Transcriptome exploration in Leymus chinensis under saline-alkaline treatment using 454 pyrosequencing
Leymus chinensis (Trin.) Tzvel. is a high saline-alkaline tolerant forage grass genus of the tribe Gramineae family, which also plays an important role in protection of natural environment. To date, little is known about the saline-alkaline tolerance of L. chinensis on the molecular level. To better...
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| description | Leymus chinensis (Trin.) Tzvel. is a high saline-alkaline tolerant forage grass genus of the tribe Gramineae family, which also plays an important role in protection of natural environment. To date, little is known about the saline-alkaline tolerance of L. chinensis on the molecular level. To better understand the molecular mechanism of saline-alkaline tolerance in L. chinensis, 454 pyrosequencing was used for the transcriptome study.
We used Roche-454 massive parallel pyrosequencing technology to sequence two different cDNA libraries that were built from the two samples of control and under saline-alkaline treatment (optimal stress concentration-Hoagland solution with 100 mM NaCl and 200 mM NaHCO(3)). A total of 363,734 reads in control group and 526,267 reads in treatment group with an average length of 489 bp and 493 bp were obtained, respectively. The reads were assembled into 104,105 unigenes with MIRA sequence assemable software, among which, 73,665 unigenes were in control group, 88,016 unigenes in treatment group and 57,576 unigenes in both groups. According to the comparative expression analysis between the two groups with the threshold of "log2 Ratio ≥1", there were 36,497 up-regulated unegenes and 18,218 down-regulated unigenes predicted to be the differentially expressed genes. After gene annotation and pathway enrichment analysis, most of them were involved in stress and tolerant function, signal transduction, energy production and conversion, and inorganic ion transport. Furthermore, 16 of these differentially expressed genes were selected for real-time PCR validation, and they were successfully confirmed with the results of 454 pyrosequencing.
This work is the first time to study the transcriptome of L. chinensis under saline-alkaline treatment based on the 454-FLX massively parallel DNA sequencing platform. It also deepened studies on molecular mechanisms of saline-alkaline in L. chinensis, and constituted a database for future studies. |
| doi_str_mv | 10.1371/journal.pone.0053632 |
| format | Article |
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We used Roche-454 massive parallel pyrosequencing technology to sequence two different cDNA libraries that were built from the two samples of control and under saline-alkaline treatment (optimal stress concentration-Hoagland solution with 100 mM NaCl and 200 mM NaHCO(3)). A total of 363,734 reads in control group and 526,267 reads in treatment group with an average length of 489 bp and 493 bp were obtained, respectively. The reads were assembled into 104,105 unigenes with MIRA sequence assemable software, among which, 73,665 unigenes were in control group, 88,016 unigenes in treatment group and 57,576 unigenes in both groups. According to the comparative expression analysis between the two groups with the threshold of "log2 Ratio ≥1", there were 36,497 up-regulated unegenes and 18,218 down-regulated unigenes predicted to be the differentially expressed genes. After gene annotation and pathway enrichment analysis, most of them were involved in stress and tolerant function, signal transduction, energy production and conversion, and inorganic ion transport. Furthermore, 16 of these differentially expressed genes were selected for real-time PCR validation, and they were successfully confirmed with the results of 454 pyrosequencing.
