Expansion and Diversification of Fluorescent Protein Genes in Fifteen Acropora Species during the Evolution of Acroporid Corals

Abstract

In addition to a purple, non-fluorescent chromoprotein (ChrP), fluorescent proteins (FPs) account for the vivid colors of corals, which occur in green (GFP), cyan (CFP), and red (RFP) FPs. To understand the evolution of the coral FP gene family, we examined the genomes of 15 Acropora species and three confamilial taxa. This genome-wide survey identified 219 FP genes. Molecular phylogeny revealed that the 15 Acropora species each have 9-18 FP genes, whereas the other acroporids examined have only two, suggesting a pronounced expansion of the FP genes in the genus Acropora. The data estimates of FP gene duplication suggest that the last common ancestor of the Acropora species that survived in the period of high sea surface temperature (Paleogene period) has already gained 16 FP genes. Different evolutionary histories of lineage-specific duplication and loss were discovered among GFP/CFPs, RFPs, and ChrPs. Synteny analysis revealed core GFP/CFP, RFP, and ChrP gene clusters, in which a tandem duplication of the FP genes was evident. The expansion and diversification of Acropora FPs may have contributed to the present-day richness of this genus.

Keywords: Acropora; Acroporidae; chromoprotein; corals; fluorescent proteins; gene expansion; tandem duplication.

Figure 2

Expansions of the fluorescent protein (FP) genes of the genus Acropora with estimated divergence times of the acroporid corals indicated at the bottom of each tree. Numbers of genes duplicated (+) or lost (–) are indicated at each branch. (A) FP gene duplications and losses. It is inferred that the Acroporidae ancestor had five FPs. Species trees with divergence time estimates, changes in sea level, and sea surface temperature are indicated [22]. Expected sea level changes are shown with a blue dotted line [59]. Estimated tropical sea surface temperature of the Eocene is indicated with an orange line [60]. The Paleocene–Eocene thermal maximum (PETM) is indicated with an arrowhead, and the Early Eocene climatic optimum (EECO) is highlighted in light grey. An approximate geological time scale is shown at the bottom. J, Jurassic period; C, Cretaceous period; P, Paleocene; E, Eocene; O, Oligocene; M, Miocene. The history of FP duplications and losses are classified into those of GFP/CFPs (B), RFPs (C), and ChrPs (D). Squares show that putative GFP evolved into RFP or ChrP.

Figure 1

Molecular phylogenetic tree of 255 fluorescent proteins (FPs) from the 18 acroporid species and the other cnidarians. The tree was generated by the maximum likelihood (ML) method. Nodes supported by bootstrap values higher than 70% are shown with a circle using iTOL software. Candidates of the RFPs and chromoproteins in the acroporid corals are classified into two different clades (red and purple stars, respectively). The others are indicated as GFP/CFP candidates that form a large clade (green star) with known GFPs and CFPs. Squares highlights the sequences that are not from acroporid corals.

Figure 3

Three core gene clusters, including nine FP genes and syntenic regions in Acropora genomes. Synteny analysis showed the probability of extensive tandem gene duplications or losses at three genomic locations in the Acropora lineages. (A) GFP/CFP (green arrow) gene clusters in Clade III Acropora (A. digitifera, A. nasuta, A. microphthalma, and A. acuminata). (B) RFP (red arrow) clusters in Clade II (A. intermedia, A. gemmifera, A. awi, and A. florida). (C) ChrP (purple arrow) clusters in Clade III (A. digitifera, A. nasuta, A. microphthalma, and A. acuminata). The clades correspond to Figure 2. The orthologous relationships between species are shown as symbols (★, ○, ■, ◇, and △) that correspond to Figure S5. The standard arrow indicates predicted complete FP genes (Table S2), and the dashed arrow indicates the predicted incomplete FP genes from this study (Table S1). Black arrows indicate neighboring genes to FPs.

Figure 4

Estimated numbers of fluorescent genes in the Acropora ancestor and diversification in the descendant lineages. It is hypothesized that ~16 FP genes have been conserved in Acropora. RFP and GFP/CFP genes may have diversified more in Clades II and IV, respectively.