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)

表S1 转录组数据信息。
表S2 基因组序列来源。
表S3 拟南芥（Arabidopsis thaliana）与幽灵兰（Epipogium aphyllum）间的1:1直系同源基因（orthologs）列表。
表S4 拟南芥（Arabidopsis thaliana）与玫瑰幽灵兰（Epipogium roseum）间的1:1直系同源基因（orthologs）列表。
表S5 拟南芥（Arabidopsis thaliana）与松下兰（Hypopitys monotropa）间的1:1直系同源基因（orthologs）列表。
表S6 幽灵兰属（Epipogium）、松下兰（Hypopitys monotropa）与其光合近缘类群间基因占比存在显著差异的基因本体术语（GO terms）完整列表。
表S7 转录组组装结果详细统计。
表S8 组装完整性分析结果。
表S9 基于TargetP分析，各物种中产物靶向至不同细胞器的基因占总基因数的比例。仅纳入具备完整5'端且至少被注释有一个基因本体术语的基因。
表S10 研究物种中目标基因的存在情况及其所受选择压力。
表S11 串联基因序列的GC含量（GC-content）。
表S12 针对幽灵兰属与松下兰质体基因组（plastomes）中丢失的核糖体蛋白编码基因，潜在替代基因的搜索结果。（XLSX格式，文件大小5745 KB）