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Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing
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| Zeitschriftentitel: | New Phytologist |
|---|---|
| Personen und Körperschaften: | , , |
| In: | New Phytologist, 213, 2017, 1, S. 413-429 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Wiley
|
| Schlagwörter: |
| author_facet |
Rothfels, Carl J. Pryer, Kathleen M. Li, Fay‐Wei Rothfels, Carl J. Pryer, Kathleen M. Li, Fay‐Wei |
|---|---|
| author |
Rothfels, Carl J. Pryer, Kathleen M. Li, Fay‐Wei |
| spellingShingle |
Rothfels, Carl J. Pryer, Kathleen M. Li, Fay‐Wei New Phytologist Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing Plant Science Physiology |
| author_sort |
rothfels, carl j. |
| spelling |
Rothfels, Carl J. Pryer, Kathleen M. Li, Fay‐Wei 0028-646X 1469-8137 Wiley Plant Science Physiology http://dx.doi.org/10.1111/nph.14111 <jats:title>Summary</jats:title><jats:p> <jats:list list-type="bullet"> <jats:list-item><jats:p>Difficulties in generating nuclear data for polyploids have impeded phylogenetic study of these groups. We describe a high‐throughput protocol and an associated bioinformatics pipeline (Pipeline for Untangling Reticulate Complexes (<jats:sc>Purc</jats:sc>)) that is able to generate these data quickly and conveniently, and demonstrate its efficacy on accessions from the fern family Cystopteridaceae. We conclude with a demonstration of the downstream utility of these data by inferring a multi‐labeled species tree for a subset of our accessions.</jats:p></jats:list-item> <jats:list-item><jats:p>We amplified four <jats:italic>c</jats:italic>. 1‐kb‐long nuclear loci and sequenced them in a parallel‐tagged amplicon sequencing approach using the PacBio platform. <jats:sc>Purc</jats:sc> infers the final sequences from the raw reads via an iterative approach that corrects <jats:styled-content style="fixed-case">PCR</jats:styled-content> and sequencing errors and removes <jats:styled-content style="fixed-case">PCR</jats:styled-content>‐mediated recombinant sequences (chimeras).</jats:p></jats:list-item> <jats:list-item><jats:p>We generated data for all gene copies (homeologs, paralogs, and segregating alleles) present in each of three sets of 50 mostly polyploid accessions, for four loci, in three PacBio runs (one run per set). From the raw sequencing reads, <jats:sc>Purc</jats:sc> was able to accurately infer the underlying sequences.</jats:p></jats:list-item> <jats:list-item><jats:p>This approach makes it easy and economical to study the phylogenetics of polyploids, and, in conjunction with recent analytical advances, facilitates investigation of broad patterns of polyploid evolution.</jats:p></jats:list-item> </jats:list> </jats:p> Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing New Phytologist |
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10.1111/nph.14111 |
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Wiley, 2017 |
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Wiley, 2017 |
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0028-646X 1469-8137 |
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rothfels2017nextgenerationpolyploidphylogeneticsrapidresolutionofhybridpolyploidcomplexesusingpacbiosinglemoleculesequencing |
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2017 |
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Wiley |
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New Phytologist |
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49 |
| title |
Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing |
| title_unstemmed |
Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing |
| title_full |
Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing |
| title_fullStr |
Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing |
| title_full_unstemmed |
Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing |
| title_short |
Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing |
| title_sort |
next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using pacbio single‐molecule sequencing |
| topic |
Plant Science Physiology |
| url |
http://dx.doi.org/10.1111/nph.14111 |
| publishDate |
2017 |
| physical |
413-429 |
| description |
<jats:title>Summary</jats:title><jats:p>
<jats:list list-type="bullet">
<jats:list-item><jats:p>Difficulties in generating nuclear data for polyploids have impeded phylogenetic study of these groups. We describe a high‐throughput protocol and an associated bioinformatics pipeline (Pipeline for Untangling Reticulate Complexes (<jats:sc>Purc</jats:sc>)) that is able to generate these data quickly and conveniently, and demonstrate its efficacy on accessions from the fern family Cystopteridaceae. We conclude with a demonstration of the downstream utility of these data by inferring a multi‐labeled species tree for a subset of our accessions.</jats:p></jats:list-item>
<jats:list-item><jats:p>We amplified four <jats:italic>c</jats:italic>. 1‐kb‐long nuclear loci and sequenced them in a parallel‐tagged amplicon sequencing approach using the PacBio platform. <jats:sc>Purc</jats:sc> infers the final sequences from the raw reads via an iterative approach that corrects <jats:styled-content style="fixed-case">PCR</jats:styled-content> and sequencing errors and removes <jats:styled-content style="fixed-case">PCR</jats:styled-content>‐mediated recombinant sequences (chimeras).</jats:p></jats:list-item>
