Elephant shark sequence reveals unique insights into the evolutionary history of vertebrate genes: a comparative analysis of the protocadherin cluster
WP Yu, V Rajasegaran, K Yew, WL Loh, BH Tay, CT Amemiya, S Brenner and B Venkatesh.
Cartilaginous fishes are the oldest living phylogenetic group of jawed vertebrates. Here
we demonstrate the value of cartilaginous fish sequences in reconstructing the
evolutionary history of vertebrate genomes by sequencing protocadherin cluster in the
relatively small genome (910 Mb) of the elephant shark (Callorhinchus milii). Human
and coelacanth contain a single protocadherin cluster with 53 and 49 genes, respectively,
that are organized in three subclusters, Pcdhα, Pcdhβ and Pcdhγ, whereas the duplicated
protocadherin clusters in fugu and zebrafish contain more than 77 and 107 genes,
respectively, that are organized in Pcdhα and Pcdhγ subclusters. By contrast, elephant
shark contains a single protocadherin cluster with 47 genes organized in four subclusters
(Pcdhδ, Pcdhε, Pcdhμ and Pcdhν). By comparison with elephant shark sequences, we
discovered a Pcdhδ subcluster in teleost fishes, coelacanth, Xenopus and chicken. Our
results suggest that the protocadherin cluster in the ancestral jawed vertebrate contained
more subclusters than modern vertebrates, and the evolution of the protocadherin cluster
is characterized by lineage-specific differential loss of entire subclusters of genes. In
contrast to teleost fish and mammalian protocadherin genes which have undergone gene
conversion events, elephant shark protocadherin genes have experienced very little gene conversion. The syntenic block of genes in the elephant shark protocadherin locus is well conserved in human but disrupted in fugu. Thus, elephant shark genome appears to be
less prone to rearrangements compared to teleost fish genomes. The small and ‘stable’
genome of the elephant shark is a valuable reference for understanding the evolution of
Published in The Proceedings of the National Academy of Sciences, USA. 105(10): 3819-3824.
For more information about B. Venkatesh and Sydney Brenner’s lab, click here.