Evolution of Protein-Mediated Biomineralization in Scleractinian Corals

Abstract

While recent strides have been made in understanding the biological process by which stony corals calcify, much remains to be revealed, including the ubiquity across taxa of specific biomolecules involved. Several proteins associated with this process have been identified through proteomic profiling of the skeletal organic matrix (SOM) extracted from three scleractinian species. However, the evolutionary history of this putative "biomineralization toolkit," including the appearance of these proteins' throughout metazoan evolution, remains to be resolved. Here we used a phylogenetic approach to examine the evolution of the known scleractinians' SOM proteins across the Metazoa. Our analysis reveals an evolutionary process dominated by the co-option of genes that originated before the cnidarian diversification. Each one of the three species appears to express a unique set of the more ancient genes, representing the independent co-option of SOM proteins, as well as a substantial proportion of proteins that evolved independently. In addition, in some instances, the different species expressed multiple orthologous proteins sharing the same evolutionary history. Furthermore, the non-random clustering of multiple SOM proteins within scleractinian-specific branches suggests the conservation of protein function between distinct species for what we posit is part of the scleractinian "core biomineralization toolkit." This "core set" contains proteins that are likely fundamental to the scleractinian biomineralization mechanism. From this analysis, we infer that the scleractinians' ability to calcify was achieved primarily through multiple lineage-specific protein expansions, which resulted in a new functional role that was not present in the parent gene.

Keywords: SOM proteins; co-option; phylogenetic analysis; skeleton evolution; stony corals.

FIGURE 1

Evolutionary origin of SOM proteins (SOMP) and duplication rates across animal taxa. (A) In the species tree, each internal node represents an ancestral lineage, where tips represent extant species. Accordingly, blue-filled bars near specific internal nodes represent the percentage of known SOM proteins that were gained in a specific ancestral lineage, based on our results. Similarly, the gray-filled bar represents the percentage of known SOM proteins that evolved from a protein whose last duplication occurred at specific ancestral species. Bottom-right bars represent gain at extant species. The mean ($\overline{x}$) and standard deviation (s.d.) values are indicated in each bar graph. Black shapes symbolize the different mineral phases of the species that form a rigid skeleton or shell. (B) The heatmap describes the occurrences of each known SOM protein from Stylophora pistillata, Acropora digitifera, and A. millepora across the different orthogroups and their coding sequence homologs among all species in this study. For a comprehensive list of the SOM proteins found in each orthogroup, see Supplementary Table 2.

FIGURE 2

Rooted gene tree of polycystin-like proteins (OG0006984) representing the independent co-option of orthologous proteins into the SOM of the Acroporidae species. Node points represent the phylum (shape) and order (color). Tips that are labeled red indicate the occurrence of scleractinian known SOM proteins. The highlighted cluster represents a “Scleractinia branch.” Node support values indicate percentage bootstrap values. Only values above 75 are indicated.

FIGURE 3

Rooted gene tree of scleractinian coral aspartic acid-rich proteins (OG0001947) representing the scleractinian-specific expansion of the gene family involving species from both the complex and robust scleractinian clades. Node points represent the phylum (shape) and order (color). Tips that are labeled red indicate the occurrence of scleractinian known SOM proteins. The two highlighted clades represent orthologous relationships between scleractinian sequences to the known SOM protein(s) in their respective “Scleractinia branch.” Node support values indicate percentage bootstrap values. Only values above 75 are indicated.

FIGURE 4

Rooted gene tree of metal transport proteins (OG0001324) representing the scleractinian-specific expansion of the gene family. Node points represent the phylum (shape) and order (color). Tips that are labeled red indicate the occurrence of scleractinian known SOM proteins. The highlighted cluster represents a “Scleractinia branch.” Node support values indicate percentage bootstrap values. Only values above 75 are indicated.

FIGURE 5

Rooted gene tree of CAP-Gly domain-containing proteins (OG0004585) representing the independent co-option of a single S. pistillata protein into the SOM. Node points represent the phylum (shape) and order (color). Tips that are labeled red indicate the occurrence of known SOM proteins. The highlighted cluster represents a “Scleractinia branch.” Node support values indicate percentage bootstrap values. Only values above 75 are indicated.