Green fluorescent protein (GFP) has been widely used as a
molecular marker in modern biological research. Before the recent report of one GFP gene in Branchiostoma floridae, GFP family members were
cloned only from other two groups of species:
Cnidaria and Copepoda. Here we describe the complete GFP gene repertoire of B. floridae which includes 13 functional genes and 2
pseudogenes, representing the largest GFP family found so far. Coupling with nine other GFP sequences from another two species of genus Branchiostoma and the sequences from
Cnidaria and Copepoda, we made a deep-level
phylogenetic analysis for GFP genes in cephalochordates and found: 1) GFP genes have experienced a divergent evolution in cephalochordates; 2) all amphioxus GFP genes form four main
clades on the tree which had diverged before the
radiation of the
last common ancestor of all extant cephalochordates; 3) GFP genes in amphioxus shared a common ancestor with that in Copepoda rather than being
derived from
horizontal gene transfer, which indicates that our ancestor was
derived from a
fluorescent organism and lost this ability after its separation from Cephalochordata, and also makes GFP a rare gene which has a rather unusual evolutionary path. In addition, we also provided evidence indicating that GFP genes have evolved divergent functions by specializing their expression profile, and different
fluorescent spectra by changing their
emission peaks. These findings spark two interesting issues: what are GFP in vivo functions in cephalochordates and why they are lost in other examined deuterostomes?
