Supplemental Material for Boatwright et al., 2018

File S1 contains Trinotate gene ontology annotations for Tragopogon dubius.
File S2 contains Trinotate annotations for T. dubius.
File S3 contains Trinotate gene ontology annotations for T. porrifolius.
File S4 contains Trinotate annotations for T. porrifolius.
File S5 contains Trinotate gene ontology annotations for T. pratensis.
File S6 contains Trinotate annotations for T. pratensis.
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.
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.
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.
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.
File S11 contains the redundancy-compressed assembly for T. dubius.
File S12 contains the redundancy-compressed assembly for T. porrifolius.
File S13 contains the redundancy-compressed assembly for T. pratensis.
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 (+).
Table S2 contains assembly isoform counts for each intermediate assembly through the initial CAP3 run.
Table S3 contains stepwise assembly statistics from the initial CAP3 run to the final redundancy-compressed assemblies.
Table S4 contains program version information.
Table S5 contains R session information including package versions.
Figure S1 depicts some possible overlaps for orthologous pairs and the identification of common orthologous regions.
Figure S1 depicts the assembly compression pipeline used in this study.
Figure S2 show some examples of common orthologous regions between ortholog sequences.
Figure S3 shows T. dubius and T. porrifolius common orthologous region lengths mean-difference plot.
Figure S4 shows T. dubius and T. pratensis common orthologous region lengths mean-difference plot.
Figure S5 shows T. dubius and T. porrifolius common orthologous region percent GC mean-difference plot.
Figure S6 shows T. dubius and T. pratensis common orthologous region percent GC mean-difference plot.
Figure S7 contains a MDS plot of the expression matrix for T. mirus and its diploid progenitors.
Figure S8 contains a voom mean-variance trend generated from the expression matrix containing T. mirus and its diploid progenitors.
Figure S9 contains a plot of the residual standard deviations after applying voom inverse-variance weights to the T. mirus expression matrix.
Figure S10 contains a MDS plot of the expression matrix for T. miscellus and its diploid progenitors.
Figure S11 contains a voom mean-variance trend generated from the expression matrix containing T. miscellus and its diploid progenitors.
Figure S12 contains a plot of the residual standard deviations after applying voom inverse-variance weights to the T. miscellus expression matrix.