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Trait‐directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus
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| Zeitschriftentitel: | New Phytologist |
|---|---|
| Personen und Körperschaften: | , , , , , , , |
| In: | New Phytologist, 201, 2014, 1, S. 144-154 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Wiley
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| Schlagwörter: |
| author_facet |
Meharg, Caroline Khan, Bayezid Norton, Gareth Deacon, Claire Johnson, David Reinhardt, Richard Huettel, Bruno Meharg, Andrew A. Meharg, Caroline Khan, Bayezid Norton, Gareth Deacon, Claire Johnson, David Reinhardt, Richard Huettel, Bruno Meharg, Andrew A. |
|---|---|
| author |
Meharg, Caroline Khan, Bayezid Norton, Gareth Deacon, Claire Johnson, David Reinhardt, Richard Huettel, Bruno Meharg, Andrew A. |
| spellingShingle |
Meharg, Caroline Khan, Bayezid Norton, Gareth Deacon, Claire Johnson, David Reinhardt, Richard Huettel, Bruno Meharg, Andrew A. New Phytologist Trait‐directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus Plant Science Physiology |
| author_sort |
meharg, caroline |
| spelling |
Meharg, Caroline Khan, Bayezid Norton, Gareth Deacon, Claire Johnson, David Reinhardt, Richard Huettel, Bruno Meharg, Andrew A. 0028-646X 1469-8137 Wiley Plant Science Physiology http://dx.doi.org/10.1111/nph.12491 <jats:title>Summary</jats:title><jats:p> <jats:list list-type="bullet"> <jats:list-item><jats:p>The aim of this study was to characterize the transcriptome of a balanced polymorphism, under the regulation of a single gene, for phosphate fertilizer responsiveness/arsenate tolerance in wild grass <jats:italic><jats:styled-content style="fixed-case">H</jats:styled-content>olcus lanatus</jats:italic> genotypes screened from the same habitat.</jats:p></jats:list-item> <jats:list-item><jats:p><jats:italic>De novo</jats:italic> transcriptome sequencing, <jats:styled-content style="fixed-case">RNA</jats:styled-content>seq (RNA sequencing) and single nucleotide polymorphism (<jats:styled-content style="fixed-case">SNP</jats:styled-content>) calling were conducted on <jats:styled-content style="fixed-case">RNA</jats:styled-content> extracted from <jats:italic><jats:styled-content style="fixed-case">H</jats:styled-content>. lanatus</jats:italic>. Roche 454 sequencing data were assembled into <jats:italic>c</jats:italic>. 22 000 isotigs, and paired‐end <jats:styled-content style="fixed-case">I</jats:styled-content>llumina reads for phosphorus‐starved (P−) and phosphorus‐treated (<jats:styled-content style="fixed-case">P</jats:styled-content>+) genovars of tolerant (<jats:styled-content style="fixed-case">T</jats:styled-content>) and nontolerant (<jats:styled-content style="fixed-case">N</jats:styled-content>) phenotypes were mapped to this reference transcriptome.</jats:p></jats:list-item> <jats:list-item><jats:p>Heatmaps of the gene expression data showed strong clustering of each <jats:styled-content style="fixed-case">P</jats:styled-content>+/<jats:styled-content style="fixed-case">P</jats:styled-content>− treated genovar, as well as clustering by <jats:styled-content style="fixed-case">N</jats:styled-content>/<jats:styled-content style="fixed-case">T</jats:styled-content> phenotype. Statistical analysis identified 87 isotigs to be significantly differentially expressed between <jats:styled-content style="fixed-case">N</jats:styled-content> and <jats:styled-content style="fixed-case">T</jats:styled-content> phenotypes and 258 between <jats:styled-content style="fixed-case">P</jats:styled-content>+ and <jats:styled-content style="fixed-case">P</jats:styled-content>− treated plants. <jats:styled-content style="fixed-case">SNP</jats:styled-content>s and transcript expression that systematically differed between <jats:styled-content style="fixed-case">N</jats:styled-content> and <jats:styled-content style="fixed-case">T</jats:styled-content> phenotypes had regulatory function, namely proteases, kinases and ribonuclear <jats:styled-content style="fixed-case">RNA</jats:styled-content>‐binding protein and transposable elements.</jats:p></jats:list-item> <jats:list-item><jats:p>A single gene for arsenate tolerance led to distinct phenotype transcriptomes and <jats:styled-content style="fixed-case">SNP</jats:styled-content> profiles, with large differences in upstream post‐translational and post‐transcriptional regulatory genes rather than in genes directly involved in P nutrition transport and metabolism <jats:italic>per se</jats:italic>.</jats:p></jats:list-item> </jats:list> </jats:p> Trait‐directed <i>de novo</i> population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, <i><scp>H</scp>olcus lanatus</i> New Phytologist |
