Comparative analysis of sugarcane root transcriptome in response to the plant growth-promoting Burkholderia anthina MYSP113
The diazotrophic Burkholderia anthina MYSP113 is a vital plant growth-promoting bacteria and sugarcane root association. The present study based on a detailed analysis of sugarcane root transcriptome by using the HiSeq-Illumina platform in response to the strain MYSP113. The bacterium was initially...
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| creator | Malviya, Mukesh Kumar Li, Chang-Ning Solanki, Manoj Kumar Singh, Rajesh Kumar Htun, Reemon Singh, Pratiksha Verma, Krishan K Yang, Li-Tao Li, Yang-Rui |
| description | The diazotrophic Burkholderia anthina MYSP113 is a vital plant growth-promoting bacteria and sugarcane root association. The present study based on a detailed analysis of sugarcane root transcriptome by using the HiSeq-Illumina platform in response to the strain MYSP113. The bacterium was initially isolated from the rhizosphere of sugarcane. To better understand biological, cellular, and molecular mechanisms, a de novo transcriptomic assembly of sugarcane root was performed. HiSeq-Illumina platformwas employed for the sequencing of an overall of 16 libraries at a 2×100 bp configuration. Differentially expressed genes (DEGs) analysis identified altered gene expression in 370 genes (total of 199 up-regulated genes and 171 down-regulated genes). Deciphering the huge datasets, concerning the functioning and production of biological systems, a high throughput genome sequencing analysis was attempted with Gene ontology functional analyses and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The report revealed a total of 148930 unigenes. 70414 (47.28%) of them were annotated successfully to Gene Ontology (GO) terms. 774 at 45 days, 4985 of 30 days and 15 days of 6846 terms were significantly regulated. GO analysis revealed that many genes involved in the metabolic, oxidation-reduction process and biological regulatory processes in response to strain MYSP113 and significantly enriched as compare to the control. Moreover, KEGG enriched results show that differentially expressed genes were classified into different pathway categories involved in various processes, such as nitrogen metabolism, plant hormone signal transduction, etc. The sample correlation analyses could help examine the similarity at the gene expression level. The reliability of the observed differential gene expression patterns was validated with quantitative real-time PCR (qRT-PCR). Additionally, plant enzymes activities such as peroxidase and superoxide dismutase were significantly increased in plant roots after the inoculation of strain MYSP113. The results of the research may help in understanding the plant growth-promoting rhizobacteria and plant interaction. |
| doi_str_mv | 10.1371/journal.pone.0231206 |
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The present study based on a detailed analysis of sugarcane root transcriptome by using the HiSeq-Illumina platform in response to the strain MYSP113. The bacterium was initially isolated from the rhizosphere of sugarcane. To better understand biological, cellular, and molecular mechanisms, a de novo transcriptomic assembly of sugarcane root was performed. HiSeq-Illumina platformwas employed for the sequencing of an overall of 16 libraries at a 2×100 bp configuration. Differentially expressed genes (DEGs) analysis identified altered gene expression in 370 genes (total of 199 up-regulated genes and 171 down-regulated genes). Deciphering the huge datasets, concerning the functioning and production of biological systems, a high throughput genome sequencing analysis was attempted with Gene ontology functional analyses and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The report revealed a total of 148930 unigenes. 70414 (47.28%) of them were annotated successfully to Gene Ontology (GO) terms. 774 at 45 days, 4985 of 30 days and 15 days of 6846 terms were significantly regulated. GO analysis revealed that many genes involved in the metabolic, oxidation-reduction process and biological regulatory processes in response to strain MYSP113 and significantly enriched as compare to the control. Moreover, KEGG enriched results show that differentially expressed genes were classified into different pathway categories involved in various processes, such as nitrogen metabolism, plant hormone signal transduction, etc. The sample correlation analyses could help examine the similarity at the gene expression level. The reliability of the observed differential gene expression patterns was validated with quantitative real-time PCR (qRT-PCR). Additionally, plant enzymes activities such as peroxidase and superoxide dismutase were significantly increased in plant roots after the inoculation of strain MYSP113. The results of the research may help in understanding the plant growth-promoting rhizobacteria and plant interaction.