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Comparative Genomics Offers Look at Epidermal Genes Behind Turtle Shell Evolution

NEW YORK (GenomeWeb) – A new study suggests that turtles owe their tough shells to expansions and other features affecting gene families associated with epidermal differentiation.

As they reported online last night in Molecular Biology and Evolution, researchers from Austria and Italy used comparative genomics to search for clues to the advent of turtle shells. Based on patterns for so-called Epidermal Differentiation Complex (EDC) gene patterns in the Western painted turtle and other turtle species, they concluded that this gene family has both expanded and undergone partial translocation to pepper other parts of the genome in turtles.

The same gene family is present across the terrestrial tetrapod lineage, the team noted, contributing to the development of claws in reptiles, feathers in birds, and skin cells that protect humans and other animals from pathogens and the like. Results from the study support the notion that specific tweaks to the epidermal differentiation process have contributed to the formation of turtles' hard, protective shells and the epidermal scutes that cover them.

"Our results reveal that the evolution of turtles involved expansions of gene families within the EDC, translocations of beta-protein and other genes to novel loci outside of the EDC, and adaptation of EDC gene expression patterns to turtle-specific integumentary structures," senior author Leopold Eckhart, a biology and pathobiology researcher at the Medical University of Vienna, and his colleagues wrote.

The team began by searching for EDC-like genes in an existing genome sequence for the Western painted turtle, Chrysemys picta bellii, with the help of known amino acid sequences for proteins encoded by the EDC in human, chicken, and lizard genomes.

The search ultimately uncovered more than 100 Western painted turtle genes that appear to originate in the EDC — a set that encompassed four-dozen or more genes coding for epidermal differentiation-associated beta-proteins, also known as beta-keratin proteins.

The researchers uncovered similar EDC gene organization in the genomes of two more previously sequenced turtles, the green sea turtle Chelonia mydas and the Chinese softshell turtle Pelodiscus sinensis, though the genome of a third turtle, the spiny softshell turtle, was too fragmented for such comparisons.

Along with biases towards specific amino acids in the products of the turtle EDC genes, the team saw signs of gene duplication, gene family expansion, and translocation to other parts of the genome in the time since the turtle lineage split from that leading to birds and crocodilians some 244 million years ago.

Finally, using existing RNA sequence data for the western painted turtle and the red-eared slider turtle, together with newly generated PCR-based expression data for various European pond turtle tissues, the researchers demonstrated that beta-proteins and other EDC genes found outside the typical EDC locus contribute to cornified keratinocytes such as those making up scutes, while other EDC genes are expressed in epidermal keratinocyte cells. 

"Collectively, the results of the present comparative genomics study and our gene expression data indicate that the evolution of the integument of turtles was associated with numerous adaptation of genes involved in epidermal differentiation and with the origin and expansion of shell-associated beta-proteins," the study's authors concluded.