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Wiley, 2014 |
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Wiley, 2014 |
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0028-646X 1469-8137 |
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meharg2014traitdirecteddenovopopulationtranscriptomedissectsgeneticregulationofabalancedpolymorphisminphosphorusnutritionarsenatetoleranceinawildgrassholcuslanatus |
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2014 |
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Wiley |
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New Phytologist |
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| title |
Trait‐directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus |
| title_unstemmed |
Trait‐directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus |
| title_full |
Trait‐directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus |
| title_fullStr |
Trait‐directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus |
| title_full_unstemmed |
Trait‐directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus |
| title_short |
Trait‐directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus |
| title_sort |
trait‐directed <i>de novo</i> population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, <i><scp>h</scp>olcus lanatus</i> |
| topic |
Plant Science Physiology |
| url |
http://dx.doi.org/10.1111/nph.12491 |
| publishDate |
2014 |
| physical |
144-154 |
| description |
<jats:title>Summary</jats:title><jats:p>
<jats:list list-type="bullet">
<jats:list-item><jats:p>The aim of this study was to characterize the transcriptome of a balanced polymorphism, under the regulation of a single gene, for phosphate fertilizer responsiveness/arsenate tolerance in wild grass <jats:italic><jats:styled-content style="fixed-case">H</jats:styled-content>olcus lanatus</jats:italic> genotypes screened from the same habitat.</jats:p></jats:list-item>
<jats:list-item><jats:p><jats:italic>De novo</jats:italic> transcriptome sequencing, <jats:styled-content style="fixed-case">RNA</jats:styled-content>seq (RNA sequencing) and single nucleotide polymorphism (<jats:styled-content style="fixed-case">SNP</jats:styled-content>) calling were conducted on <jats:styled-content style="fixed-case">RNA</jats:styled-content> extracted from <jats:italic><jats:styled-content style="fixed-case">H</jats:styled-content>. lanatus</jats:italic>. Roche 454 sequencing data were assembled into <jats:italic>c</jats:italic>. 22 000 isotigs, and paired‐end <jats:styled-content style="fixed-case">I</jats:styled-content>llumina reads for phosphorus‐starved (P−) and phosphorus‐treated (<jats:styled-content style="fixed-case">P</jats:styled-content>+) genovars of tolerant (<jats:styled-content style="fixed-case">T</jats:styled-content>) and nontolerant (<jats:styled-content style="fixed-case">N</jats:styled-content>) phenotypes were mapped to this reference transcriptome.</jats:p></jats:list-item>
<jats:list-item><jats:p>Heatmaps of the gene expression data showed strong clustering of each <jats:styled-content style="fixed-case">P</jats:styled-content>+/<jats:styled-content style="fixed-case">P</jats:styled-content>− treated genovar, as well as clustering by <jats:styled-content style="fixed-case">N</jats:styled-content>/<jats:styled-content style="fixed-case">T</jats:styled-content> phenotype. Statistical analysis identified 87 isotigs to be significantly differentially expressed between <jats:styled-content style="fixed-case">N</jats:styled-content> and <jats:styled-content style="fixed-case">T</jats:styled-content> phenotypes and 258 between <jats:styled-content style="fixed-case">P</jats:styled-content>+ and <jats:styled-content style="fixed-case">P</jats:styled-content>− treated plants. <jats:styled-content style="fixed-case">SNP</jats:styled-content>s and transcript expression that systematically differed between <jats:styled-content style="fixed-case">N</jats:styled-content> and <jats:styled-content style="fixed-case">T</jats:styled-content> phenotypes had regulatory function, namely proteases, kinases and ribonuclear <jats:styled-content style="fixed-case">RNA</jats:styled-content>‐binding protein and transposable elements.</jats:p></jats:list-item>
