Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta)

Devos, Nicolas; Szövényi, Péter; Weston, David J.; Rothfels, Carl J.; Johnson, Matthew G.; Shaw, A. Jonathan

doi:10.1111/nph.13887

Title: Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta)

Journal Article · Mon Feb 22 00:00:00 EST 2016 · New Phytologist

DOI:https://doi.org/10.1111/nph.13887· OSTI ID:1326556

Devos, Nicolas ^[1]; Szövényi, Péter ^[2]; Weston, David J. ^[3]; Rothfels, Carl J. ^[4]; Johnson, Matthew G. ^[5]; Shaw, A. Jonathan ^[1]

Duke Univ., Durham, NC (United States)
Univ. of Zurich, Zurich (Switzerland); Swiss Institute of Bioinformatics, Lausanne (Switzerland)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Univ. of California, Berkeley, CA (United States)
Chicago Botanic Garden, Glencoe, IL (United States)

Summary The goal of this research was to investigate whether there has been a whole‐genome duplication ( WGD ) in the ancestry of Sphagnum (peatmoss) or the class Sphagnopsida, and to determine if the timing of any such duplication(s) and patterns of paralog retention could help explain the rapid radiation and current ecological dominance of peatmosses. RNA sequencing ( RNA ‐seq) data were generated for nine taxa in Sphagnopsida (Bryophyta). Analyses of frequency plots for synonymous substitutions per synonymous site ( K _s ) between paralogous gene pairs and reconciliation of 578 gene trees were conducted to assess evidence of large‐scale or genome‐wide duplication events in each transcriptome. Both K _s frequency plots and gene tree‐based analyses indicate multiple duplication events in the history of the Sphagnopsida. The most recent WGD event predates divergence of Sphagnum from the two other genera of Sphagnopsida. Duplicate retention is highly variable across species, which might be best explained by local adaptation. Our analyses indicate that the last WGD could have been an important factor underlying the diversification of peatmosses and facilitated their rise to ecological dominance in peatlands. The timing of the duplication events and their significance in the evolutionary history of peat mosses are discussed.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Laboratory Directed Research and Development (LDRD) Program

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1326556

Alternate ID(s):: OSTI ID: 1379979

Journal Information:: New Phytologist, Vol. 211, Issue 1; ISSN 0028-646X

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 36 works

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The sphagnome project: enabling ecological and evolutionary insights through a genus-level sequencing project Weston, David J.; Turetsky, Merritt R.; Johnson, Matthew G. Wiley-Blackwell Publishing, Inc. https://doi.org/10.5167/uzh-141244	text	January 2018
The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data Perroud, Pierre-François; Haas, Fabian B.; Hiss, Manuel Wiley-Blackwell Publishing, Inc. https://doi.org/10.5167/uzh-161740	text	January 2018
Assessing the performance of Ks plots for detecting ancient whole genome duplications Tiley, George P.; Barker, Michael S.; Burleigh, J. Gordon Genome Biology and Evolution https://doi.org/10.1093/gbe/evy200	journal	September 2018
Integrated phylogenomic analyses reveal recurrent ancestral large-scale duplication events in mosses Gao, Bei; Chen, Moxian; Li, Xiaoshuang BioRxiv https://doi.org/10.1101/603191	posted_content	April 2019

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