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Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond
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| Zeitschriftentitel: | The Plant Journal |
|---|---|
| Personen und Körperschaften: | , , , , , , , , , , , , , , , , , , , , , , |
| In: | The Plant Journal, 76, 2013, 3, S. 494-505 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Wiley
|
| Schlagwörter: |
| author_facet |
Mascher, Martin Richmond, Todd A. Gerhardt, Daniel J. Himmelbach, Axel Clissold, Leah Sampath, Dharanya Ayling, Sarah Steuernagel, Burkhard Pfeifer, Matthias D'Ascenzo, Mark Akhunov, Eduard D. Hedley, Pete E. Gonzales, Ana M. Morrell, Peter L. Kilian, Benjamin Blattner, Frank R. Scholz, Uwe Mayer, Klaus F.X. Flavell, Andrew J. Muehlbauer, Gary J. Waugh, Robbie Jeddeloh, Jeffrey A. Stein, Nils Mascher, Martin Richmond, Todd A. Gerhardt, Daniel J. Himmelbach, Axel Clissold, Leah Sampath, Dharanya Ayling, Sarah Steuernagel, Burkhard Pfeifer, Matthias D'Ascenzo, Mark Akhunov, Eduard D. Hedley, Pete E. Gonzales, Ana M. Morrell, Peter L. Kilian, Benjamin Blattner, Frank R. Scholz, Uwe Mayer, Klaus F.X. Flavell, Andrew J. Muehlbauer, Gary J. Waugh, Robbie Jeddeloh, Jeffrey A. Stein, Nils |
|---|---|
| author |
Mascher, Martin Richmond, Todd A. Gerhardt, Daniel J. Himmelbach, Axel Clissold, Leah Sampath, Dharanya Ayling, Sarah Steuernagel, Burkhard Pfeifer, Matthias D'Ascenzo, Mark Akhunov, Eduard D. Hedley, Pete E. Gonzales, Ana M. Morrell, Peter L. Kilian, Benjamin Blattner, Frank R. Scholz, Uwe Mayer, Klaus F.X. Flavell, Andrew J. Muehlbauer, Gary J. Waugh, Robbie Jeddeloh, Jeffrey A. Stein, Nils |
| spellingShingle |
Mascher, Martin Richmond, Todd A. Gerhardt, Daniel J. Himmelbach, Axel Clissold, Leah Sampath, Dharanya Ayling, Sarah Steuernagel, Burkhard Pfeifer, Matthias D'Ascenzo, Mark Akhunov, Eduard D. Hedley, Pete E. Gonzales, Ana M. Morrell, Peter L. Kilian, Benjamin Blattner, Frank R. Scholz, Uwe Mayer, Klaus F.X. Flavell, Andrew J. Muehlbauer, Gary J. Waugh, Robbie Jeddeloh, Jeffrey A. Stein, Nils The Plant Journal Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond Cell Biology Plant Science Genetics |
| author_sort |
mascher, martin |
| spelling |
Mascher, Martin Richmond, Todd A. Gerhardt, Daniel J. Himmelbach, Axel Clissold, Leah Sampath, Dharanya Ayling, Sarah Steuernagel, Burkhard Pfeifer, Matthias D'Ascenzo, Mark Akhunov, Eduard D. Hedley, Pete E. Gonzales, Ana M. Morrell, Peter L. Kilian, Benjamin Blattner, Frank R. Scholz, Uwe Mayer, Klaus F.X. Flavell, Andrew J. Muehlbauer, Gary J. Waugh, Robbie Jeddeloh, Jeffrey A. Stein, Nils 0960-7412 1365-313X Wiley Cell Biology Plant Science Genetics http://dx.doi.org/10.1111/tpj.12294 <jats:title>Summary</jats:title><jats:p>Advanced resources for genome‐assisted research in barley (<jats:italic><jats:styled-content style="fixed-case">H</jats:styled-content>ordeum vulgare</jats:italic>) including a whole‐genome shotgun assembly and an integrated physical map have recently become available. These have made possible studies that aim to assess genetic diversity or to isolate single genes by whole‐genome resequencing and <jats:italic>in silico</jats:italic> variant detection. However such an approach remains expensive given the 5 Gb size of the barley genome. Targeted sequencing of the m<jats:styled-content style="fixed-case">RNA</jats:styled-content>‐coding exome reduces barley genomic complexity more than 50‐fold, thus dramatically reducing this heavy sequencing and analysis load. We have developed and employed an in‐solution hybridization‐based sequence capture platform to selectively enrich for a 61.6 megabase coding sequence target that includes predicted genes from the genome assembly of the cultivar <jats:styled-content style="fixed-case">M</jats:styled-content>orex as well as publicly available full‐length c<jats:styled-content style="fixed-case">DNA</jats:styled-content>s and <jats:italic>de novo</jats:italic> assembled RNA‐Seq consensus sequence contigs. The platform provides a highly specific capture with substantial and reproducible enrichment of targeted exons, both for cultivated barley and related species. We show that this exome capture platform provides a clear path towards a broader and deeper understanding of the natural variation residing in the m<jats:styled-content style="fixed-case">RNA</jats:styled-content>‐coding part of the barley genome and will thus constitute a valuable resource for applications such as mapping‐by‐sequencing and genetic diversity analyzes.</jats:p> Barley whole exome capture: a tool for genomic research in the genus <i>Hordeum</i> and beyond The Plant Journal |
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Wiley, 2013 |
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Wiley, 2013 |
