Insights into bilaterian evolution from three spiralian genomes

Abstract

Current genomic perspectives on animal diversity neglect two prominent phyla, the molluscs and annelids, that together account for nearly one-third of known marine species and are important both ecologically and as experimental systems in classical embryology. Here we describe the draft genomes of the owl limpet (Lottia gigantea), a marine polychaete (Capitella teleta) and a freshwater leech (Helobdella robusta), and compare them with other animal genomes to investigate the origin and diversification of bilaterians from a genomic perspective. We find that the genome organization, gene structure and functional content of these species are more similar to those of some invertebrate deuterostome genomes (for example, amphioxus and sea urchin) than those of other protostomes that have been sequenced to date (flies, nematodes and flatworms). The conservation of these genomic features enables us to expand the inventory of genes present in the last common bilaterian ancestor, establish the tripartite diversification of bilaterians using multiple genomic characteristics and identify ancient conserved long- and short-range genetic linkages across metazoans. Superimposed on this broadly conserved pan-bilaterian background we find examples of lineage-specific genome evolution, including varying rates of rearrangement, intron gain and loss, expansions and contractions of gene families, and the evolution of clade-specific genes that produce the unique content of each genome.

Figure 1. Full-genome evidence resolves metazoan relationships and verifies the monophyly of lophotrochozoans and spiralians

a, A protein tree inferred from 299,129 amino acid positions gathered from 827 slow-evolving orthologues using RAxML and modelling heterogeneity of substitution processes using a LG + Γ4 model with each gene partitioned. Strong support is obtained for the monophyly of lophotrochozoans. b, Intron tree obtained from a matrix of 5,377 introns analysed using MrBayes and an asymmetric binary model (probability of gain: 0.01). c, Indel tree reconstructed from a matrix of 1,928 indel sites using a regular binary model. Circles at nodes indicate a bootstrap support of >0.90 (a) or a posterior probability of >0.95 (b and c). In b and c, arrows indicate species that do not follow the protein family tree topology.

Figure 2. Clustering of metazoan genomes in a multidimensional space of molecular functions

The first two principal components are displayed, accounting for 20% and 15% of variation, respectively. At least three clusters are evident, including a vertebrate cluster (far right), a non-bilaterian metazoan, invertebrate deuterostome or spiralian cluster (centre, top), and an ecdysozoan group (lower left). Drosophila and Tribolium (lower left) are outliers. Aqu, Amphimedon queenslandica (demosponge); Bfl, Branchiostoma floridae (amphioxus); Cel, Caenorhabditis elegans; Cte, Capitella teleta (polychaete); Cin, Ciona intestinalis (sea squirt); Dme, Drosophila melanogaster; Dpu, Daphnia pulex (water flea); Dre, Danio rerio (zebrafish); Isc, Ixodes scapularis (tick); Gga, Gallus gallus (chicken); Hsa, Homo sapiens (human); Hma, Hydra magnipapillata; Hro, Helobdella robusta (leech); Lgi, Lottia gigantea (limpet); Mmu, Mus musculus (mouse); Nve, Nematostella vectensis (sea anemone); Sma, Schistosoma mansoni; Sme, Schmidtea mediterranea (planarian); Spu, Strongylocentrotus purpuratus (sea urchin); Tad, Trichoplax adhaerens (placozoan); Tca, Tribolium castaneum (flour beetle); Xtr, Xenopus tropicalis (clawed frog).

Figure 3. Macrosynteny between spiralians, humans and Trichoplax

a, The location of genes in scaffolds of L. gigantea, C. teleta and Trichoplax (a non-bilaterian outgroup that conserves synteny) relative to the position of their orthologues in the human genome. The human chromosome segments have been grouped according to their ancestral linkage group (ALG); chromosome segment identifiers are also shown (see ref. 10). Human genes in ALG 2 have their orthologues co-located on a limited set of scaffolds in L. gigantea, C. teleta and Trichoplax, indicating conserved linkage of this group of genes across eumetazoan lineages. In contrast, although ALG 17 and ALG 9 are preserved separately in Trichoplax, scaffolds of L. gigantea and C. teleta have homologous gene content either with ALG 9 or with both ALG 9 and ALG 17, indicating a translocation of one or more chromosome segments from ALG 17 to ALG 9 in the common ancestor of molluscs and annelids, after the divergence of the spiralian and vertebrate lineages. Genes inferred to derive from this translocated segment are shown in red. Subsequent intra-chromosomal rearrangement has dispersed the translocated genes among the genes of ALG 9. b, The scenario in panel a represented schematically on a phylogenetic tree, with chromosomes of ancestral and living genomes represented as horizontal blue bars and the translocated segment represented in red. c, The positions of human genes and their L. gigantea, C. teleta and Trichoplax adhaerens orthologues compared in dot plots schematically (and in the real data; see panel a) for three ALGs.

Figure 4. The Hox gene complement and linkage in the three lophotrochozoan genomes and selected bilaterians

Arrows indicate direction of transcription (orientation between scaffolds is arbitrary). Scaffolds with ends marked by black dots may be part of a larger Hox complex because the Hox gene is at the end of the scaffold. B. floridae, Branchiostoma floridae. Colours indicate unambiguously assigned paralogy groups (Hox1, Hox2, Hox3, Hox4, central class and posterior class).

Figure 5. Examples of conserved orthologous gene clusters

a–c, Clusters of linked genes across diverse species. Within each panel, genes in the same colour are members of the same orthologous group, with the gene identifiers of defining members of the group indicated: C7orf42, (human) chromosome 7 open reading frame 42; Exoc7, exocyst complex component 7; FAM100, family with sequence similarity 100; FoxJ, forkhead box protein J; HDC, histidine decarboxylase; MGRN E3 Ub ligase, mahogunin ring finger E3 ubiquitin ligase; MORC, MORC family CW-type zinc finger; PSMG1, proteasome (prosome, macropain) assembly chaperone 1; ROX/MINT, Max-binding protein family member; SYAP1, synapse-associated protein 1; WBP11, WW domain binding protein 11; ZMPSTE24, zinc metallopeptidase, STE24 homologue. Scaffold positions for all displayed linkages are listed in Supplementary Note 7.2. d, Cumulative rates of microsynteny change plotted on a fixed metazoan tree topology. Branch lengths are proportional to the number of inferred genomic rearrangements. A. queenslandica, Amphimedon queenslandica; C. intestinalis, Ciona intestinalis; D. melanogaster, Drosophila melanogaster; D. pulex, Daphnia pulex; D. rerio, Danio rerio; G. gallus, Gallus gallus; H. magnipapillata, Hydra magnipapillata; I. scapularis, Ixodes scapularis; M. musculus, Mus musculus; N. vectensis, Nematostella vectensis; Ub, ubiquitin; X. tropicalis, Xenopus tropicalis.