<jats:list-item><jats:p>A single gene for arsenate tolerance led to distinct phenotype transcriptomes and <jats:styled-content style="fixed-case">SNP</jats:styled-content> profiles, with large differences in upstream post‐translational and post‐transcriptional regulatory genes rather than in genes directly involved in P nutrition transport and metabolism <jats:italic>per se</jats:italic>.</jats:p></jats:list-item>
</jats:list>
</jats:p> |
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| author | Meharg, Caroline, Khan, Bayezid, Norton, Gareth, Deacon, Claire, Johnson, David, Reinhardt, Richard, Huettel, Bruno, Meharg, Andrew A. |
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| description | <jats:title>Summary</jats:title><jats:p> <jats:list list-type="bullet"> <jats:list-item><jats:p>The aim of this study was to characterize the transcriptome of a balanced polymorphism, under the regulation of a single gene, for phosphate fertilizer responsiveness/arsenate tolerance in wild grass <jats:italic><jats:styled-content style="fixed-case">H</jats:styled-content>olcus lanatus</jats:italic> genotypes screened from the same habitat.</jats:p></jats:list-item> <jats:list-item><jats:p><jats:italic>De novo</jats:italic> transcriptome sequencing, <jats:styled-content style="fixed-case">RNA</jats:styled-content>seq (RNA sequencing) and single nucleotide polymorphism (<jats:styled-content style="fixed-case">SNP</jats:styled-content>) calling were conducted on <jats:styled-content style="fixed-case">RNA</jats:styled-content> extracted from <jats:italic><jats:styled-content style="fixed-case">H</jats:styled-content>. lanatus</jats:italic>. Roche 454 sequencing data were assembled into <jats:italic>c</jats:italic>. 22 000 isotigs, and paired‐end <jats:styled-content style="fixed-case">I</jats:styled-content>llumina reads for phosphorus‐starved (P−) and phosphorus‐treated (<jats:styled-content style="fixed-case">P</jats:styled-content>+) genovars of tolerant (<jats:styled-content style="fixed-case">T</jats:styled-content>) and nontolerant (<jats:styled-content style="fixed-case">N</jats:styled-content>) phenotypes were mapped to this reference transcriptome.</jats:p></jats:list-item> <jats:list-item><jats:p>Heatmaps of the gene expression data showed strong clustering of each <jats:styled-content style="fixed-case">P</jats:styled-content>+/<jats:styled-content style="fixed-case">P</jats:styled-content>− treated genovar, as well as clustering by <jats:styled-content style="fixed-case">N</jats:styled-content>/<jats:styled-content style="fixed-case">T</jats:styled-content> phenotype. Statistical analysis identified 87 isotigs to be significantly differentially expressed between <jats:styled-content style="fixed-case">N</jats:styled-content> and <jats:styled-content style="fixed-case">T</jats:styled-content> phenotypes and 258 between <jats:styled-content style="fixed-case">P</jats:styled-content>+ and <jats:styled-content style="fixed-case">P</jats:styled-content>− treated plants. <jats:styled-content style="fixed-case">SNP</jats:styled-content>s and transcript expression that systematically differed between <jats:styled-content style="fixed-case">N</jats:styled-content> and <jats:styled-content style="fixed-case">T</jats:styled-content> phenotypes had regulatory function, namely proteases, kinases and ribonuclear <jats:styled-content style="fixed-case">RNA</jats:styled-content>‐binding protein and transposable elements.</jats:p></jats:list-item> <jats:list-item><jats:p>A single gene for arsenate tolerance led to distinct phenotype transcriptomes and <jats:styled-content style="fixed-case">SNP</jats:styled-content> profiles, with large differences in upstream post‐translational and post‐transcriptional regulatory genes rather than in genes directly involved in P nutrition transport and metabolism <jats:italic>per se</jats:italic>.</jats:p></jats:list-item> </jats:list> </jats:p> |