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| title |
Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond |
| title_unstemmed |
Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond |
| title_full |
Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond |
| title_fullStr |
Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond |
| title_full_unstemmed |
Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond |
| title_short |
Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond |
| title_sort |
barley whole exome capture: a tool for genomic research in the genus <i>hordeum</i> and beyond |
| topic |
Cell Biology Plant Science Genetics |
| url |
http://dx.doi.org/10.1111/tpj.12294 |
| publishDate |
2013 |
| physical |
494-505 |
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<jats:title>Summary</jats:title><jats:p>Advanced resources for genome‐assisted research in barley (<jats:italic><jats:styled-content style="fixed-case">H</jats:styled-content>ordeum vulgare</jats:italic>) including a whole‐genome shotgun assembly and an integrated physical map have recently become available. These have made possible studies that aim to assess genetic diversity or to isolate single genes by whole‐genome resequencing and <jats:italic>in silico</jats:italic> variant detection. However such an approach remains expensive given the 5 Gb size of the barley genome. Targeted sequencing of the m<jats:styled-content style="fixed-case">RNA</jats:styled-content>‐coding exome reduces barley genomic complexity more than 50‐fold, thus dramatically reducing this heavy sequencing and analysis load. We have developed and employed an in‐solution hybridization‐based sequence capture platform to selectively enrich for a 61.6 megabase coding sequence target that includes predicted genes from the genome assembly of the cultivar <jats:styled-content style="fixed-case">M</jats:styled-content>orex as well as publicly available full‐length c<jats:styled-content style="fixed-case">DNA</jats:styled-content>s and <jats:italic>de novo</jats:italic> assembled RNA‐Seq consensus sequence contigs. The platform provides a highly specific capture with substantial and reproducible enrichment of targeted exons, both for cultivated barley and related species. We show that this exome capture platform provides a clear path towards a broader and deeper understanding of the natural variation residing in the m<jats:styled-content style="fixed-case">RNA</jats:styled-content>‐coding part of the barley genome and will thus constitute a valuable resource for applications such as mapping‐by‐sequencing and genetic diversity analyzes.</jats:p> |
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| author | Mascher, Martin, Richmond, Todd A., Gerhardt, Daniel J., Himmelbach, Axel, Clissold, Leah, Sampath, Dharanya, Ayling, Sarah, Steuernagel, Burkhard, Pfeifer, Matthias, D'Ascenzo, Mark, Akhunov, Eduard D., Hedley, Pete E., Gonzales, Ana M., Morrell, Peter L., Kilian, Benjamin, Blattner, Frank R., Scholz, Uwe, Mayer, Klaus F.X., Flavell, Andrew J., Muehlbauer, Gary J., Waugh, Robbie, Jeddeloh, Jeffrey A., Stein, Nils |
| author_facet | Mascher, Martin, Richmond, Todd A., Gerhardt, Daniel J., Himmelbach, Axel, Clissold, Leah, Sampath, Dharanya, Ayling, Sarah, Steuernagel, Burkhard, Pfeifer, Matthias, D'Ascenzo, Mark, Akhunov, Eduard D., Hedley, Pete E., Gonzales, Ana M., Morrell, Peter L., Kilian, Benjamin, Blattner, Frank R., Scholz, Uwe, Mayer, Klaus F.X., Flavell, Andrew J., Muehlbauer, Gary J., Waugh, Robbie, Jeddeloh, Jeffrey A., Stein, Nils, Mascher, Martin, Richmond, Todd A., Gerhardt, Daniel J., Himmelbach, Axel, Clissold, Leah, Sampath, Dharanya, Ayling, Sarah, Steuernagel, Burkhard, Pfeifer, Matthias, D'Ascenzo, Mark, Akhunov, Eduard D., Hedley, Pete E., Gonzales, Ana M., Morrell, Peter L., Kilian, Benjamin, Blattner, Frank R., Scholz, Uwe, Mayer, Klaus F.X., Flavell, Andrew J., Muehlbauer, Gary J., Waugh, Robbie, Jeddeloh, Jeffrey A., Stein, Nils |
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| description | <jats:title>Summary</jats:title><jats:p>Advanced resources for genome‐assisted research in barley (<jats:italic><jats:styled-content style="fixed-case">H</jats:styled-content>ordeum vulgare</jats:italic>) including a whole‐genome shotgun assembly and an integrated physical map have recently become available. These have made possible studies that aim to assess genetic diversity or to isolate single genes by whole‐genome resequencing and <jats:italic>in silico</jats:italic> variant detection. However such an approach remains expensive given the 5 Gb size of the barley genome. Targeted sequencing of the m<jats:styled-content style="fixed-case">RNA</jats:styled-content>‐coding exome reduces barley genomic complexity more than 50‐fold, thus dramatically