The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants Li, Linzhou; Wang, Sibo; Wang, Hongli; Sahu, Sunil Kumar; Marin, Birger; Li, Haoyuan; Xu, Yan; Liang, Hongping; Li, Zhen; Cheng, Shifeng; Reder, Tanja; Çebi, Zehra; Wittek, Sebastian; Petersen, Morten; Melkonian, Barbara; Du, Hongli; Yang, Huanming; Wang, Jian; Wong, Gane Ka-Shu; Xu, Xun; Liu, Xin; Van de Peer, Yves; Melkonian, Michael; Liu, Huan Published in: Nature Ecology and Evolution DOI: 10.1038/s41559-020-1221-7 Publication date: 2020 Document version Publisher's PDF, also known as Version of record Document license: CC BY Citation for published version (APA): Li, L., Wang, S., Wang, H., Sahu, S. K., Marin, B., Li, H., ... Liu, H. (2020). The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants. Nature Ecology and Evolution, 4(9), 1220- 1231. https://doi.org/10.1038/s41559-020-1221-7 Download date: 10. Sep. 2020 ARTICLES https://doi.org/10.1038/s41559-020-1221-7 The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants Linzhou Li1,2,13, Sibo Wang1,3,13, Hongli Wang1,4, Sunil Kumar Sahu 1, Birger Marin 5, Haoyuan Li1, Yan Xu1,4, Hongping Liang1,4, Zhen Li 6, Shifeng Cheng1, Tanja Reder5, Zehra Çebi5, Sebastian Wittek5, Morten Petersen3, Barbara Melkonian5,7, Hongli Du8, Huanming Yang1, Jian Wang1, Gane Ka-Shu Wong 1,9, Xun Xu 1,10, Xin Liu 1, Yves Van de Peer 6,11,12 ✉ , Michael Melkonian5,7 ✉ and Huan Liu 1,3 ✉ Genome analysis of the pico-eukaryotic marine green alga Prasinoderma coloniale CCMP 1413 unveils the existence of a novel phylum within green plants (Viridiplantae), the Prasinodermophyta, which diverged before the split of Chlorophyta and Streptophyta. Structural features of the genome and gene family comparisons revealed an intermediate position of the P. colo- niale genome (25.3 Mb) between the extremely compact, small genomes of picoplanktonic Mamiellophyceae (Chlorophyta) and the larger, more complex genomes of early-diverging streptophyte algae. Reconstruction of the minimal core genome of Viridiplantae allowed identification of an ancestral toolkit of transcription factors and flagellar proteins. Adaptations of P. coloniale to its deep-water, oligotrophic environment involved expansion of light-harvesting proteins, reduction of early light-induced proteins, evolution of a distinct type of C4 photosynthesis and carbon-concentrating mechanism, synthesis of the metal-complexing metabolite picolinic acid, and vitamin B1, B7 and B12 auxotrophy. The P. coloniale genome provides first insights into the dawn of green plant evolution. ne of the most important biological events in the history later studies20. M. viride is now recognized as an early-diverging of life was the successful colonization of the terrestrial member of the Streptophyta21,22. While the majority of the Olandscape by green plants (Viridiplantae) that paved the early-diverging lineages in the Chlorophyta consisted of (mostly way for terrestrial animal evolution, altering geomorphology marine) scaly flagellates, some lineages were represented by very and changes in the Earth’s climate1–3. The Viridiplantae comprise small, non-flagellate unicells often surrounded by cell walls23,24. perhaps 500,000 species, ranging from the smallest to the largest One of these lineages, provisionally termed ‘Prasinococcales’23 eukaryotes4,5. Divergence time estimates from molecular data sug- (clade VI), could not be reliably positioned in phylogenetic gest that Viridiplantae may be close to 1 billion years old6,7. All trees24,25. A major step forward was made when it was discovered extant green plants are classified in either of two divisions/phyla, that an enigmatic, non-cultured group of deep-water, oceanic Chlorophyta and Streptophyta, which differ structurally, bio- macroscopic algae of palmelloid organization comprising the chemically and molecularly8–12. The Streptophyta contain the land genera Verdigellas and Palmophyllum formed a deeply diverg- plants (embryophytes) and a paraphyletic assemblage of algae ing lineage of Viridiplantae that included the Prasinococcales26. known as the streptophyte algae, whereas all other green algae Later, the class Palmophyllophyceae was established for these comprise the Chlorophyta. The reconstruction of phylogenetic organisms as the first divergence in Chlorophyta, that is sister to relationships across green plants using transcriptomic or genomic all other Chlorophyta27. Phylogenies based on nuclear-encoded data provided evidence that unicellular, often scaly, flagellate ribosomal RNA genes (4,579 positions), however, placed