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Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing.

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Date
2017-01
Authors
Rothfels, Carl J
Pryer, Kathleen M
Li, Fay-Wei
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Abstract
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 (Purc)) 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. We amplified four c. 1-kb-long nuclear loci and sequenced them in a parallel-tagged amplicon sequencing approach using the PacBio platform. Purc infers the final sequences from the raw reads via an iterative approach that corrects PCR and sequencing errors and removes PCR-mediated recombinant sequences (chimeras). 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, Purc was able to accurately infer the underlying sequences. 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.
Type
Journal article
Subject
Sequence Analysis, DNA
Hybridization, Genetic
Computational Biology
Phylogeny
Recombination, Genetic
Base Sequence
Consensus Sequence
Polyploidy
Alleles
Databases, Genetic
Biological Evolution
Permalink
https://hdl.handle.net/10161/21753
Published Version (Please cite this version)
10.1111/nph.14111
Publication Info
Rothfels, Carl J; Pryer, Kathleen M; & Li, Fay-Wei (2017). Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing. The New phytologist, 213(1). pp. 413-429. 10.1111/nph.14111. Retrieved from https://hdl.handle.net/10161/21753.
This is constructed from limited available data and may be imprecise. To cite this article, please review & use the official citation provided by the journal.
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Pryer

Kathleen M. Pryer

Professor of Biology
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