reducing this heavy sequencing and analysis load. We have developed and employed an in‐solution hybridization‐based sequence capture platform to selectively enrich for a 61.6 megabase coding sequence target that includes predicted genes from the genome assembly of the cultivar <jats:styled-content style="fixed-case">M</jats:styled-content>orex as well as publicly available full‐length c<jats:styled-content style="fixed-case">DNA</jats:styled-content>s and <jats:italic>de novo</jats:italic> assembled RNA‐Seq consensus sequence contigs. The platform provides a highly specific capture with substantial and reproducible enrichment of targeted exons, both for cultivated barley and related species. We show that this exome capture platform provides a clear path towards a broader and deeper understanding of the natural variation residing in the m<jats:styled-content style="fixed-case">RNA</jats:styled-content>‐coding part of the barley genome and will thus constitute a valuable resource for applications such as mapping‐by‐sequencing and genetic diversity analyzes.</jats:p> |
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| spelling | Mascher, Martin Richmond, Todd A. Gerhardt, Daniel J. Himmelbach, Axel Clissold, Leah Sampath, Dharanya Ayling, Sarah Steuernagel, Burkhard Pfeifer, Matthias D'Ascenzo, Mark Akhunov, Eduard D. Hedley, Pete E. Gonzales, Ana M. Morrell, Peter L. Kilian, Benjamin Blattner, Frank R. Scholz, Uwe Mayer, Klaus F.X. Flavell, Andrew J. Muehlbauer, Gary J. Waugh, Robbie Jeddeloh, Jeffrey A. Stein, Nils 0960-7412 1365-313X Wiley Cell Biology Plant Science Genetics http://dx.doi.org/10.1111/tpj.12294 <jats:title>Summary</jats:title><jats:p>Advanced resources for genome‐assisted research in barley (<jats:italic><jats:styled-content style="fixed-case">H</jats:styled-content>ordeum vulgare</jats:italic>) including a whole‐genome shotgun assembly and an integrated physical map have recently become available. These have made possible studies that aim to assess genetic diversity or to isolate single genes by whole‐genome resequencing and <jats:italic>in silico</jats:italic> variant detection. However such an approach remains expensive given the 5 Gb size of the barley genome. Targeted sequencing of the m<jats:styled-content style="fixed-case">RNA</jats:styled-content>‐coding exome reduces barley genomic complexity more than 50‐fold, thus dramatically reducing this heavy sequencing and analysis load. We have developed and employed an in‐solution hybridization‐based sequence capture platform to selectively enrich for a 61.6 megabase coding sequence target that includes predicted genes from the genome assembly of the cultivar <jats:styled-content style="fixed-case">M</jats:styled-content>orex as well as publicly available full‐length c<jats:styled-content style="fixed-case">DNA</jats:styled-content>s and <jats:italic>de novo</jats:italic> assembled RNA‐Seq consensus sequence contigs. The platform provides a highly specific capture with substantial and reproducible enrichment of targeted exons, both for cultivated barley and related species. We show that this exome capture platform provides a clear path towards a broader and deeper understanding of the natural variation residing in the m<jats:styled-content style="fixed-case">RNA</jats:styled-content>‐coding part of the barley genome and will thus constitute a valuable resource for applications such as mapping‐by‐sequencing and genetic diversity analyzes.</jats:p> Barley whole exome capture: a tool for genomic research in the genus <i>Hordeum</i> and beyond The Plant Journal |
| spellingShingle | Mascher, Martin, Richmond, Todd A., Gerhardt, Daniel J., Himmelbach, Axel, Clissold, Leah, Sampath, Dharanya, Ayling, Sarah, Steuernagel, Burkhard, Pfeifer, Matthias, D'Ascenzo, Mark, Akhunov, Eduard D., Hedley, Pete E., Gonzales, Ana M., Morrell, Peter L., Kilian, Benjamin, Blattner, Frank R., Scholz, Uwe, Mayer, Klaus F.X., Flavell, Andrew J., Muehlbauer, Gary J., Waugh, Robbie, Jeddeloh, Jeffrey A., Stein, Nils, The Plant Journal, Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond, Cell Biology, Plant Science, Genetics |
| title | Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond |
| title_full | Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond |
| title_fullStr | Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond |
| title_full_unstemmed | Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond |
| title_short | Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond |
| title_sort | barley whole exome capture: a tool for genomic research in the genus <i>hordeum</i> and beyond |
| title_unstemmed | Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond |
| topic | Cell Biology, Plant Science, Genetics |
| url | http://dx.doi.org/10.1111/tpj.12294 |