Additional file 1: of RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of fully mycoheterotrophic plants

Table S1. Information on transcriptome data. Table S2. Sources of genome sequences. Table S3. List of 1–1 orthologs between Arabidopsis thaliana and Epipogium aphyllum. Table S4. List of 1–1 orthologs between Arabidopsis thaliana and Epipogium roseum. Table S5. List of 1–1 orthologs between Arabidopsis thaliana and Hypopitys monotropa. Table S6. Complete list of GO terms for which the fractions of genes differed significantly among Epipogium, Hypopitys monotropa and their photosynthetic relatives. Table S7. Detailed statistics of the transcriptome assemblies. Table S8. Analysis of the completeness of the assemblies. Table S9. Proportions of genes whose products are targeted to various organelles relative to the total numbers of genes in the species according to TargetP analysis. Only genes with complete 5′ ends and at least one assigned GO term are considered. Table S10. Presence of genes of interest in the studied species and selective pressures acting on them. Table S11. GC-content of concatenated genes’ sequences. Table S12. Results of a search for possible substitutes for ribosomal proteins whose genes have been lost from the plastomes of Epipogium and Hypopitys monotropa. (XLSX 5745 kb