SUPPORTING INFORMATION Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary Kevin Vanneste1,2, Guy Baele3, Steven Maere1,2,*, and Yves Van de Peer1,2,4,* 1 Department of Plant Systems Biology, VIB, Ghent, Belgium 2 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium 3 Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium 4 Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria, South Africa *Corresponding authors Yves Van de Peer Steven Maere VIB / Ghent University VIB / Ghent University Technologiepark 927 Technologiepark 927 Gent (9052), Belgium Gent (9052), Belgium Tel: +32 (0)9 331 3807 Tel: +32 (0)9 331 3805 Fax: +32 (0)9 331 3809 Fax: +32 (0)9 331 3809 E-mail:
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[email protected] Overview Species grouping topology ................................................ 3 Calibrations and constraints .............................................. 5 Alternative calibrations and constraints ............................ 13 Relative rate tests ............................................................. 27 Re-dating the Pyrus bretschneideri WGD ......................... 30 WGD age estimates from literature ................................... 33 Eschscholzia californica and Acorus americanus ............. 34 2 Species grouping topology In order to date the node joining the homeologous pair, orthogroups were constructed consisting of both homeologs and orthologs from other plant species for which full genome sequence information was available. Different plant species were grouped into ‘species groups’ for which one ortholog was selected and added to the orthogroup, in order to keep the orthogroup topology fixed and to facilitate automation on the one hand, but also to allow enough orthogroups to be constructed on the other hand (see Material and methods).