Supplemental Material for Cartwright and Lott, 2020

Figure S1 contains PCA plots for transcript abundance in all crosses.Figure S2 contains plots for all the types of regulatory changes for maternally deposited transcripts in each set of pairwise comparisons between species.Figure S3 contains plots for all the types of regulatory changes for mostly zygotic genes in each set of pairwise comparisons between species.Figure S4 shows the transcript abundance from parental lines for <i>M1BP</i>, <i>Dref</i>, and <i>BEAF-32</i> at stage 2.Figure S5 contains the GO terms for mostly zygotic genes that change in <i>trans </i>regulation and are unique to a specific cross.<br>Table S1 lists the primers used for determining embryo sex (Y chromosomal genes <i>ORY</i> and <i>kl3</i>, and autosomal control gene <i>ftz</i>).Table S2 is an ortholog table.Table S3 contains the correlation coefficients for pairwise comparisons of parental and hybrid samples.Table S4 contains the enriched motifs found in the upstream regions of maternally deposited genes.Table S5 contains a list of enriched GO categories for mostly zygotic genes changing in <i>trans </i>regulation.Table S6 lists the number of genes in every cross that fall into each pattern of inheritance in the hybrid. File S1 is a script that produces a file with the variant sites assigned to chromosomal locations.File S2 is a script that will get the count of reads at each variant site in a given sample, using the file generated from the script in File S1.File S3 is a script that organizes the count information from the output of the script in File S2.File S4 is a script that will merge and normalize the data after organizing the read counts for each species using File S3.