organisms were positioned near the base of the radiation in both Palmophyllophyceae as the earliest divergence in Viridiplantae, phyla13–16, corroborating earlier proposals based on ultrastruc- but monophyly of Chlorophyta + Streptophyta to the exclusion of tural analyses that the common ancestor of all green plants may Palmophyllophyceae, received no support in these analyses27. have been a scaly flagellate17,18. The search for an extant relative To date, genomic resources for the Palmophyllophyceae have of such a flagellate, however, has been in vain, although an initial been limited to organelle genomes. Here we present the first report suggested that Mesostigma viride diverged before the split nuclear genome sequence of a unicellular member of this lineage, of Chlorophyta and Streptophyta19, a result not corroborated by Prasinoderma coloniale (Fig. 1a). Based on phylogenomic analyses, 1State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China. 2Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark. 3Department of Biology, University of Copenhagen, Copenhagen, Denmark. 4BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China. 5Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany. 6Department of Plant Biotechnology and Bioinformatics (Ghent University) and Center for Plant Systems Biology, Ghent, Belgium. 7Central Collection of Algal Cultures, Faculty of Biology, University of Duisburg-Essen, Essen, Germany. 8School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China. 9Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta, Canada. 10Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China. 11College of Horticulture, Nanjing Agricultural University, Nanjing, China. 12Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa. 13These authors contributed equally: Linzhou Li, Sibo Wang. ✉e-mail: [email protected]; [email protected]; [email protected] 1220 NATURE EcOLOgy & EVOLUTION | VOL 4 | SEPTEMBER 2020 | 1220–1231 | www.nature.com/natecolevol NATURE ECOLOGY & EVOLUTION ARTICLES a c Arabidopsis thaliana 0.05 91/57/1 Pinus taeda 69/-/- Angiopteris lygodiifolia/fokiensis Embryophyta Equisetum arvense/diffusum Huperzia selago/lucidula Tracheophytes Physcomitrella patens Polytrichum juniperinum Diphyscium fulvifolium Mosses 95/58/1 Takakia lepidozioides Marchantia polymorpha Treubia lacunosa Liverworts Nardia compressa Nothoceros vincentianus Phaeoceros sp. Hornworts Cosmarium ochthodes 97/100/1 Penium margaritaceum Netrium digitus Zygnematophyceae 57/–/– Mougeotia sp. 56/100/- 68/63/1 Mesotaenium caldariorum Cylindrocystis cushleckae Cylindrocystis brebissonii Mesotaenium endlicherianum 94/ Chaetosphaeridium globosum 76/1 Coleochaete scutata Coleochaetophyceae Nitella hyalina Chara braunii Charophyceae Klebsormidium nitens Entransia fimbriata Klebsormidiophyceae Spirotaenia condensata Chlorokybus atmophyticus Streptophyta Mesostigma viride Mesostigmatophyceae Ulva mutabilis 10 µm 95/89/1 Desmochloris halophila 100/93/1 Ignatius tetrasporus Ulvophyceae Chlorophyta Oltmannsiellopsis sp. Volvox carteri 81/81/1 94/86/1 Eudorina sp. Chlorophyceae 97/96/1 Yamagishiella unicocca Chlamydomonas reinhardtii Spermatozopsis exsultans –/70/– Hydrodictyonre ticulatum b Chromochloris zofingiensis Stigeoclonium helveticum 89/99/1 Tetraselmis cordiformis Arabidopsis thaliana 94/98/1 Tetraselmis striata Chlorodendrophyceae 100/1 Scherffelia dubia Stichococcus bacillaris 100/1 Chara braunii Koliella longiseta Trebouxiophyceae Streptophyta Coccomyxa subellipsoidea 100/1 Klebsormidium nitens Botryococcus braunii Auxenochlorella protothecoides Chlorella variabilis Chlorokybus atmophyticus 85/98/1 Chlorella vulgaris 100/1 Pedinomonas minor Mesostigma viride Marsupiomonas pelliculata Pedinophyceae 94/96/1 Chloropicon primus Chloropicophyceae/Pseudoscourfieldiales 82/99/1 Pycnococcus provasolii 0.1 100/1 Volvox carteri Nephroselmis pyriformis Nephroselmis olivacea Nephroselmidophyceae Gonium pectorale Micromonas bravo 56/83/0.98 100/1 Micromonas commoda Mamiellophyceae 100/1 Chlamydomonas reinhardtii Mamiella gilva Ostrecoccus tauri 96/98/1 100/1 100/1 95/91/1 Ostreococcus lucimarinus Chromochloris zofingiensis Bathycoccus prasinos Dolichomastix tenuilepis Ulva mutabilis 75/55/1 Crustomastix stigmatica Monomastix opisthostigma 100/1 Monomastix sp. Auxenochlorella protothecoides 96/98/1 Pyramimona s parkeae 100/1 Pyramimona s olivacea Pyramimonadophyceae Chlorella variabilis Chlorophyta Pyramimona s tetrarhynchus 100/1 Cymbomona s tetramitiformis Viridiplantae Coccomyxa subellipsoidea