This work is the first time to study the transcriptome of L. chinensis under saline-alkaline treatment based on the 454-FLX massively parallel DNA sequencing platform. It also deepened studies on molecular mechanisms of saline-alkaline in L. chinensis, and constituted a database for future studies.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0053632</identifier><identifier>PMID: 23365637</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Abiotic stress ; Alkalies - pharmacology ; Annotations ; Barley ; Biology ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; Education ; Energy Metabolism - genetics ; Engineering research ; Exploration ; Forage ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Library ; Gene sequencing ; Genes ; Genetic aspects ; Genomes ; Genomics ; Genotypes ; Germplasm ; Glycine max ; Grasses ; High-Throughput Nucleotide Sequencing ; Ion transport ; Ion Transport - genetics ; Leymus chinensis ; Life sciences ; Lipid peroxidation ; Molecular modelling ; Molecular Sequence Annotation ; Observations ; Pharmaceuticals ; Plant hardiness ; Poaceae - drug effects ; Poaceae - genetics ; Poaceae - metabolism ; Properties ; Real-Time Polymerase Chain Reaction ; Salinity ; Salt Tolerance - genetics ; Salt-Tolerant Plants - drug effects ; Salt-Tolerant Plants - genetics ; Salt-Tolerant Plants - metabolism ; Signal Transduction - genetics ; Sodium Bicarbonate - pharmacology ; Sodium chloride ; Sodium Chloride - pharmacology ; Stress concentration ; Stress, Physiological - genetics ; Studies ; Transcription (Genetics) ; Transcriptome - genetics ; Transduction</subject><ispartof>PloS one, 2013-01, Vol.8 (1), p.e53632-e53632</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Sun et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://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>2013 Sun et al 2013 Sun et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-1b16b94477bc4915d1e5df9362c950e187c202891187339df940f9bd918fba743</citedby><cites>FETCH-LOGICAL-c692t-1b16b94477bc4915d1e5df9362c950e187c202891187339df940f9bd918fba743</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/PMC3554714/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3554714/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2100,2926,23865,27923,27924,53790,53792,79371,79372</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23365637$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Shiu, Shin-Han</contributor><creatorcontrib>Sun, Yepeng</creatorcontrib><creatorcontrib>Wang, Fawei</creatorcontrib><creatorcontrib>Wang, Nan</creatorcontrib><creatorcontrib>Dong, Yuanyuan</creatorcontrib><creatorcontrib>Liu, Qi</creatorcontrib><creatorcontrib>Zhao, Lei</creatorcontrib><creatorcontrib>Chen, Huan</creatorcontrib><creatorcontrib>Liu, Weican</creatorcontrib><creatorcontrib>Yin, Hailong</creatorcontrib><creatorcontrib>Zhang, Xiaomei</creatorcontrib><creatorcontrib>Yuan, Yanxi</creatorcontrib><creatorcontrib>Li, Haiyan</creatorcontrib><title>Transcriptome exploration in Leymus chinensis under saline-alkaline treatment using 454 pyrosequencing</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Leymus chinensis (Trin.) Tzvel. is a high saline-alkaline tolerant forage grass genus of the tribe Gramineae family, which also plays an important role in protection of natural environment. To date, little is known about the saline-alkaline tolerance of L. chinensis on the molecular level. To better understand the molecular mechanism of saline-alkaline tolerance in L. chinensis, 454 pyrosequencing was used for the transcriptome study.
We used Roche-454 massive parallel pyrosequencing technology to sequence two different cDNA libraries that were built from the two samples of control and under saline-alkaline treatment (optimal stress concentration-Hoagland solution with 100 mM NaCl and 200 mM NaHCO(3)). A total of 363,734 reads in control group and 526,267 reads in treatment group with an average length of 489 bp and 493 bp were obtained, respectively. The reads were assembled into 104,105 unigenes with MIRA sequence assemable software, among which, 73,665 unigenes were in control group, 88,016 unigenes in treatment group and 57,576 unigenes in both groups. According to the comparative expression analysis between the two groups with the threshold of "log2 Ratio ≥1", there were 36,497 up-regulated unegenes and 18,218 down-regulated unigenes predicted to be the differentially expressed genes. After gene annotation and pathway enrichment analysis, most of them were involved in stress and tolerant function, signal transduction, energy production and conversion, and inorganic ion transport. Furthermore, 16 of these differentially expressed genes were selected for real-time PCR validation, and they were successfully confirmed with the results of 454 pyrosequencing.
This work is the first time to study the transcriptome of L. chinensis under saline-alkaline treatment based on the 454-FLX massively parallel DNA sequencing platform. It also deepened studies on molecular mechanisms of saline-alkaline in L. chinensis, and constituted a database for future studies.