Supplementary Materials: Phylogenomics provides new insights into gains and losses of selenoproteins among Archaeplastida Hongping Liang1,2,3#, Tong Wei2,3,4#, Yan Xu1,2,3#, Linzhou Li2,3,6, Sunil Kumar Sahu2,3,4, Hongli Wang1,2,3, Haoyuan Li1,2, Xian Fu2,3, Gengyun Zhang2,4, Michael Melkonian7, Xin Liu2,3,4, Sibo Wang2,4,5*,Huan Liu2,4,5* 1 BGI Education Center, University of Chinese Academy of Sciences, Beijing, China. 2 BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China. 3 China National Gene Bank, Institute of New Agricultural Resources, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China. 4 State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China. 5 Department of Biology, University of Copenhagen, Copenhagen, Denmark. 6 School of Biology and Biological Engineering, South China University of Technology, 510006, China. 7 Botanical Institute, Cologne Biocenter, University of Cologne, Cologne D-50674, Germany. #these authors contributed equally to this work * Correspondence: *[email protected] Supplementary Figure S1: Completeness of genome assemblies and Stop codon statistics. The genome quality was assessed by the BUSCO program. The number of single, multiple, missing and fragmented genes are shown in the middle histogram. The stop codon usage of genes is shown on the right histograms. The species that lost the Sec machinery are marked with an asterisk in the tree. Each group was colored in different background in the left column. Group Species Numbers Stop Codon Arabidopsis thaliana Oryza sativa japonica Embryophyte Selaginella moellendorffii BUSCO Gene Number: Marchantia polymorpha Physcomitrella patens Single Mesotaenium endlicherianum Multiple “Spirotaenia sp.” Coleochaete scutata Fragmented Streptophyte Chara braunii Klebsormidium nitens Missing Chlorokybus atmophyticus Mesostigma viride Volvox carteri Gonium pectorale Gene Stop Codon: Chlamydomonas reinhardtii TGA Chlamydomonas eustigma TAG Chlorophyte Chromochloris zofingiensis Monoraphidium neglectum TAA Ulva mutabilis Chlorella sorokiniana Chlorella variabilis Loss of Sec trait: Coccomyxa subellipsoidea Ostreococcus sp. Ostreococcus lucimarinus Ostreococcus tauri Bathycoccus prasinos Micromonas commoda Micromonas pusilla Porphyra umbilicalis Pyropia yezoensis Chondrus crispus Rhodoplantae Porphyridium purpureum Galdieria sulphuraria Cyanidioschyzon merolae Glaucoplantae Cyanophora paradoxa Aureococcus_anophagefferens Protist Thalassiosira pseudonana Emiliana huxleyi 3 53 103 153 203 253 303 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Cys-homologs Selenoprotein 2 2 2 Other homologs Selenoprotein families: GPx AhpC SelW SelM MSP FrnE SelT TR msra_b EhSEP2 selenou Ostsp3 SelH Ostsp2 di_b Sel15 ars_s MsrA SelK prx SelO rhor SelS Ostsp1 fdha SPS SelR gpx_b prx_like ugsc gst grx rsam Arabidopsis thaliana 8 1 2 2 3 1 14 2 1 1 1 1 1 4 1 1 9 2 1 3 16 6 Oryza sativa japonica 4 1 1 2 1 3 1 10 2 1 2 1 3 1 1 8 1 2 3 1 3 2 1 1 2 2 8 8 Selaginella moellendorffii 6 2 2 2 2 8 4 