Supplemental Material for Boatwright et al., 2018

<div>File S1 contains Trinotate gene ontology annotations for Tragopogon dubius. </div><div>File S2 contains Trinotate annotations for T. dubius. </div><div>File S3 contains Trinotate gene ontology annotations for T. porrifolius. </div><div>File S4 contains Trinotate annotations for T. porrifolius. </div><div>File S5 contains Trinotate gene ontology annotations for T. pratensis. </div><div>File S6 contains Trinotate annotations for T. pratensis. </div><div>File S7 is a BED file containing the coordinates for the T. dubius common orthologous region sequence from the T.dubius-T.porrifolius orthologous pair. </div><div>File S8 is a BED file containing the coordinates for the T. dubius common orthologous region sequence from the T.dubius-T.pratensis orthologous pair. </div><div>File S9 is a BED file containing the coordinates for the T. porrifolius common orthologous region sequence from the T.dubius-T.porrifolius orthologous pair. </div><div>File S10 is a BED file containing the coordinates for the T. pratensis common orthologous region sequence from the T.dubius-T.pratensis orthologous pair. </div><div>File S11 contains the redundancy-compressed assembly for T. dubius. </div><div>File S12 contains the redundancy-compressed assembly for T. porrifolius. </div><div>File S13 contains the redundancy-compressed assembly for T. pratensis. </div><div>Table S1 contains the transcriptome read statistics for T. dubius, T. porrifolius and T. pratensis when reads were raw or trimmed and head (10) cropped (-) or not (+). </div><div>Table S2 contains assembly isoform counts for each intermediate assembly through the initial CAP3 run. </div><div>Table S3 contains stepwise assembly statistics from the initial CAP3 run to the final redundancy-compressed assemblies. </div><div>Table S4 contains program version information. </div><div>Table S5 contains R session information including package versions. </div><div>Figure S1 depicts some possible overlaps for orthologous pairs and the identification of common orthologous regions. </div><div>Figure S1 depicts the assembly compression pipeline used in this study. </div><div>Figure S2 show some examples of common orthologous regions between ortholog sequences. </div><div>Figure S3 shows T. dubius and T. porrifolius common orthologous region lengths mean-difference plot. </div><div>Figure S4 shows T. dubius and T. pratensis common orthologous region lengths mean-difference plot. </div><div>Figure S5 shows T. dubius and T. porrifolius common orthologous region percent GC mean-difference plot. </div><div>Figure S6 shows T. dubius and T. pratensis common orthologous region percent GC mean-difference plot. </div><div>Figure S7 contains a MDS plot of the expression matrix for T. mirus and its diploid progenitors. </div><div>Figure S8 contains a voom mean-variance trend generated from the expression matrix containing T. mirus and its diploid progenitors. </div><div>Figure S9 contains a plot of the residual standard deviations after applying voom inverse-variance weights to the T. mirus expression matrix. </div><div>Figure S10 contains a MDS plot of the expression matrix for T. miscellus and its diploid progenitors. </div><div>Figure S11 contains a voom mean-variance trend generated from the expression matrix containing T. miscellus and its diploid progenitors. </div><div>Figure S12 contains a plot of the residual standard deviations after applying voom inverse-variance weights to the T. miscellus expression matrix. </div><div><br></div>