Supplement: Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140 year old naturally established neo-allopolyploid monkeyflower Patrick P. Edger1,*, Ronald Smith2, Michael R. McKain3, Arielle M. Cooley4, Mario Vallejo-Marin5, Yaowu Yuan6, Adam J. Bewick7, Lexiang Ji7, Adrian E. Platts8, Megan Bowman9, Kevin Childs9, Robert J. Schmitz7, Gregory D. Smith2, J. Chris Pires10 and Joshua R. Puzey11,*,a 1Department of Horticulture, Michigan State University, East Lansing, MI 2Department of Applied Science, College of William and Mary, Williamsburg, VA 3Donald Danforth Plant Science Center, St. Louis, MO 4Biology Department, Whitman College, Walla Walla, WA 5Biological and Environmental Sciences, University of Stirling, Stirling, UK 6Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 7Department of Genetics, University of Georgia, Athens, GA 8McGill Centre for Bioinformatics, McGill University, Montreal, QC, Canada H3A 0E9 9Department of Plant Biology, Michigan State University, East Lansing, MI 10Division of Biological Sciences, University of Missouri, Columbia, MO 65211 11Department of Biology, College of William and Mary, Williamsburg, VA *These authors contributed equally aAuthor for correspondance:
[email protected] Contents 1 Methods 3 1 1.1 Genome assembly and annotation . .3 1.2 Whole genome alignments and phylogenetic analyses . .3 1.3 RNA-sequencing and quantification of gene expression . .3 1.4 Whole genome methylation sequencing and analysis . .4 1.5 LRT to detect homeolog expression bias . .4 1.6 Methods for Transposon annotation . .6 1.6.1 Autonomous cut-and-paste TEs . .6 1.6.2 Helitrons . .7 1.6.3 LTR retrotransposons . .7 1.6.4 LINEs . .8 1.6.5 SINEs .