RESEARCH ARTICLE Figures and figure supplements Dynamics of genomic innovation in the unicellular ancestry of animals Xavier Grau-Bove´ et al Grau-Bove´ et al. eLife 2017;6:e26036. DOI: 10.7554/eLife.26036 1 of 28 Research article Genes and Chromosomes Genomics and Evolutionary Biology 500bp A. Phylogeny and genome statistics B. Phenotypic traits Metazoa+ Metazoa Choanoflagellata Source Abreviation Genome size# scaffolds(Mb) L75 N50 (kb) # genes % BUSCOorthologs % GC Monosiga brevicollis † Mbre 41.6 218 27 1,073.6 9,172 78.6% 54.9 Choanoflagellata Single-celled flagellates, Filozoa Choano- colonial forms ( Salpingoeca ) flagellata Salpingoeca rosetta † Sros 55.4 154 25 1,519.5 11,624 80.6% 56.0 Capsaspora owczarzaki † Cowc 27.9 84 11 1,617.7 8,741 86.6% 53.8 Filasterea Single-celled filopodiated amoebas, Filasterea Ministeria vibrans ‡ Mvib - - - - - - - aggregative stage ( Capsaspora ) Creolimax fragrantissima Cfra 42.9 83 17 1,585.0 8,694 86.7% 40.5 Ichthyosporea Ichthyophonida Sphaeroforma arctica * Sarc 120.9 15,618 1,442 116.1 18,319 77.15% 42.0 Coenocytic clonal growth, schizogony and propagule Holozoa * dispersal (by amoebas, Ichthyo- Ichthyophonus hoferi Ihof 88.1 1,633 515 106.7 6,351 63.2% 33.4 flagellated or not) phonida Amoebidium parasiticum *‡ Apar - - - - - - - Ichthyo- Abeoforma whisleri Awhi 101.9 51,561 25,133 2.4 17,283 11.9% 30.24 Teretosporea sporea Pirum gemmata ** Pgem 84.4 50,415 25,440 1.9 21,835 17.0% 29.11 Opisthokonta ** Dermocystida Chromosphaera perkinsii Cper 34.6 3,994 187 120.2 12,463 85.5% 42.13 Coenocytic clonal growth, Dermo- ** flagellated amoeboid dispersal stage cystida Sphaerothecum destruens ‡ Sdes - - - - - - - Corallochytrium limacisporum Clim 24.1 287 86 180.5 7,535 83.4% 51.2 Corallochytrea Obazoa Colonies with palintomic division, ** amoeboid dispersal stage (cryptic ? Fungi Unikonta/ flagellum hypothesized) Amorphea Holomycota Discicristoidea Apusomonadida LECA Amoebozoa Diaphoratickes+Excavata / Bikonta Figure 1. Evolutionary framework and genome statistics of the study. (A) Schematic phylogenetic tree of eukaryotes, with a focus on the Holozoa. The adjacent table summarizes genome assembly/annotation statistics. Data sources: red asterisks denote Teretosporea genomes reported here; double asterisks denote organisms sequenced for this study; † previously sequenced genomes (King et al., 2008; Fairclough et al., 2013; Suga et al., 2013); ‡ organisms for which transcriptomic data exists but no genome is available (Torruella et al., 2015). (B) Overview of the phenotypic traits of each group of unicellular Holozoa, focusing on their multicellular-like characteristics. For further details, see (Torruella et al., 2015; Mendoza et al., 2002; Marshall et al., 2008; Glockling et al., 2013). Figure 1—source data 1 and 2. DOI: 10.7554/eLife.26036.003 The following source data is available for figure 1: Source data 1. Table of genome structure statistics, from the data-set of eukaryotic genomes used in the study. DOI: 10.7554/eLife.26036.004 Source data 2. List of genome and transcriptome assemblies and annotations, including abbreviations, taxonomic classification and data sources. DOI: 10.7554/eLife.26036.005 