13 3 1 1 2 2 16 2 1 5 2 6 2 2 9 3 8 11 Physcomitrella patens 4 1 1 2 2 3 1 21 7 1 2 1 1 12 1 1 1 3 1 2 4 8 Marchantia polymorpha 2 1 1 2 1 2 1 7 1 1 1 6 1 1 2 1 2 4 4 Mesotaenium endlicherianum 1 1 1 4 1 1 2 1 3 1 1 1 1 1 9 1 5 5 1 1 5 3 6 2 2 4 3 1 1 1 “Spirotaenia sp.” 2 4 1 3 1 4 1 2 8 6 1 4 1 1 2 3 2 13 3 1 3 6 1 1 8 3 7 6 3 Coleochaete scutata 1 2 1 1 1 1 1 1 1 3 1 17 1 1 1 1 6 1 3 7 1 1 1 1 2 2 8 2 1 Chara braunii 1 1 1 1 1 2 3 2 19 1 1 1 1 1 5 1 2 1 2 2 1 4 2 8 4 3 1 Klebsormidium flaccidum 1 1 1 1 2 2 10 1 1 1 1 1 1 2 5 1 1 1 3 3 3 2 1 Chlorokybus atmophyticus 1 1 1 1 1 1 6 1 1 1 5 1 1 3 1 2 2 1 1 Mesostigma viride 1 1 1 1 1 1 6 1 1 1 1 1 2 8 1 1 1 1 1 1 1 10 2 5 3 10 1 3 1 7 2 1 2 4 8 2 1 Volvox carteri 1 1 1 1 1 1 1 1 1 3 5 1 1 1 1 1 2 1 1 1 1 1 1 3 2 1 1 1 3 1 2 2 1 1 2 1 Gonium pectorale 1 1 1 1 2 2 1 1 2 2 5 1 1 1 1 1 2 1 1 5 3 1 2 1 2 3 2 1 1 1 1 1 Chlamydomonas reinhardtii 1 2 1 1 1 1 1 1 1 1 3 1 1 1 1 1 1 1 1 1 4 1 1 1 1 3 1 4 1 3 3 2 3 Chlamydomonas eustigma 1 1 1 1 1 1 4 1 1 1 1 2 5 1 2 3 1 4 1 1 2 2 1 1 2 1 2 1 1 1 1 3 9 1 1 1 1 1 9 1 1 1 1 3 2 3 3 1 Each column corresponds to a selenoprotein Chromochloris zofingiensis Monoraphidium neglectum 2 1 1 2 1 1 1 3 1 1 1 1 1 1 1 2 1 3 1 1 1 4 1 1 2 1 2 1 1 Ulva mutabilis 1 1 1 1 1 5 1 1 1 1 1 1 4 2 3 1 1 1 1 1 2 1 3 Chlorella variabilis 2 2 1 1 3 1 1 3 1 5 3 1 2 2 6 2 1 1 1 1 5 1 1 1 1 1 1 1 1 1 1 Chlorella sorokiniana 2 1 1 1 1 1 3 1 1 1 3 1 1 1 1 3 1 1 1 1 2 1 Coccomyxa subellipsoidea 1 1 1 1 1 1 3 5 1 1 1 1 2 3 1 1 1 1 1 2 1 1 2 1 Ostreococcus sp. RCC809 4 1 1 2 1 1 1 1 1 1 1 1 4 1 15 2 1 1 1 1 1 1 1 1 1 2 3 1 1 1 4 1 1 1 3 3 1 1 Ostreococcus lucimarinus 5 1 1 2 1 1 2 1 1 1 3 1 1 16 2 1 1 1 1 1 1 1 1 1 1 4 2 4 1 1 1 5 1 1 1 1 3 1 1 2 1 1 Ostreococcus tauri 5 1 1 2 2 1 1 2 1 1 1 1 1 4 1 1 17 1 1 1 1 1 1 1 1 1 3 2 2 2 4 1 1 1 3 1 1 2 2 1 Bathycoccus prasinos 4 2 2 1 1 1 2 1 1 2 3 1 19 1 1 1 1 1 1 1 4 1 2 6 1 1 3 1 2 2 1 Micromonas commoda 5 2 1 1 2 1 2 1 1 1 2 4 2 19 2 1 1 1 1 1 1 1 1 1 3 1 3 3 1 1 4 2 8 1 1 Micromonas pusilla 6 2 1 1 1 2 1 2 1 1 1 2 2 2 2 23 1 1 1 1 1 2 1 1 1 1 1 1 6 4 1 1 6 1 1 1 3 1 2 2 7 1 1 Porphyra umbilicalis 2 1 1 1 1 1 3 16 2 2 1 1 91 5 1 2 4 1 2 4 1 1 8 Pyropia yezoensis 2 1 1 2 1 11 1 1 1 8 3 1 2 1 2 1 1 4 1 1 3 2 7 1 Chondrus crispus 1 1 1 1 1 1 1 3 9 12 7 1 1 4 1 1 1 2 1 1 7 1 Porphyridium purpureum 2 1 1 1 1 11 1 1 1 1 1 4 1 5 1 1 2 8 1 1 2 9 1 Galdieria sulphuraria 1 1 1 1 6 1 2 4 2 1 1 1 1 1 1 2 3 1 Cyanidioschyzon merolae 1 1 1 8 1 1 1 6 1 2 1 1 1 1 1 3 1 1 Cyanophora paradoxa 1 1 1 1 5 1 3 1 2 2 1 1 1 1 13 4 2 1 3 2 1 1 1 2 2 1 1 3 1 1 Aureococcus anophagefferens 2 1 1 4 4 1 2 3 2 5 6 1 1 3 4 8 2 3 29 2 2 1 1 1 1 2 2 1 2 1 1 2 13 2 1 2 2 1 10 1 4 9 1 2 1 4 1 3 1 1 6 1 1 Thalassiosira pseudonana 1 1 1 1 1 2 2 1 1 1 1 4 2 20 1 2 1 1 1 1 3 1 1 4 1 4 1 1 2 1 3 1 1 6 3 1 9 2 7 2 4 7 1 7 2 2 3 1 1 2 14 2 8 36 3 1 3 7 4 5 2 2 1 3 1 5 4 3 4 1 3 5 1 1 18 3 1 2 2 1 2 8 2 1 Emiliana huxleyi the number of selenoproteins. -containing gene were selected for the analysis.