Abstract
The vertebrate gene repertoire is characterized by “cryptic” genes whose identification has been hampered by their absence from the genomes of well-studied species. One example is the Bmp16 gene, a paralog of the developmental key genes Bmp2 and -4. We focus on the Bmp2/4/16 group of genes to study the evolutionary dynamics following gen(om)e duplications with special emphasis on the poorly studied Bmp16 gene. We reveal the presence of Bmp16 in chondrichthyans in addition to previously reported teleost fishes and reptiles. Using comprehensive, vertebrate-wide gene sampling, our phylogenetic analysis complemented with synteny analyses suggests that Bmp2, -4 and -16 are remnants of a gene quartet that originated during the two rounds of whole-genome duplication (2R-WGD) early in vertebrate evolution. We confirm that Bmp16 genes were lost independently in at least three lineages (mammals, archelosaurs and amphibians) and report that they have elevated rates of sequence evolution. This finding agrees with their more “flexible” deployment during development; while Bmp16 has limited embryonic expression domains in the cloudy catshark, it is broadly expressed in the green anole lizard. Our study illustrates the dynamics of gene family evolution by integrating insights from sequence diversification, gene repertoire changes, and shuffling of expression domains.
Highlights
Bmp2/4 genes have been studied for almost 50 years since the 1970s1, but one member of the class, designated as Bmp[16], was discovered as late as 20092
To obtain an inventory of Bmp2/4/16 homologs present in the genomes of extant vertebrates, we used RT-PCR screening, RNA sequencing (RNA-seq) and exhaustive database searches
Degenerate RT-PCR using cDNA derived from brain tissue of the same species identified a sequence that is highly similar to the Bmp2/4/16-A sequence identified in the genome assembly of E. burgeri
Summary
Bmp2/4 genes have been studied for almost 50 years since the 1970s1, but one member of the class, designated as Bmp[16], was discovered as late as 20092 It was first found in ray-finned fishes (actinopterygians) including zebrafish, and orthologs have since only been reported in the African coelacanth and the green anole lizard[3]. Two cleavage sites (S1 and S2) have been described for BMP2/4 proteins, and only proteins cleaved at both sites are fully active and able to convey long-range signals[23]. Another level of regulation in Bmp signalling is receptor binding. It is currently not fully understood to what extent these structural characteristics described for BMP2/4 proteins apply to BMP16 proteins, there is evidence that zebrafish bmp2a, -2b, -4 and -16 are all able to activate the BMP-signalling pathway in vitro[3]
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