Comparative Analysis of Epidermal Differentiation Genes of Crocodilians Suggests New Models for the Evolutionary Origin of Avian Feather Proteins

Abstract

The epidermis of amniotes forms a protective barrier against the environment and the differentiation program of keratinocytes, the main cell type in the epidermis, has undergone specific alterations in the course of adaptation of amniotes to a broad variety of environments and lifestyles. The epidermal differentiation complex (EDC) is a cluster of genes expressed at late stages of keratinocyte differentiation in both sauropsids and mammals. In the present study, we identified and analyzed the crocodilian equivalent of the EDC. The gene complement of the EDC of both the American alligator and the saltwater crocodile were determined by comparative genomics, de novo gene prediction and identification of EDC transcripts in published transcriptome data. We found that crocodilians have an organization of the EDC similar to that of their closest living relatives, the birds, with which they form the clade Archosauria. Notable differences include the specific expansion of a subfamily of EDC genes in crocodilians and the loss of distinct ancestral EDC genes in birds. Identification and comparative analysis of crocodilian orthologs of avian feather proteins suggest that the latter evolved by cooption and sequence modification of ancestral EDC genes, and that the amplification of an internal highly cysteine-enriched amino acid sequence motif gave rise to the feather component epidermal differentiation cysteine-rich protein in the avian lineage. Thus, sequence diversification of EDC genes contributed to the evolutionary divergence of the crocodilian and avian integuments.

Review: Evolution and diversification of corneous beta‐proteins, the characteristic epidermal proteins of reptiles and birds

“…In crocodilians 22 CBP genes have been detected in both the American alligator ( A. mississippiensis ) and the saltwater crocodile ( C. porosus ; Holthaus et al, ), which is similar to the 20 and 21 genes identified in a previous study (Greenwold & Sawyer, ). Remarkably no less than 42 CBP genes were found in the Chinese alligator (Figure ; Supporting Information Figure S1, As), suggesting some variation in the number of these structural proteins among crocodilians.…”

“…The cladogram is based on Dalla Valle, Nardi, Gelmi, et al () and 2010a that report these main subdivisions. The source for the number of CBPs was for snakes Holthaus et al (); for anolis Dalla Valle, Nardi, Bonazza, et al (2010b); for the Japanese gecko Liu et al (); for birds Greenwold et al (); for crocodilians Holthaus et al () and this review; for turtles Li et al () [Color figure can be viewed at wileyonlinelibrary.com]…”

“…The recent sequencing of various reptile and bird genomes has made it possible not only to identify the CBP gene cluster in all major sauropsid clades, but also to apply comparative genomics (Zheng et al, ) to address the relationship between corneous proteins in sauropsids and mammals (Mlitz et al, ; Strasser et al, ; Figure ). The CBP cluster was found in the EDC on chromosome 25 of the chicken (Alibardi & Toni, ; Greenwold & Sawyer, , ), and in the EDC of all major sauropsid clades (Holthaus et al, , , ; Strasser et al, ). Therefore, proteins formerly termed beta‐keratins have their genes included in the EDC, and are themselves “epidermal differentiation” or “corneous” proteins and not keratins (IF‐proteins).…”

“…In crocodilians a special type of CBP (As_Beta39, Figure ; Supporting Information S5), which is particularly long, rich in glycine (G), serine (S), tyrosine (Y), and arginine (R), and contains several amino acid residues rare in other CBPs, such as glutamic acid (E), has been identified (Holthaus et al, ). Whether this richness in glycine stretches imparts hydrophobicity to the skin of these water dwellers predators remains to be proved.…”

“…Initially the archosaur claw and scale subfamily were similar (Triassic), but possibly during the early Jurassic Period the avian lineage rapidly diversified, giving rise to the feather CBP genes, likely from duplication and diversification from the scale subfamily (Alibardi, ; Greenwold & Sawyer, , ; Gregg & Rogers, ). The analyzed members of the crocodilians display a different number (from 0 to 5) of claw CBPs (see Holthaus et al, ; Supporting Information Figure S1, As), and compared with birds and turtles they seem to have lost most members of the claw subfamily (Figure e).…”