Grau-Bove´ et al. eLife 2017;6:e26036. DOI: 10.7554/eLife.26036 2 of 28 Research article Genes and Chromosomes Genomics and Evolutionary Biology Pair-wise comparisons of 1-to-1 orthologs' lenghts Salpingoeca Monosiga Capsaspora Sphaeroforma Creolimax Abeoforma Pirum Ichthyophonus Chromosphaera Corallochytrium Salpingoeca 1000 100 Monosiga 1000 100 Capsaspora 1000 100 Sphaeroforma 1000 100 Creolimax 1000 100 length Abeoforma 1000 100 1000 Pirum 100 Ichthyophonus 1000 100 Chromosphaera 1000 100 Corallochytrium 1000 100 100 1000 100 1000 100 1000 100 1000 100 1000 100 1000 100 1000 100 1000 100 1000 100 1000 length Choanoflagellata Density Filasterea Ichthyosporea 10 20 30 40 50 Corallochytrium Figure 1—figure supplement 1. Comparisons of gene length of one-to-one orthologs from pair-wise comparisons of all 10 unicellular Holozoa. Dots around the diagonal lines indicate that orthologs from both organisms have identical lengths. Note that Abeoforma and Pirum have abundant incomplete orthologous sequences. Figure 1—figure supplement 1 continued on next page Grau-Bove´ et al. eLife 2017;6:e26036. DOI: 10.7554/eLife.26036 3 of 28 Research article Genes and Chromosomes Genomics and Evolutionary Biology Figure 1—figure supplement 1 continued DOI: 10.7554/eLife.26036.006 Grau-Bove´ et al. eLife 2017;6:e26036. DOI: 10.7554/eLife.26036 4 of 28 Research article Genes and Chromosomes Genomics and Evolutionary Biology Supports: Xenopus tropicalis Metazoa 99/1 ML LG+R7+C60 / Branchiostoma floridae BI LG+ 7+i Saccoglossus kowalevskii Distance: Lottia gigantea 0.2 Capitella teleta Daphnia pulex Acropora digitifera Nematostella vectensis 100/0.9 Hydra magnipapillata 95/1 Trichoplax adhaerens Oscarella carmela Amphimedon queenslandica Mnemiopsis leidyi Didymoeca costata Choanoflagellata Helgoeca nana Salpingoeca rosetta Monosiga brevicollis Capsaspora owczarzaki Filasterea Ministeria vibrans Ichthyophonus hoferi Washington Ichthyo- Ichthyosporea Holozoa Ichthyophonus hoferi Alaska phonida Amoebidium parasiticum Creolimax fragrantissima Sphaeroforma arctica Abeoforma whisleri Teretosporea 98/1 Pirum gemmata Chromosphaera perkinsii Dermo- 93/0.85 Sphaerothecum destruens cystida Corallochytrium limacisporum Hawaii Corallochytrea Corallochytrium limacisporum India Mucor circinelloides Fungi Rhizopus oryzae 98/NA Opisthokonta Mortierella verticillata Rhizophagus irregularis Cryptococcus neoformans Ustilago maydis Schizosaccharomyces pombe 64/1 Coemansia reversa Conidiobolus coronatus Allomyces macrogynus 84/0.95 Catenaria anguillulae Piromyces sp. E2 94/1 Gonapodya prolifera Spizellomyces punctatus Holomycota Batrachochytrium dendrobatidis Rozella allomycis Parvularia atlantis (Nuclearia sp. ) Nucleariids Fonticula alba Thecamonas trahens Apusomonadida Manchomonas bermudensis Breviata anathema Breviatea Subulatomonas tetraspora Pygsuia biforma Dictyostelium discoideum Amoebozoa Polysphondylium pallidum Physarum polycephalum Acanthamoeba castellanii Figure 2. Phylogenomic tree of Unikonta/Amorphea. Phylogenomic analysis of the BVD57 taxa matrix. Tree topology is the consensus of two Markov chain Monte Carlo chains run for 1231 generations, saving every 20 trees and