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

Abstract

SummaryDifficulties 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.

Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

“…Additional work identifying parental lineages of putative hybrid species using allelic information from single‐copy nuclear genes – for example, statistical phasing of alleles from sequence capture data and/or isolating individual alleles via molecular cloning and/or bioinformatically from high‐throughput amplicon datasets (e.g. Pyron et al ., ; Uribe‐Convers et al ., ; Motazedi et al ., ; Rothfels et al ., ; Blischak et al ., ) – remains to be done in Lachemilla . Kamneva et al .…”

Characterizing the allopolyploid species among the wild relatives of soybean: Utility of reduced representation genotyping methodologies

“…Research into the origin of polyploid species and their subsequent adaptation will continue to benefit from the advent of short read and other sequencing technologies (Burrell et al, 2015;Qi et al, 2015;Rothfels et al, 2017;Stetter & Schmid, 2017). Newly developed data analysis methods will make the identification of allopolyploids and studies of their evolution tractable (Jones et al, 2013;McKinney et al, 2017;Gompert & Mock, 2017).…”

Sex and Rosaceae apomicts

“…We need molecular methods with which to document reticulate evolution in diploid-polyploid complexes. Next-generation sequencing can provide the raw data, but new strategies are needed such as the one suggested by Rothfels & al. (2016).…”