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

Rio Kashimoto,Chuya Shinzato,Kanako Hisata,Noriyuki Satoh,Eiichi Shoguchi

doi:10.3390/genes12030397

Rio Kashimoto, Chuya Shinzato + Show 3 more

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https://doi.org/10.3390/genes12030397

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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.

Highlights

Animal color patterns involving fluorescent proteins (FPs) are critical to providing colors to corals and are known to have expanded in these animals, and Fluorescent Protein (FP) are perhaps nowhere more exploited than by corals [1,2,3,4]
We identified candidate FP genes by analyzing the assembled genomes of 18 acroporid species (Acropora and three other confamilial taxa) using BLASTP searches with 40 protein sequences as queries (Table 1) and using Pfam domain searches
By comparing the gene numbers encoding FPs between species, we found that the 15 Acropora species have 9–18 FP genes, whereas the two Montipora species and Astrepora myriophthalma have only two (Table 2)

Summary

Introduction

Animal color patterns involving fluorescent proteins (FPs) are critical to providing colors to corals and are known to have expanded in these animals, and FPs are perhaps nowhere more exploited than by corals [1,2,3,4]. Coral colors are due primarily to green (GFP), cyan (CFP), and red (RFP) FP emission, as well as in combination with purple or blue non-fluorescent chromoproteins (ChrPs) [5,6,7,8]. Cnidarian GFPs are composed of ~230 amino acids [3,9], which are excited by blue light (maximum 395 nm with a minor peak at 470 nm) and emit green light (peak emission between 509 and 540 nm) [10,11,12]. FPs fluoresce based on the tripeptide chromophore—XYG—[13]. Aequorin is a bioluminescent protein that, through energy transfer, excites GFPs. Aequorin and GFPs were discovered by Osamu Shimomura in the jellyfish Aequorea victoria [14]. FPs have been widely used as reporters of gene expression

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