after a burn-in of 32%. Statistical supports are indicated at each node: (i) non-parametric maximum likelihood ultrafast-bootstrap (UFBS) values obtained from 1000 replicates using IQ-TREE and the LG + R7+C60 model; (ii) Bayesian posterior probabilities (BPP) under the LG+G7 + CAT model as implemented in Phylobayes. Nodes with maximum support values (BPP = 1 and UFBS = 100) are indicated by a black bullet. See Figure 2—figure supplement 1 for raw trees with complete statistical supports. Figure 2—source data 1. DOI: 10.7554/eLife.26036.007 The following source data is available for figure 2: Source data 1. BVD57 phylogenomic dataset (Torruella et al., 2015) including 87 unaligned protein domains (with PFAM accession number) per species. DOI: 10.7554/eLife.26036.008 Grau-Bove´ et al. eLife 2017;6:e26036. DOI: 10.7554/eLife.26036 5 of 28 Research article Genes and Chromosomes Genomics and Evolutionary Biology A. Phylogenomic analysis: BVD57, ML (LG+R7+C60) B. Phylogenomic analysis: BVD57, ML (LG+R7+PMSF) 100/100 Xenopus tropicalis 99 Xenopus tropicalis 0 . 2 0 . 0 9 99.1/99 Branchiostoma floridae 96 Branchiostoma floridae Saccoglossus kowalevskii Saccoglossus kowalevskii 100/100 100 100/100 Lottia gigantea 100 Lottia gigantea 100/100 Capitella teleta 100 Capitella teleta 100/100 Daphnia pulex 59 Daphnia pulex 100/100 Acropora digitifera 100 Acropora digitifera 99.9/100 100/100 Nematostella vectensis 98 Nematostella vectensis 93.5/95 Hydra magnipapillata 99 43 Hydra magnipapillata Trichoplax adhaerens Trichoplax adhaerens 100/100 100 100/100 Oscarella carmela 99 Oscarella carmela Amphimedon queenslandica Amphimedon queenslandica 100/100 Mnemiopsis leidyi 100 Mnemiopsis leidyi 100/100 Didymoeca costata 100 Didymoeca costata 100/100 Helgoeca nana 100 Helgoeca nana 100/100 68 100/100 Salpingoeca rosetta 100 Salpingoeca rosetta Monosiga brevicollis Monosiga brevicollis 100/100 Capsaspora owczarzaki 100 Capsaspora owczarzaki Ministeria vibrans Ministeria vibrans 100/100 Ichthyophonus hoferi Washington 100 Ichthyophonus hoferi Washington 100/100 Ichthyophonus hoferi Alaska 100 Ichthyophonus hoferi Alaska 100/100 100 100/100 Amoebidium parasiticum 100 Amoebidium parasiticum 100/100 Creolimax fragrantissima 100 Creolimax fragrantissima 100/100 Sphaeroforma arctica 100 Sphaeroforma arctica 100/100 Abeoforma whisleri 100 Abeoforma whisleri 98.1/98 Pirum gemmata 59 Pirum gemmata 100/100 Chromoshpaera perkinsii 100 Chromoshpaera perkinsii 84.9/93 Sphaerothecum destruens 58 Sphaerothecum destruens 100/100 Corallochytrium limacisporum Hawaii 100 Corallochytrium limacisporum Hawaii Corallochytrium limacisporum India Corallochytrium limacisporum India 100/100 Mucor circinelloides 100 Mucor circinelloides 99.2/100 Rhizopus oryzae 98 Rhizopus oryzae 99.2/98 Mortierella verticillata 98 Mortierella verticillata 100/100 Rhizophagus irregularis 100 Rhizophagus irregularis 100/100 97 100/100 Cryptococcus neoformans 100 Cryptococcus neoformans 100/100 Ustilago maydis 100 Ustilago maydis 100 100/100 Schizosaccharomyces pombe Schizosaccharomyces pombe 100/100 Coemansia reversa 100 Coemansia reversa Conidiobolus coronatus 71 Conidiobolus coronatus 17.5/64 100/100 Allomyces