Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing.
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 articleSubject
Sequence Analysis, DNAHybridization, Genetic
Computational Biology
Phylogeny
Recombination, Genetic
Base Sequence
Consensus Sequence
Polyploidy
Alleles
Databases, Genetic
Biological Evolution
Permalink
https://hdl.handle.net/10161/21753Published Version (Please cite this version)
10.1111/nph.14111Publication 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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Show full item recordScholars@Duke
Kathleen M. Pryer
Professor of Biology

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