Additional file 1: Table S1. of Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants

Average GC%, size, protein-encoding gene count and density per M. pusilla CCMP1545 chromosome. Finished chromosomes are indicated. Table S2. Ortholog similarity in prasinophytes. The gene fraction is the ortholog count divided by the number of proteins in the smaller set. Table S3. OrthoGroups numbers across the Class II prasinophytes (see also Fig. 4) and number of OrthoGroups with >1 protein from the respective taxon in this analysis. Note that the higher redundancy of transcriptome-based proteomes of D. tenuilepis and CCMP2099 is likely due to artefacts of the method used. Table S4. Predicted proteins present in Micromonas and Dolichomastix, but not in Bathycoccus or Ostreococcus. Table S5. Genes encoding proteins in the peptidoglycan biosynthesis pathway identified here in prasinophytes, streptophytes and glaucophytes. Gene IDs from the new annotation generated here as shown in the JGI system (CCMP1545, RCC299, Ostreococcus RCC809), CAMPEP (CCMP2099, D. tenuilepis, N. pyriformis, P. salinarum, G. wittrockiana, see www.iplantcollaborative.org ), Genbank (O. tauri, O. lucimarinus, and B. prasinos) and Phytozome version 11 (all others). tblastn: Gene found using tblastn against the genome (streptophytes) or transcriptome (CCMP2099, D. tenuilepis), no corresponding gene model exists. Table S6. EST support for Viridiplantae peptidoglycan genes (tblastn with predicted peptide, E-value cutoff 10â 15). A maximum of five ESTs are listed for each. Table S7. Signal peptides on Viridiplantae peptidoglycan pathway enzymes found using TargetP. C: Chloroplast; M: Mitochondrion; S: secreted; â : no signal; n/a: protein was located by tblastn in the genome and no corresponding gene model exists. Table S8. Greencut2 family proteins in prasinophytes. (XLSX 167 kb)

本数据集包含微小单胞藻（Micromonas pusilla）CCMP1545每条染色体的平均GC含量、染色体长度、编码蛋白基因数及基因密度，已完成组装的染色体已标注。表S2：普林藻类（prasinophytes）的直系同源相似性，其中基因占比为直系同源基因数与较小蛋白组中蛋白数的比值。表S3：II类普林藻类的直系同源组（OrthoGroups）数量（详见图4），以及本分析中各分类群对应直系同源组内包含1条以上蛋白的直系同源组数量。注：纤细双鞭藻（D. tenuilepis）与CCMP2099的转录组蛋白组冗余度较高，可能源于所用分析方法引入的实验伪影。表S4：仅在微单胞藻属（Micromonas）和长鞭藻属（Dolichomastix）中存在，而不在深绿藻属（Bathycoccus）或原沟藻属（Ostreococcus）中存在的预测蛋白。表S5：本研究在普林藻类、链型植物（Streptophyta）及灰藻门（Glaucophyta）中鉴定到的肽聚糖生物合成通路相关蛋白编码基因。基因ID来自本研究新生成的注释结果，对应数据库如下：联合基因组研究所（Joint Genome Institute, JGI）系统（CCMP1545、RCC299、原沟藻属RCC809）、CAMPEP数据库（CCMP2099、纤细双鞭藻、N. pyriformis、P. salinarum、G. wittrockiana，详见www.iplantcollaborative.org）、GenBank基因数据库（O. tauri、O. lucimarinus及B. prasinos）以及Phytozome第11版（其余所有物种）。tblastn注释说明：通过tblastn比对基因组（链型植物）或转录组（CCMP2099、纤细双鞭藻）得到的基因，无对应基因模型。表S6：绿色植物（Viridiplantae）肽聚糖基因的表达序列标签（Expressed Sequence Tag, EST）支持数据（使用预测肽段进行tblastn比对，E值阈值为10^-15），每个基因最多列出5条EST。表S7：通过TargetP预测得到的绿色植物肽聚糖通路酶的信号肽信息：C：叶绿体定位；M：线粒体定位；S：分泌型；–：无信号肽；n/a：通过tblastn在基因组中定位到但无对应基因模型的蛋白。表S8：普林藻类中的Greencut2家族蛋白。（XLSX 167 kb）