Additional file 2 of Time-series transcriptomic screening of factors contributing to the cross-tolerance to UV radiation and anhydrobiosis in tardigrades

Additional file 2: Table S1. Statistics of RNA-Seq data obtained in this study. Statistics of each RNA-Seq data sequenced in this study. Mapping ratio for BWA mapping are shown. Table S2. Highly expressed or regulated genes in Short time-course. Genes with TPM values > 1,000 and fold change > 4 are highlighted in purple and orange, respectively. Table S3. Highly expressed or regulated genes in Long time-course. Genes with TPM values > 1,000 and fold change > 4 are highlighted in purple and orange, respectively. Table S4. Annotation of conserved genes. Details of the genes with Swiss-Prot homologs. Table S5. Annotation of novel genes. Details of the genes without Swiss-Prot homologs. Conservation profiles within Tardigrada based on OrthoFinder results, domains identified by InterProScan and the amino acid sequences are indicated. Table S6. OG0000231 and OG0000230 orthologs within Tardigrada identified by BLASTP. Coding sequences of OG0000230 and OG0000231 proteins were submitted to BLASTP search against predicted proteome sequences of indicated species in our in-house genome database and additional transcriptome assemblies. Table S7. OG0000231 copy numbers within Tardigrada identified by Orthofinder. Number of genes classified as OG0000231 orthologs by Orthofinder. Table S8. OG0000230 copy numbers within Tardigrada identified by Orthofinder. Number of genes classified as OG0000230 orthologs by Orthofinder. Table S9. Expression of OG0000230 orthologs. TPM values of OG0000230 orthologs in R. varieornatus UVC response and anhydrobiosis. Table S10. Expression of OG0000231 orthologs. TPM values of OG0000231 orthologs in R. varieornatusUVC response and anhydrobiosis. Table S11. Refinement of OG0000231 gene regions. Mispredicted OG0000231 orthologs in R. varieornatus genome. Table S12. HGT statistics of OG0000230 orthologs from previous studies. HGT statistics calculated in our previous study [11] for OG0000230 orthologs. Table S13. OG0000230 orthologs identified from NCBI nr database. List of orthologs identified by Diamond BLASTP search (E-value < 1E-5) against NCBI nr database. Tardigrade, non-tardigrade eukaryotic, and bacterial hits were each colored in gray, yellow, and green. H. exemplaris orthologs colored in red had gene annotations, but validation by RNA-Seq data mapping indicated that these genes may be mis-predicted. Table S14. OG0000230 orthologs identified from RefSeq database. List of orthologs identified by Diamond BLASTP search (E-value < 1E-5) against NCBI Bacteria RefSeq complete genome sequences. Genes before and after OG000023 orthologs are shown. Table S15. Gene synteny of OG0000231 and OG0000230 orthologs in R. varieornatus. Annotation of five genes prior and after OG0000231 orthologs in R. varieornatus. OG0000231 and OG0000230 orthologs are highlighted in red. Table S16. Data collection and refinement statistics for g12777. Crystal parameters and refinement statistics for Mn2+- and Zn2+-bound g12777 protein catalytic domain are summarized. One crystal for each structure was used for diffraction data collection. Table S17. Metal ion affinity of recombinant proteins. Affinity values for metal ions with g12777 proteins.

附加文件2：表S1。本研究获得的RNA测序（RNA-Seq）数据统计信息。本研究中所有测序的RNA测序数据的统计详情，展示了BWA比对的比对率。
表S2。短期时间进程中高表达或差异调控基因。其中，每百万转录本数（TPM）大于1000的基因以紫色标注，倍数变化大于4的基因以橙色标注。
表S3。长期时间进程中高表达或差异调控基因。其中，TPM大于1000的基因以紫色标注，倍数变化大于4的基因以橙色标注。
表S4。保守基因注释信息。包含具有Swiss-Prot同源序列的基因的详细信息。
表S5。新基因注释信息。包含无Swiss-Prot同源序列的基因的详细信息，同时标注了基于OrthoFinder分析结果得到的缓步动物门（Tardigrada）内保守特征、通过InterProScan鉴定的结构域，以及氨基酸序列。
表S6。通过BLASTP鉴定的缓步动物门（Tardigrada）内OG0000231与OG0000230同源基因。将OG0000230与OG0000231蛋白的编码序列提交至BLASTP检索，比对本实验室内部基因组数据库及额外转录组组装结果中指定物种的预测蛋白质组序列。
表S7。通过OrthoFinder鉴定的缓步动物门（Tardigrada）内OG0000231基因拷贝数。统计经OrthoFinder归类为OG0000231同源基因的基因数量。
表S8。通过OrthoFinder鉴定的缓步动物门（Tardigrada）内OG0000230基因拷贝数。统计经OrthoFinder归类为OG0000230同源基因的基因数量。
表S9。OG0000230同源基因的表达谱。展示了R. varieornatus在短波紫外线（UVC）应答与脱水隐生（anhydrobiosis）过程中，OG0000230同源基因的TPM值。
表S10。OG0000231同源基因的表达谱。展示了R. varieornatus在短波紫外线（UVC）应答与脱水隐生（anhydrobiosis）过程中，OG0000231同源基因的TPM值。
表S11。OG0000231基因区域的校正信息。包含R. varieornatus基因组中被错误预测的OG0000231同源基因相关内容。
表S12。既往研究中OG0000230同源基因的水平基因转移（HGT）统计。本团队前期研究[11]针对OG0000230同源基因计算的水平基因转移统计信息。
表S13。从NCBI非冗余（NCBI nr）数据库中鉴定的OG0000230同源基因。展示了通过Diamond BLASTP检索（E值<1E-5）NCBI nr数据库得到的同源基因列表。其中，缓步动物、非缓步动物真核生物及细菌的比对结果分别以灰色、黄色和绿色标注。以红色标注的海氏缓步虫（H. exemplaris）同源基因虽已完成基因注释，但经RNA测序数据比对验证后发现，这些基因可能存在预测错误。
表S14。从RefSeq参考序列数据库中鉴定的OG0000230同源基因。展示了通过Diamond BLASTP检索（E值<1E-5）NCBI细菌RefSeq完整基因组序列得到的同源基因列表，并标注了OG0000230同源基因上下游的基因信息。
表S15。R. varieornatus中OG0000231与OG0000230同源基因的基因共线性信息。标注了R. varieornatus基因组中OG0000231同源基因上下游各5个基因的注释信息，其中OG0000231与OG0000230同源基因以红色高亮显示。
表S16。g12777蛋白的数据收集与校正统计。总结了结合Mn²+与Zn²+的g12777蛋白催化结构域的晶体参数及校正统计信息，每个结构均采用单颗晶体完成衍射数据收集。
表S17。重组蛋白的金属离子结合亲和力。展示了g12777蛋白与各类金属离子的亲和力数值。