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Elephant Shark Protocadherin Sequence Offers Peek Into Vertebrate Evolution

NEW YORK (GenomeWeb News) - Elephant shark genetic sequences are helping researchers unravel vertebrate evolutionary history, according to new research.
Researchers from Singapore and the US sequenced the elephant shark’s protocadherin gene cluster in order to piece together the history of jawed vertebrates.
Their results, published online today in the Proceedings of the National Academy of Sciences, indicate that the elephant shark protocadherin cluster has undergone surprisingly little gene conversion and that jawed vertebrates have lost protocadherin subgroups through evolutionary history.
The elephant shark, also called the elephant fish or ghost shark, belongs to Chondrichthyes, a group of cartilaginous fishes — the oldest living jawed vertebrates — that also includes sharks, skates, and rays. The other living, jawed vertebrates belong to Osteichthyes, the bony vertebrates.
“Because they are the most ancient phylogenetic group of jawed vertebrate, cartilaginous fishes not only provide a better insight into the now-extinct ancestral jawed vertebrate genome but also serve as an outgroup that helps in identifying lineage-specific adaptive changes in different lineages of bony vertebrates,” the authors wrote.
Consequently, researchers have been probing the elephant shark genome for several years. For this paper, senior authors Sydney Brenner and Byrappa Venkatesh of Singapore’s Institute of Molecular and Cell Biology and their colleagues focused on protocadherin cluster genes. These genes code for cadherin-like proteins involved in cell adhesion.
Because protocadherins are found at synaptic membranes, there is speculation that the proteins are linked to synaptic complexity and the emergence of complex central nervous systems. The region is also incredibly dynamic evolutionarily and often undergoes gene loss, duplication, or conversion.
To identify the elephant shark protocadherin cluster, the team used TBLASTN searches of the elephant shark whole-genome shotgun sequence with human protocadherin amino acid sequence. Using the two sequences they found this way, they probed an elephant shark BAC library to pull out ten clones. They then sequenced three overlapping clones using standard shotgun sequencing.
The protocadherin cluster sequence, comprised of roughly 409,000 bases, contained 47 exon regions in four subclusters. In contrast, humans have 53 genes organized into just three subclusters. Coelacanths, a type of fleshy-finned bony fish, have 49 genes in three subclusters. On the other hand, bony fish such as fugu and zebrafish have around hundred protocadherin genes in two unlinked clusters.
Taken together, the authors propose that this indicates that modern vertebrates may have lost clusters of protocadherin genes through evolution from ancestral jawed vertebrates. By extrapolating back into history, the authors suggest that the last common ancestor of jawed vertebrates had around seven protocadherin subclusters.
Based on their amino acid sequence alignments of elephant shark protocadherin genes with one another and with the genes of other animals, they were also able to construct phylogenetic trees to track protocadherin evolution. Interestingly, the authors reported that the elephant shark protocadherin cluster doesn’t undergo as many rearrangements as other animals and seems to be evolving slower than that of bony fish or coelacanths.
“The relatively small and slowly evolving genome of the elephant shark, therefore, is an important ‘reference’ for understanding the evolution of vertebrate genomes,” the authors wrote.