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)补充表S1：转录组数据信息。补充表S2：基因组序列来源。补充表S3：拟南芥（Arabidopsis thaliana）与无叶假水晶兰（Epipogium aphyllum）之间的1:1直系同源基因列表。补充表S4：拟南芥与玫瑰假水晶兰（Epipogium roseum）之间的1:1直系同源基因列表。补充表S5：拟南芥与松下兰（Hypopitys monotropa）之间的1:1直系同源基因列表。补充表S6：假水晶兰属、松下兰与其光合近缘类群间基因占比存在显著差异的GO（Gene Ontology）术语完整列表。补充表S7：转录组组装的详细统计数据。补充表S8：组装完整性分析结果。补充表S9：基于TargetP分析，各物种中产物靶向至不同细胞器的基因占物种总基因数的比例。本次分析仅纳入具有完整5'端且至少分配有一个GO术语的基因。补充表S10：研究物种中目标基因的存在情况及其所受选择压力。补充表S11：串联基因序列的GC含量。补充表S12：假水晶兰属与松下兰质体基因组（plastome）中丢失的核糖体蛋白基因的潜在替代基因搜索结果。（XLSX格式，文件大小5745 KB）