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.