<jats:list-item><jats:p>We generated data for all gene copies (homeologs, paralogs, and segregating alleles) present in each of three sets of 50 mostly polyploid accessions, for four loci, in three PacBio runs (one run per set). From the raw sequencing reads, <jats:sc>Purc</jats:sc> was able to accurately infer the underlying sequences.</jats:p></jats:list-item>
<jats:list-item><jats:p>This approach makes it easy and economical to study the phylogenetics of polyploids, and, in conjunction with recent analytical advances, facilitates investigation of broad patterns of polyploid evolution.</jats:p></jats:list-item>
</jats:list>
</jats:p> |
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| author | Rothfels, Carl J., Pryer, Kathleen M., Li, Fay‐Wei |
| author_facet | Rothfels, Carl J., Pryer, Kathleen M., Li, Fay‐Wei, Rothfels, Carl J., Pryer, Kathleen M., Li, Fay‐Wei |
| author_sort | rothfels, carl j. |
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| description | <jats:title>Summary</jats:title><jats:p> <jats:list list-type="bullet"> <jats:list-item><jats:p>Difficulties in generating nuclear data for polyploids have impeded phylogenetic study of these groups. We describe a high‐throughput protocol and an associated bioinformatics pipeline (Pipeline for Untangling Reticulate Complexes (<jats:sc>Purc</jats:sc>)) that is able to generate these data quickly and conveniently, and demonstrate its efficacy on accessions from the fern family Cystopteridaceae. We conclude with a demonstration of the downstream utility of these data by inferring a multi‐labeled species tree for a subset of our accessions.</jats:p></jats:list-item> <jats:list-item><jats:p>We amplified four <jats:italic>c</jats:italic>. 1‐kb‐long nuclear loci and sequenced them in a parallel‐tagged amplicon sequencing approach using the PacBio platform. <jats:sc>Purc</jats:sc> infers the final sequences from the raw reads via an iterative approach that corrects <jats:styled-content style="fixed-case">PCR</jats:styled-content> and sequencing errors and removes <jats:styled-content style="fixed-case">PCR</jats:styled-content>‐mediated recombinant sequences (chimeras).</jats:p></jats:list-item> <jats:list-item><jats:p>We generated data for all gene copies (homeologs, paralogs, and segregating alleles) present in each of three sets of 50 mostly polyploid accessions, for four loci, in three PacBio runs (one run per set). From the raw sequencing reads, <jats:sc>Purc</jats:sc> was able to accurately infer the underlying sequences.</jats:p></jats:list-item> <jats:list-item><jats:p>This approach makes it easy and economical to study the phylogenetics of polyploids, and, in conjunction with recent analytical advances, facilitates investigation of broad patterns of polyploid evolution.</jats:p></jats:list-item> </jats:list> </jats:p> |
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| spelling | Rothfels, Carl J. Pryer, Kathleen M. Li, Fay‐Wei 0028-646X 1469-8137 Wiley Plant Science Physiology http://dx.doi.org/10.1111/nph.14111 <jats:title>Summary</jats:title><jats:p> <jats:list list-type="bullet"> <jats:list-item><jats:p>Difficulties in generating nuclear data for polyploids have impeded phylogenetic study of these groups. We describe a high‐throughput protocol and an associated bioinformatics pipeline (Pipeline for Untangling Reticulate Complexes (<jats:sc>Purc</jats:sc>)) that is able to generate these data quickly and conveniently, and demonstrate its efficacy on accessions from the fern family Cystopteridaceae. We conclude with a demonstration of the downstream utility of these data by inferring a multi‐labeled species tree for a subset of our accessions.</jats:p></jats:list-item> <jats:list-item><jats:p>We amplified four <jats:italic>c</jats:italic>. 1‐kb‐long nuclear loci and sequenced them in a parallel‐tagged amplicon sequencing approach using the PacBio platform. <jats:sc>Purc</jats:sc> infers the final sequences from the raw reads via an iterative approach that corrects <jats:styled-content style="fixed-case">PCR</jats:styled-content> and sequencing errors and removes <jats:styled-content style="fixed-case">PCR</jats:styled-content>‐mediated recombinant sequences (chimeras).</jats:p></jats:list-item> <jats:list-item><jats:p>We generated data for all gene copies (homeologs, paralogs, and segregating alleles) present in each of three sets of 50 mostly polyploid accessions, for four loci, in three PacBio runs (one run per set). From the raw sequencing reads, <jats:sc>Purc</jats:sc> was able to accurately infer the underlying sequences.</jats:p></jats:list-item> <jats:list-item><jats:p>This approach makes it easy and economical to study the phylogenetics of polyploids, and, in conjunction with recent analytical advances, facilitates investigation of broad patterns of polyploid evolution.</jats:p></jats:list-item> </jats:list> </jats:p> Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing New Phytologist |
| spellingShingle | Rothfels, Carl J., Pryer, Kathleen M., Li, Fay‐Wei, New Phytologist, Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing, Plant Science, Physiology |
| title | Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing |
| title_full | Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing |
| title_fullStr | Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing |
| title_full_unstemmed | Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing |
| title_short | Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing |
| title_sort | next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using pacbio single‐molecule sequencing |
| title_unstemmed | Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing |
| topic | Plant Science, Physiology |
| url | http://dx.doi.org/10.1111/nph.14111 |