</description><subject>Abiotic stress</subject><subject>Alkalies - pharmacology</subject><subject>Annotations</subject><subject>Barley</subject><subject>Biology</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>Education</subject><subject>Energy Metabolism - genetics</subject><subject>Engineering research</subject><subject>Exploration</subject><subject>Forage</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Plant</subject><subject>Gene Library</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotypes</subject><subject>Germplasm</subject><subject>Glycine max</subject><subject>Grasses</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Ion transport</subject><subject>Ion Transport - genetics</subject><subject>Leymus chinensis</subject><subject>Life sciences</subject><subject>Lipid peroxidation</subject><subject>Molecular modelling</subject><subject>Molecular Sequence Annotation</subject><subject>Observations</subject><subject>Pharmaceuticals</subject><subject>Plant hardiness</subject><subject>Poaceae - drug effects</subject><subject>Poaceae - genetics</subject><subject>Poaceae - metabolism</subject><subject>Properties</subject><subject>Real-Time Polymerase Chain Reaction</subject><subject>Salinity</subject><subject>Salt Tolerance - genetics</subject><subject>Salt-Tolerant Plants - drug effects</subject><subject>Salt-Tolerant Plants - genetics</subject><subject>Salt-Tolerant Plants - metabolism</subject><subject>Signal Transduction - genetics</subject><subject>Sodium Bicarbonate - pharmacology</subject><subject>Sodium chloride</subject><subject>Sodium Chloride - pharmacology</subject><subject>Stress concentration</subject><subject>Stress, Physiological - genetics</subject><subject>Studies</subject><subject>Transcription (Genetics)</subject><subject>Transcriptome - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sun, Yepeng</au><au>Wang, Fawei</au><au>Wang, Nan</au><au>Dong, Yuanyuan</au><au>Liu, Qi</au><au>Zhao, Lei</au><au>Chen, Huan</au><au>Liu, Weican</au><au>Yin, Hailong</au><au>Zhang, Xiaomei</au><au>Yuan, Yanxi</au><au>Li, Haiyan</au><au>Shiu, Shin-Han</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Transcriptome exploration in Leymus chinensis under saline-alkaline treatment using 454 pyrosequencing</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2013-01-24</date><risdate>2013</risdate><volume>8</volume><issue>1</issue><spage>e53632</spage><epage>e53632</epage><pages>e53632-e53632</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Leymus chinensis (Trin.) Tzvel. is a high saline-alkaline tolerant forage grass genus of the tribe Gramineae family, which also plays an important role in protection of natural environment. To date, little is known about the saline-alkaline tolerance of L. chinensis on the molecular level. To better understand the molecular mechanism of saline-alkaline tolerance in L. chinensis, 454 pyrosequencing was used for the transcriptome study.
We used Roche-454 massive parallel pyrosequencing technology to sequence two different cDNA libraries that were built from the two samples of control and under saline-alkaline treatment (optimal stress concentration-Hoagland solution with 100 mM NaCl and 200 mM NaHCO(3)). A total of 363,734 reads in control group and 526,267 reads in treatment group with an average length of 489 bp and 493 bp were obtained, respectively. The reads were assembled into 104,105 unigenes with MIRA sequence assemable software, among which, 73,665 unigenes were in control group, 88,016 unigenes in treatment group and 57,576 unigenes in both groups. According to the comparative expression analysis between the two groups with the threshold of "log2 Ratio ≥1", there were 36,497 up-regulated unegenes and 18,218 down-regulated unigenes predicted to be the differentially expressed genes. After gene annotation and pathway enrichment analysis, most of them were involved in stress and tolerant function, signal transduction, energy production and conversion, and inorganic ion transport. Furthermore, 16 of these differentially expressed genes were selected for real-time PCR validation, and they were successfully confirmed with the results of 454 pyrosequencing.
This work is the first time to study the transcriptome of L. chinensis under saline-alkaline treatment based on the 454-FLX massively parallel DNA sequencing platform. It also deepened studies on molecular mechanisms of saline-alkaline in L. chinensis, and constituted a database for future studies.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>23365637</pmid><doi>10.1371/journal.pone.0053632</doi><tpages>e53632</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2013-01, Vol.8 (1), p.e53632-e53632 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1327798868 |
| source | MEDLINE; Public Library of Science (PLoS) Journals Open Access; DOAJ Directory of Open Access Journals; PubMed Central (Training); EZB-FREE-00999 freely available EZB journals; Free Full-Text Journals in Chemistry |
| subjects | Abiotic stress Alkalies - pharmacology Annotations Barley Biology Deoxyribonucleic acid DNA DNA sequencing Education Energy Metabolism - genetics Engineering research Exploration Forage Gene expression Gene Expression Profiling Gene Expression Regulation, Plant Gene Library Gene sequencing Genes Genetic aspects Genomes Genomics Genotypes Germplasm Glycine max Grasses High-Throughput Nucleotide Sequencing Ion transport Ion Transport - genetics Leymus chinensis Life sciences Lipid peroxidation Molecular modelling Molecular Sequence Annotation Observations Pharmaceuticals Plant hardiness Poaceae - drug effects Poaceae - genetics Poaceae - metabolism Properties Real-Time Polymerase Chain Reaction Salinity Salt Tolerance - genetics Salt-Tolerant Plants - drug effects Salt-Tolerant Plants - genetics Salt-Tolerant Plants - metabolism Signal Transduction - genetics Sodium Bicarbonate - pharmacology Sodium chloride Sodium Chloride - pharmacology Stress concentration Stress, Physiological - genetics Studies Transcription (Genetics) Transcriptome - genetics Transduction |
| title | Transcriptome exploration in Leymus chinensis under saline-alkaline treatment using 454 pyrosequencing |
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