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| spelling | Meharg, Caroline Khan, Bayezid Norton, Gareth Deacon, Claire Johnson, David Reinhardt, Richard Huettel, Bruno Meharg, Andrew A. 0028-646X 1469-8137 Wiley Plant Science Physiology http://dx.doi.org/10.1111/nph.12491 <jats:title>Summary</jats:title><jats:p> <jats:list list-type="bullet"> <jats:list-item><jats:p>The aim of this study was to characterize the transcriptome of a balanced polymorphism, under the regulation of a single gene, for phosphate fertilizer responsiveness/arsenate tolerance in wild grass <jats:italic><jats:styled-content style="fixed-case">H</jats:styled-content>olcus lanatus</jats:italic> genotypes screened from the same habitat.</jats:p></jats:list-item> <jats:list-item><jats:p><jats:italic>De novo</jats:italic> transcriptome sequencing, <jats:styled-content style="fixed-case">RNA</jats:styled-content>seq (RNA sequencing) and single nucleotide polymorphism (<jats:styled-content style="fixed-case">SNP</jats:styled-content>) calling were conducted on <jats:styled-content style="fixed-case">RNA</jats:styled-content> extracted from <jats:italic><jats:styled-content style="fixed-case">H</jats:styled-content>. lanatus</jats:italic>. Roche 454 sequencing data were assembled into <jats:italic>c</jats:italic>. 22 000 isotigs, and paired‐end <jats:styled-content style="fixed-case">I</jats:styled-content>llumina reads for phosphorus‐starved (P−) and phosphorus‐treated (<jats:styled-content style="fixed-case">P</jats:styled-content>+) genovars of tolerant (<jats:styled-content style="fixed-case">T</jats:styled-content>) and nontolerant (<jats:styled-content style="fixed-case">N</jats:styled-content>) phenotypes were mapped to this reference transcriptome.</jats:p></jats:list-item> <jats:list-item><jats:p>Heatmaps of the gene expression data showed strong clustering of each <jats:styled-content style="fixed-case">P</jats:styled-content>+/<jats:styled-content style="fixed-case">P</jats:styled-content>− treated genovar, as well as clustering by <jats:styled-content style="fixed-case">N</jats:styled-content>/<jats:styled-content style="fixed-case">T</jats:styled-content> phenotype. Statistical analysis identified 87 isotigs to be significantly differentially expressed between <jats:styled-content style="fixed-case">N</jats:styled-content> and <jats:styled-content style="fixed-case">T</jats:styled-content> phenotypes and 258 between <jats:styled-content style="fixed-case">P</jats:styled-content>+ and <jats:styled-content style="fixed-case">P</jats:styled-content>− treated plants. <jats:styled-content style="fixed-case">SNP</jats:styled-content>s and transcript expression that systematically differed between <jats:styled-content style="fixed-case">N</jats:styled-content> and <jats:styled-content style="fixed-case">T</jats:styled-content> phenotypes had regulatory function, namely proteases, kinases and ribonuclear <jats:styled-content style="fixed-case">RNA</jats:styled-content>‐binding protein and transposable elements.</jats:p></jats:list-item> <jats:list-item><jats:p>A single gene for arsenate tolerance led to distinct phenotype transcriptomes and <jats:styled-content style="fixed-case">SNP</jats:styled-content> profiles, with large differences in upstream post‐translational and post‐transcriptional regulatory genes rather than in genes directly involved in P nutrition transport and metabolism <jats:italic>per se</jats:italic>.</jats:p></jats:list-item> </jats:list> </jats:p> Trait‐directed <i>de novo</i> population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, <i><scp>H</scp>olcus lanatus</i> New Phytologist |
| spellingShingle | Meharg, Caroline, Khan, Bayezid, Norton, Gareth, Deacon, Claire, Johnson, David, Reinhardt, Richard, Huettel, Bruno, Meharg, Andrew A., New Phytologist, Trait‐directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus, Plant Science, Physiology |
| title | Trait‐directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus |
| title_full | Trait‐directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus |
| title_fullStr | Trait‐directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus |
| title_full_unstemmed | Trait‐directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus |
| title_short | Trait‐directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus |
| title_sort | trait‐directed <i>de novo</i> population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, <i><scp>h</scp>olcus lanatus</i> |
| title_unstemmed | Trait‐directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus |
| topic | Plant Science, Physiology |
| url | http://dx.doi.org/10.1111/nph.12491 |