The Capsaspora genome reveals a complex unicellular prehistory of animals

Abstract

To reconstruct the evolutionary origin of multicellular animals from their unicellular ancestors, the genome sequences of diverse unicellular relatives are essential. However, only the genome of the choanoflagellate Monosiga brevicollis has been reported to date. Here we completely sequence the genome of the filasterean Capsaspora owczarzaki, the closest known unicellular relative of metazoans besides choanoflagellates. Analyses of this genome alter our understanding of the molecular complexity of metazoans' unicellular ancestors showing that they had a richer repertoire of proteins involved in cell adhesion and transcriptional regulation than previously inferred only with the choanoflagellate genome. Some of these proteins were secondarily lost in choanoflagellates. In contrast, most intercellular signalling systems controlling development evolved later concomitant with the emergence of the first metazoans. We propose that the acquisition of these metazoan-specific developmental systems and the co-option of pre-existing genes drove the evolutionary transition from unicellular protists to metazoans.

Figure 1. The filasterean Capsaspora owczarzaki.

(a,b) Differential interference contrast microscopy (a) and scanning electron microscopy (b) images of C. owczarzaki. Scale bar, 10 μm (a) and 1 μm (b). (c), Phylogenetic position of C. owczarzaki. Four different analyses on the basis of two independent data sets and two different methods indicate an identical topology, except for the clustering of all non-sponge metazoans (white circle). Details are in Supplementary Note 2. Gray and black circles indicate ≥90% (0.90) and ≥99% (0.99) of bootstrap values and Bayesian posterior probabilities, respectively, for all four analyses.

Figure 2. Gain and loss of protein domains within the Opisthokonta.

(a) The number of Pfam protein domains that were gained or lost at each evolutionary period was inferred by Dollo parsimony, which does not consider multiple independent evolution of a domain. Total number of protein domains, and the inferred numbers of domain gain (+) and loss (−) events are depicted at the tree edges. The full list of domains is in Supplementary Table S4. (b,c) GO terms that were enriched by the evolution of protein domains (b) or depleted by the loss of protein domains (c) were sought via the topology-weighted algorithm. The significant GO terms (P<1.0e−3) are shown at the tree edges together with the number of included Pfam domains. Terms including fewer than seven gained or lost domains are not shown. The list of domains included in each GO is in Supplementary Tables S5 and S6.

Figure 3. Capsaspora owczarzaki enrichment of metazoan-biased protein domains.

The number of genes encoding proteins that contain each of the selected InterPro domains were analysed (the InterPro short names are shown on the right) for 19 eukaryote genomes. We chose 106 domains that are significantly (Fisher’s exact test; P<1.0e−20) enriched in the metazoan genomes compared with the genomes of non-holozoan lineages. Redundant domains are not exhaustively shown. Domains present only in a single taxon are not shown (available in Supplementary Fig. S12). Values were normalized by the number of all protein-coding genes in the genomes, and relative values to the maximum were calculated. Numbers were manually entered for the protein tyrosine kinase catalytic domain (Tyr_kinase_cat_dom) to exclude mispredicted serine/threonine kinase domains (see Supplementary Note 5). Protein domains were manually classified into 12 functional categories, shown on the right. In this figure, the categories ‘Zinc-fingers’, ‘cytoskeleton and its control’, ‘Functions on DNA or RNA molecules’, ‘Virus and transposons’ and ‘Other/diverse functions’ are collapsed (only leucine-rich repeats are shown; full figure available in the Supplementary Fig. S13). Domains with high relative gene counts (>0.65) in Capsaspora are depicted in red. Hsap, H. sapiens; Dmel, D. melanogaster; Cele, C. elegans; Hmag, H. magnipapillata; Nvec, N. vectensis; Tadh, T. adhaerens; Aque, A. queenslandica; Mbre, M. brevicollis; Cowc, C. owczarzaki; Ncra, N. crassa; Lbic, L. bicolor; Ddis, D. discoideum; Ehis, E. histolytica; Atha, A. thaliana; Crei, C. reinhardtii; Pfal, P. falciparum; Lmaj, L. major; Ptet, P. tetraurelia; Esil, E. siliculosus. A widely-accepted phylogeny among species is depicted on the bottom.

Figure 4. Schematic representation of the putative Capsaspora owczarzaki cell.

Protein components of major metazoan cell adhesion complexes (green background) and various signalling pathways including receptors (yellow background) are depicted. Components with red and blue backgrounds indicate those found both in C. owczarzaki and M. brevicollis and those found in C. owczarzaki but not in M. brevicollis, respectively. Dotted components are absent in the C. owczarzaki genome; greyed when M. brevicollis has them. A grey striped line represents an actin filament, to which the cell–ECM–adhesion complexes bind. See Supplementary Note 5 for details. *, two domains hedge and hog are found in different proteins in M. brevicollis. **, receptor-type proteins with domain architectures similar to Notch and Delta proteins are present in C. owczarzaki. ***, proteins with similar domain architectures are present in M. brevicollis, but not confidently mapped to those metazoan families by phylogenetic analyses. ****, the repertoires of RTKs are totally different between C. owczarzaki, M. brevicollis and metazoans, and thus likely to have diversified independently in each lineage. 4E-BP1, eukaryotic initiation factor 4E-binding protein 1; CK1, Casein kinase 1; C-Lectin, C-type lectin; CSL, CBF1/RBP-Jκ/suppressor of hairless/LAG-1; CTKs, cytoplasmic tyrosine kinases; DB, Dystrobrevin; DG, Dystroglycan; DP, Dystrophin; Dsh, Dishevelled; Ets, E-twenty six; FOX, Forkhead box; Gα, G-protein-α subunit; GluR, glutamate receptor; GPR108, G-protein-coupled receptor 108; GSK3, glycogen synthetase kinase 3; Grh, Grainy head; HD, homeodomain; IgCAM, Immunoglobulin-like cell adhesion molecule; ILK, Integrin-linked kinase; ITR, intimal thickness-related receptor; JNK, c-Jun N-terminal kinase; NRPTPs, non-receptor protein tyrosine phosphatases; OA1, Ocular albinism 1-like; PDE, phosphodiesterase; RGS, regulator of G-protein signalling; RTKs, receptor tyrosine kinases; RPTP, receptor protein tyrosine phosphatase; S6K p70; 70kDa ribosomal protein S6 kinase; SAV, Salvador; Sd, Scalloped; SG, Sarcoglycan; SSPN, Sarcospan; SYN, Syntrophin; TALE, three amino-acid loop extension-class homeodomain; TGFβ, Transforming growth factor β; TOR, Target of rapamycin; YAP, Yes-associated protein.