4425</issn><issn>2073-4425</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNpVkUtPGzEUhUdVK0CUJdvKUtfT-jGex6ZSQJAiRS1Kwtry407idLBT2xOVf9WfWI9CEXjja_vc7x75FMUlwV8Y6_DXDTiIBBOCO4rfFWcUN6ysKsrfv6pPi4sYdzivClOM-UlxykhDWlyRs-Lv8scMreD3CE5bt0FLOIAcIlpvZUJXPm3RTFmfrEbSGXR1LFcpQIzlEuLeu2gPgOaTESQDoDtnRg0GmTFMvJs_-0lrvUO-z40QvDVyQPPhSXs5_JJDPiPr0L1PMnm0HhUEtBrVDnTKmHy1sJttmkA-jgE-Fh_6bBAunvfz4uH2Zn39vVz8nN9dzxalrghPJbAKDAEDRqlaU9Vy3uqubTQ0BuuqZn1DMe1Jx2nHO0V6qVvW8bqiVGEtGTsvvh25-1E9gtHgUpCD2Af7KMOT8NKKty_ObsXGH0TddjWp6wz4_AwIPn9vTGLnx-CyZ0F5lYcxhqcx5VGlg48xQP8ygWAxZSzeZJz1n17belH_T5T9A2clpnM</recordid><startdate>20191111</startdate><enddate>20191111</enddate><creator>Zhang, Weina</creator><creator>Zuo, Cunwu</creator><creator>Chen, Zhongjian</creator><creator>Kang, Yichen</creator><creator>Qin, Shuhao</creator><general>MDPI AG</general><general>MDPI</general><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>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>5PM</scope></search><sort><creationdate>20191111</creationdate><title>RNA Sequencing Reveals That Both Abiotic and Biotic Stress-Responsive Genes are Induced during Expression of Steroidal Glycoalkaloid in Potato Tuber Subjected to Light Exposure</title><author>Zhang, Weina ; Zuo, Cunwu ; Chen, Zhongjian ; Kang, Yichen ; Qin, Shuhao</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c415t-e34ed1ededbb6c2b8558c987ce7d0c463f7202f1952959b1fac83956422b0ca33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Biodegradation</topic><topic>Bioinformatics</topic><topic>Biosynthesis</topic><topic>Calvin cycle</topic><topic>Cultivars</topic><topic>Disease resistance</topic><topic>Disease Resistance - genetics</topic><topic>Flavonoids</topic><topic>Gene expression</topic><topic>Gene Expression Regulation, Plant - radiation effects</topic><topic>Gene regulation</topic><topic>Genomes</topic><topic>Light</topic><topic>Plant diseases</topic><topic>Plant resistance</topic><topic>Plant Tubers - genetics</topic><topic>Plant Tubers - metabolism</topic><topic>Plant Tubers - radiation effects</topic><topic>Potatoes</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA-Seq</topic><topic>Secondary Metabolism - genetics</topic><topic>Software</topic><topic>Solanine - analogs & derivatives</topic><topic>Solanine - metabolism</topic><topic>Solanum tuberosum - physiology</topic><topic>Stress, Physiological - genetics</topic><topic>Transcription</topic><topic>Transcriptome - radiation effects</topic><topic>Whole Exome Sequencing</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhang, Weina</creatorcontrib><creatorcontrib>Zuo, Cunwu</creatorcontrib><creatorcontrib>Chen, Zhongjian</creatorcontrib><creatorcontrib>Kang, Yichen</creatorcontrib><creatorcontrib>Qin, Shuhao</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genes</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhang, Weina</au><au>Zuo, Cunwu</au><au>Chen, Zhongjian</au><au>Kang, Yichen</au><au>Qin, Shuhao</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>RNA Sequencing Reveals That Both Abiotic and Biotic Stress-Responsive Genes are Induced during Expression of Steroidal Glycoalkaloid in Potato Tuber Subjected to Light Exposure</atitle><jtitle>Genes</jtitle><addtitle>Genes (Basel)</addtitle><date>2019-11-11</date><risdate>2019</risdate><volume>10</volume><issue>11</issue><spage>920</spage><pages>920-</pages><issn>2073-4425</issn><eissn>2073-4425</eissn><abstract>Steroidal glycoalkaloids (SGAs), which are widely produced by potato, even in other
plants, are a class of potentially toxic compounds, but are beneficial to host resistance. However, changes of the other metabolic process along with SGA accumulation are still poorly understood and researched. Based on RNA sequencing (RNA-seq) and bioinformatics analysis, the global gene expression profiles of potato variety Helan 15 (Favorita) was investigated at four-time points during light exposure. The data was further verified by using quantitative Real-time PCR (qRT-PCR). When compared to the control group, 1288, 1592, 1737, and 1870 differentially expressed genes (DEGs) were detected at 6 h, 24 h, 48 h, and 8 d, respectively. The results of both RNAseq and qRT-PCR showed that SGA biosynthetic genes were up-regulated in the potato tuber under light exposure. Functional enrichment analysis revealed that genes related to PS light reaction and Protein degradation were significantly enriched in most time points of light exposure. Additionally, enriched Bins included Receptor kinases, Secondary metabolic process in flavonoids, Abiotic stress, and Biotic stress in the early stage of light exposure, but PS Calvin cycle, RNA regulation of transcription, and UDP glucosyl and glucoronyl transferases in the later stage. Most of the DEGs involved in PS light reaction and Abiotic stress were up-regulated at all four time points, whereas DEGs that participated in biotic stresses were mainly up-regulated at the later stage (48 h and 8 d).
-element prediction and co-expression assay were used to confirm the expressional correlation between genes that are responsible for SGA biosynthesis and disease resistance. In conclusion, the expressions of genes involved in PS light reaction, Abiotic stress, and Biotic stress were obviously aroused during the accumulation of SGAs induced by light exposure. Moreover, an increased defense response might contribute to the potato resistance to the infection by phytopathogenic microorganisms.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>31718041</pmid><doi>10.3390/genes10110920</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Biodegradation Bioinformatics Biosynthesis Calvin cycle Cultivars Disease resistance Disease Resistance - genetics Flavonoids Gene expression Gene Expression Regulation, Plant - radiation effects Gene regulation Genomes Light Plant diseases Plant resistance Plant Tubers - genetics Plant Tubers - metabolism Plant Tubers - radiation effects Potatoes Ribonucleic acid RNA RNA-Seq Secondary Metabolism - genetics Software Solanine - analogs & derivatives Solanine - metabolism Solanum tuberosum - physiology Stress, Physiological - genetics Transcription Transcriptome - radiation effects Whole Exome Sequencing |
| title | RNA Sequencing Reveals That Both Abiotic and Biotic Stress-Responsive Genes are Induced during Expression of Steroidal Glycoalkaloid in Potato Tuber Subjected to Light Exposure |
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