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0231206</identifier><identifier>PMID: 32267863</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Agriculture ; Bacteria ; Biochemistry ; Biological activity ; Biology and Life Sciences ; Biotechnology ; Burkholderia ; Cellular signal transduction ; Comparative analysis ; Corn ; Correlation analysis ; DNA sequencing ; Encyclopedias ; Enzymes ; Gene expression ; Gene sequencing ; Genes ; Genomes ; Genomics ; Growth ; Hormones ; Inoculation ; Laboratories ; Medicine and Health Sciences ; Metabolism ; Molecular modelling ; Nitrogen ; Nitrogen metabolism ; Oxidation ; Oxidation-reduction potential ; Oxidation-reduction reactions ; Pathogens ; Peroxidase ; Plant growth ; Plant hormones ; Plant roots ; Research and analysis methods ; Rhizosphere ; Sequence analysis ; Signal processing ; Signal transduction ; Sugarcane ; Superoxide dismutase ; Superoxides ; Time</subject><ispartof>PloS one, 2020-04, Vol.15 (4), p.e0231206-e0231206</ispartof><rights>COPYRIGHT 2020 Public Library of Science</rights><rights>2020 Malviya et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2020 Malviya et al 2020 Malviya et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-815485ead80a3c3f62d4ef3751e31948d878602c93dac099838185f9522f8dad3</citedby><cites>FETCH-LOGICAL-c692t-815485ead80a3c3f62d4ef3751e31948d878602c93dac099838185f9522f8dad3</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/PMC7141665/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7141665/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32267863$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Malviya, Mukesh Kumar</creatorcontrib><creatorcontrib>Li, Chang-Ning</creatorcontrib><creatorcontrib>Solanki, Manoj Kumar</creatorcontrib><creatorcontrib>Singh, Rajesh Kumar</creatorcontrib><creatorcontrib>Htun, Reemon</creatorcontrib><creatorcontrib>Singh, Pratiksha</creatorcontrib><creatorcontrib>Verma, Krishan K</creatorcontrib><creatorcontrib>Yang, Li-Tao</creatorcontrib><creatorcontrib>Li, Yang-Rui</creatorcontrib><title>Comparative analysis of sugarcane root transcriptome in response to the plant growth-promoting Burkholderia anthina MYSP113</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The diazotrophic Burkholderia anthina MYSP113 is a vital plant growth-promoting bacteria and sugarcane root association. The present study based on a detailed analysis of sugarcane root transcriptome by using the HiSeq-Illumina platform in response to the strain MYSP113. The bacterium was initially isolated from the rhizosphere of sugarcane. To better understand biological, cellular, and molecular mechanisms, a de novo transcriptomic assembly of sugarcane root was performed. HiSeq-Illumina platformwas employed for the sequencing of an overall of 16 libraries at a 2×100 bp configuration. Differentially expressed genes (DEGs) analysis identified altered gene expression in 370 genes (total of 199 up-regulated genes and 171 down-regulated genes). Deciphering the huge datasets, concerning the functioning and production of biological systems, a high throughput genome sequencing analysis was attempted with Gene ontology functional analyses and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The report revealed a total of 148930 unigenes. 70414 (47.28%) of them were annotated successfully to Gene Ontology (GO) terms. 774 at 45 days, 4985 of 30 days and 15 days of 6846 terms were significantly regulated. GO analysis revealed that many genes involved in the metabolic, oxidation-reduction process and biological regulatory processes in response to strain MYSP113 and significantly enriched as compare to the control. Moreover, KEGG enriched results show that differentially expressed genes were classified into different pathway categories involved in various processes, such as nitrogen metabolism, plant hormone signal transduction, etc. The sample correlation analyses could help examine the similarity at the gene expression level. The reliability of the observed differential gene expression patterns was validated with quantitative real-time PCR (qRT-PCR). Additionally, plant enzymes activities such as peroxidase and superoxide dismutase were significantly increased in plant roots after the inoculation of strain MYSP113. The results of the research may help in understanding the plant growth-promoting rhizobacteria and plant interaction.</description><subject>Agriculture</subject><subject>Bacteria</subject><subject>Biochemistry</subject><subject>Biological activity</subject><subject>Biology and Life Sciences</subject><subject>Biotechnology</subject><subject>Burkholderia</subject><subject>Cellular signal transduction</subject><subject>Comparative analysis</subject><subject>Corn</subject><subject>Correlation analysis</subject><subject>DNA sequencing</subject><subject>Encyclopedias</subject><subject>Enzymes</subject><subject>Gene expression</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Growth</subject><subject>Hormones</subject><subject>Inoculation</subject><subject>Laboratories</subject><subject>Medicine and Health Sciences</subject><subject>Metabolism</subject><subject>Molecular modelling</subject><subject>Nitrogen</subject><subject>Nitrogen metabolism</subject><subject>Oxidation</subject><subject>Oxidation-reduction potential</subject><subject>Oxidation-reduction reactions</subject><subject>Pathogens</subject><subject>Peroxidase</subject><subject>Plant growth</subject><subject>Plant hormones</subject><subject>Plant roots</subject><subject>Research and analysis methods</subject><subject>Rhizosphere</subject><subject>Sequence analysis</subject><subject>Signal processing</subject><subject>Signal transduction</subject><subject>Sugarcane</subject><subject>Superoxide 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analysis of sugarcane root transcriptome in response to the plant growth-promoting Burkholderia anthina MYSP113</title><author>Malviya, Mukesh Kumar ; Li, Chang-Ning ; Solanki, Manoj Kumar ; Singh, Rajesh Kumar ; Htun, Reemon ; Singh, Pratiksha ; Verma, Krishan K ; Yang, Li-Tao ; Li, Yang-Rui</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-815485ead80a3c3f62d4ef3751e31948d878602c93dac099838185f9522f8dad3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Agriculture</topic><topic>Bacteria</topic><topic>Biochemistry</topic><topic>Biological activity</topic><topic>Biology and Life Sciences</topic><topic>Biotechnology</topic><topic>Burkholderia</topic><topic>Cellular signal transduction</topic><topic>Comparative analysis</topic><topic>Corn</topic><topic>Correlation analysis</topic><topic>DNA sequencing</topic><topic>Encyclopedias</topic><topic>Enzymes</topic><topic>Gene 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Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Malviya, Mukesh Kumar</au><au>Li, Chang-Ning</au><au>Solanki, Manoj Kumar</au><au>Singh, Rajesh Kumar</au><au>Htun, Reemon</au><au>Singh, Pratiksha</au><au>Verma, Krishan K</au><au>Yang, Li-Tao</au><au>Li, Yang-Rui</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparative analysis of sugarcane root transcriptome in response to the plant growth-promoting Burkholderia anthina MYSP113</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2020-04-08</date><risdate>2020</risdate><volume>15</volume><issue>4</issue><spage>e0231206</spage><epage>e0231206</epage><pages>e0231206-e0231206</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The diazotrophic Burkholderia anthina MYSP113 is a vital plant growth-promoting bacteria and sugarcane root association. The present study based on a detailed analysis of sugarcane root transcriptome by using the HiSeq-Illumina platform in response to the strain MYSP113. The bacterium was initially isolated from the rhizosphere of sugarcane. To better understand biological, cellular, and molecular mechanisms, a de novo transcriptomic assembly of sugarcane root was performed. HiSeq-Illumina platformwas employed for the sequencing of an overall of 16 libraries at a 2×100 bp configuration. Differentially expressed genes (DEGs) analysis identified altered gene expression in 370 genes (total of 199 up-regulated genes and 171 down-regulated genes). Deciphering the huge datasets, concerning the functioning and production of biological systems, a high throughput genome sequencing analysis was attempted with Gene ontology functional analyses and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The report revealed a total of 148930 unigenes. 70414 (47.28%) of them were annotated successfully to Gene Ontology (GO) terms. 774 at 45 days, 4985 of 30 days and 15 days of 6846 terms were significantly regulated. GO analysis revealed that many genes involved in the metabolic, oxidation-reduction process and biological regulatory processes in response to strain MYSP113 and significantly enriched as compare to the control. Moreover, KEGG enriched results show that differentially expressed genes were classified into different pathway categories involved in various processes, such as nitrogen metabolism, plant hormone signal transduction, etc. The sample correlation analyses could help examine the similarity at the gene expression level. The reliability of the observed differential gene expression patterns was validated with quantitative real-time PCR (qRT-PCR). Additionally, plant enzymes activities such as peroxidase and superoxide dismutase were significantly increased in plant roots after the inoculation of strain MYSP113. The results of the research may help in understanding the plant growth-promoting rhizobacteria and plant interaction.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>32267863</pmid><doi>10.1371/journal.pone.0231206</doi><tpages>e0231206</tpages><oa>free_for_read</oa></addata></record> |
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| source | DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Free Full-Text Journals in Chemistry; Public Library of Science (PLoS) |
| subjects | Agriculture Bacteria Biochemistry Biological activity Biology and Life Sciences Biotechnology Burkholderia Cellular signal transduction Comparative analysis Corn Correlation analysis DNA sequencing Encyclopedias Enzymes Gene expression Gene sequencing Genes Genomes Genomics Growth Hormones Inoculation Laboratories Medicine and Health Sciences Metabolism Molecular modelling Nitrogen Nitrogen metabolism Oxidation Oxidation-reduction potential Oxidation-reduction reactions Pathogens Peroxidase Plant growth Plant hormones Plant roots Research and analysis methods Rhizosphere Sequence analysis Signal processing Signal transduction Sugarcane Superoxide dismutase Superoxides Time |
| title | Comparative analysis of sugarcane root transcriptome in response to the plant growth-promoting Burkholderia anthina MYSP113 |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-05T21%3A29%3A46IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Comparative%20analysis%20of%20sugarcane%20root%20transcriptome%20in%20response%20to%20the%20plant%20growth-promoting%20Burkholderia%20anthina%20MYSP113&rft.jtitle=PloS%20one&rft.au=Malviya,%20Mukesh%20Kumar&rft.date=2020-04-08&rft.volume=15&rft.issue=4&rft.spage=e0231206&rft.epage=e0231206&rft.pages=e0231206-e0231206&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0231206&rft_dat=%3Cgale_plos_%3EA619784802%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2387634033&rft_id=info:pmid/32267863&rft_galeid=A619784802&rft_doaj_id=oai_doaj_org_article_d41d3b6187b94ff99a3c2f59306cf145&rfr_iscdi=true |