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

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

Research output: Contribution to journalArticle

9 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)855-870
Number of pages16
JournalNew Phytologist
Volume217
Issue number2
DOIs
StatePublished - Jan 1 2018

Fingerprint

Caryophyllales
Polyploidy
allopolyploidy
Transcriptome
transcriptome
polyploidy
autopolyploidy
sampling
Gene Duplication
gene duplication
History
Genome
genomics
history
genome
phylogeny
methodology
Datasets

Keywords

  • Caryophyllales
  • Ks plot
  • allopolyploidy
  • genome duplication
  • modified phylome
  • polyploidy

Cite this

Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events. / Yang, Ya; Moore, Michael J.; Brockington, Samuel F.; Mikenas, Jessica; Olivieri, Julia; Walker, Joseph F.; Smith, Stephen A.

In: New Phytologist, Vol. 217, No. 2, 01.01.2018, p. 855-870.

Research output: Contribution to journalArticle

Yang, Ya ; Moore, Michael J. ; Brockington, Samuel F. ; Mikenas, Jessica ; Olivieri, Julia ; Walker, Joseph F. ; Smith, Stephen A. / Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events. In: New Phytologist. 2018 ; Vol. 217, No. 2. pp. 855-870.
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