Additional file 1: Table S1. of Parallel evolution of highly conserved plastid genome architecture in red seaweeds and seed plants

Gene compositions of red algal plastid genomes. Table S2. Representative homologous gene sets of red algal plastid genes. Table S3. Intron prediction of plastid intronic proteins in five basal red algal taxa. Tables S4, S7, and S15. List of concatenated proteins used in the ML tree searches. Tables S5 and S6. Types of angiosperm and gymnosperm plastid genomes. Tables S8 and S9. Taxon sampling of cyanobacterial genomes and their gene groups. Table S10. Predicted primary plastid orthologous gene families compared with cyanobacterial 297 OGF. Table S11. Predicted nuclear-encoded OGFs in the primary plastid groups. Table S12. EGT trees information. Table S13. Composition of OGFs in the primary plastid groups. Table S14. Sample and strain information. Table S16. Cyanobacterial proteins from four strains used in the primary plastid ML tree. Table S17. Taxon sampling of primary plastid groups in orthologous family analysis. Table S18. Number of species and genes in OGF analysis. Table S19. Taxon samples and their genes in the primary endosymbiosis groups. (XLSX 2166 kb)

本数据集涵盖红藻质体基因组的基因组成相关内容，具体附表信息如下：
表S2：红藻质体基因的代表性同源基因集
表S3：5个基底红藻类群的质体内含蛋白的内含子预测结果
表S4、S7及S15：最大似然树（Maximum Likelihood Tree，ML树）搜索所用的串联蛋白列表
表S5、S6：被子植物与裸子植物的质体基因组类型
表S8、S9：蓝藻基因组及其基因家族的类群采样信息
表S10：与蓝藻297个直系同源基因家族（Orthologous Gene Family，OGF）比对得到的预测初级质体直系同源基因家族
表S11：初级质体类群中预测的核编码直系同源基因家族
表S12：内共生基因转移（Endosymbiotic Gene Transfer，EGT）树相关信息
表S13：初级质体类群中的直系同源基因家族组成
表S14：样本与菌株信息
表S16：用于初级质体最大似然树分析的4个蓝藻菌株的蛋白序列
表S17：直系同源家族分析中初级质体类群的类群采样信息
表S18：直系同源基因家族分析中的物种与基因数量
表S19：初级内共生类群的类群样本及其对应基因
本数据集文件格式为XLSX，大小为2166 KB。