The genome of Aiptasia, a sea anemone model for coral symbiosis

Abstract

The most diverse marine ecosystems, coral reefs, depend upon a functional symbiosis between a cnidarian animal host (the coral) and intracellular photosynthetic dinoflagellate algae. The molecular and cellular mechanisms underlying this endosymbiosis are not well understood, in part because of the difficulties of experimental work with corals. The small sea anemone Aiptasia provides a tractable laboratory model for investigating these mechanisms. Here we report on the assembly and analysis of the Aiptasia genome, which will provide a foundation for future studies and has revealed several features that may be key to understanding the evolution and function of the endosymbiosis. These features include genomic rearrangements and taxonomically restricted genes that may be functionally related to the symbiosis, aspects of host dependence on alga-derived nutrients, a novel and expanded cnidarian-specific family of putative pattern-recognition receptors that might be involved in the animal-algal interactions, and extensive lineage-specific horizontal gene transfer. Extensive integration of genes of prokaryotic origin, including genes for antimicrobial peptides, presumably reflects an intimate association of the animal-algal pair also with its prokaryotic microbiome.

Keywords: coral reefs; dinoflagellate; endosymbiosis; horizontal gene transfer; pattern-recognition receptors.

Fig. 1.

Phylogenetic position and different symbiotic states of Aiptasia. (A) Partial phylogenetic tree (see SI Appendix, SI Materials and Methods and Fig. S1A for details) shows Aiptasia grouped with other anthozoans among the cnidarians. Numbers on nodes denote bootstrap values. (B–D) An aposymbiotic Aiptasia polyp (B) and symbiotic polyps viewed under white light (C) or by fluorescence microscopy to visualize the red chlorophyll autofluorescence of the endosymbiotic Symbiodinium algae (D).

Fig. 2.

Genomic rearrangements in Aiptasia. (A) Correlation between a period of speciation and a period of high TE activity. (Top) Approximate times of divergence of Aiptasia from the anemone species S. elegans, V. paguri, and Bartholomea annulata based on Nei–Gojobori synonymous substitution rates in the COX3 gene (SI Appendix, SI Materials and Methods), which correspond to the Jukes–Cantor distances used to estimate the times of past TE activity. Aiptasia and B. annulata are symbiotic with dinoflagellates; V. paguri and S. elegans are not. (Bottom) The dynamics of seven distinct TE classes, plotted as the cumulative percentage of the genome covered by each class (ordinate) at given Jukes–Cantor substitution distances [abscissa; calculated based on the nucleotide differences between the individual genomic TEs and the consensus sequence for the corresponding TE family (SI Appendix, SI Materials and Methods)]. (B) Arrangements of HOX gene clusters in three anthozoans. N. vectensis and A. digitifera genes are named as described previously (15); Aiptasia genes are named based on the sequence similarities as shown in SI Appendix, Fig. S3C. Arrows indicate directions of transcription. Blue, other homeobox genes; green, HOX and HOX-related genes.

Fig. 3.

Differential expression and nonrandom chromosomal clustering of taxonomically restricted genes (TRGs) in Aiptasia. (A) Heat map of FPKM expression values (SI Appendix, SI Materials and Methods) for 63 putative TRGs with expression-level changes of ≥eightfold (up or down) between partially (Partial) or fully (Sym) infected anemones and anemones without dinoflagellates (Apo). (B) To evaluate genomic clustering, the observed numbers of clusters of two or more putative TRGs without intervening genes were compared with the expectations based on a random distribution of such genes in the genome (SI Appendix, SI Materials and Methods). Error bars indicate SDs; numbers in parentheses indicate the actual numbers of clusters of those sizes.

Fig. 4.

Cnidarian ficolin-like proteins (CniFLs), a newly recognized family of putative PRRs. (A) Maximum-likelihood phylogenetic tree of all CniFLs identified in Aiptasia and stony corals (A. digitifera and Stylophora pistillata) and of all canonical ficolins (Fcns) found in stony corals and the anemone N. vectensis (Dataset S1.7). A human and a mouse ficolin (one of three and two, respectively, in those species) were also included as an out-group. The tree is based on an alignment of a 113-amino-acid sequence (with gaps removed) that spans portions of the collagen and fibrinogen domains. Most of the identified CniFLs contain three central Ig domains, but five (indicated by an asterisk) contain only two. Numbers on nodes denote bootstrap values. (B) Components of the lectin-complement pathway that are encoded in the Aiptasia genome (based on KEGG analysis; SI Appendix, SI Materials and Methods) and may be involved in signaling downstream of the CniFLs. BF, complement factor B; C2, C3, and C3b, complement components 2 and 3 and the cleavage product of C3; C4BP, complement component 4 binding protein; CR, complement receptor; HF1, complement factor H; MASP, mannose-binding-lectin–associated serine protease. Complement component C4 was not unequivocally identified in the currently available sequence but is included here for the sake of completeness (Dataset S1.8).

Fig. 5.

Evidence for horizontal gene transfer (HGT) in Aiptasia. (A) Cumulative-distribution plot of intron numbers in Aiptasia-specific (green) and cnidarian-specific (blue) HGT candidates and in all 29,269 Aiptasia gene models (yellow). Because of the smaller sample sizes of the first two categories (275 and 823, respectively), 95% binomial-proportion confidence intervals (SI Appendix, SI Materials and Methods) are shown for them. (B) Maximum-likelihood phylogenetic tree for the Aiptasia Tox-Art-HYD1 domains apparently derived by intraspecific duplications after an HGT event. For simplicity, the numerous and varied bacterial species whose Tox-Art-HYD1 domains form the outer branches of the tree are not shown individually (SI Appendix, Fig. S7E). Numbers on nodes denote bootstrap values. An asterisk represents the three proteins in one genomic region.