Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events.

Ya Yang,Michael J Moore,Joseph F Walker,Stephen A Smith,Jessica Mikenas,Julia Olivieri,Samuel F Brockington

doi:10.1111/nph.14812

Abstract

Studies of the macroevolutionary legacy of polyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications. We assembled a data set of transcriptomes and genomes from 168 species in Caryophyllales, of which 43 transcriptomes were newly generated for this study, representing one of the most densely sampled genomic-scale data sets available. We carried out phylogenomic analyses using a modified phylome strategy to reconstruct the species tree. We mapped the phylogenetic distribution of polyploidy events by both tree-based and distance-based methods, and explicitly tested scenarios for allopolyploidy. We identified 26 ancient and more recent polyploidy events distributed throughout Caryophyllales. Two of these events were inferred to be allopolyploidy. Through dense phylogenomic sampling, we show the propensity of polyploidy throughout the evolutionary history of Caryophyllales. We also provide a framework for utilizing transcriptome data to detect allopolyploidy, which is important as it may have different macroevolutionary implications compared with autopolyploidy.

Highlights

The prevalence and evolutionary consequences of polyploidy in plants have been discussed at length in the fields of macroevolution (Soltis et al, 2015; Lohaus & Van de Peer, 2016)
We provide a framework for utilizing transcriptome data to detect allopolyploidy, which is important as it may have different macro-evolutionary implications compared to autopolyploidy
Scripts used were archived in Dryad, with notes and updates for modified phylomes available from https://bitbucket.org/yangya/genome_walking_2016 and those for building lineage-specific homologs and mapping polyploidy events available from https://bitbucket.org/blackrim/clustering

Summary

Introduction

The prevalence and evolutionary consequences of polyploidy in plants have been discussed at length in the fields of macroevolution (Soltis et al, 2015; Lohaus & Van de Peer, 2016). Most studies of polyploidy have employed either dating synonymous distances (Ks) among paralogous gene pairs (Vanneste et al, 2013) or ancestral character reconstruction of chromosome counts (Mayrose et al, 2010; Glick & Mayrose, 2014). Ks plots between syntenic blocks from individual sequenced genomes have the advantage of being sensitive enough to detect ancient and nested polyploidy events (Jaillon et al, 2007; Jiao et al, 2011, 2012, 2014). This technique suffers from the typically sparse taxon sampling available in whole genome data. This method has the best signal for recent events and is most often restricted to the genus level or below (Wood et al, 2009; Mayrose et al, 2010, 2011)

Methods

Results

Conclusion