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

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      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.

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      Multiple sequence alignment with hierarchical clustering.

       F Corpet (1988)
      An algorithm is presented for the multiple alignment of sequences, either proteins or nucleic acids, that is both accurate and easy to use on microcomputers. The approach is based on the conventional dynamic-programming method of pairwise alignment. Initially, a hierarchical clustering of the sequences is performed using the matrix of the pairwise alignment scores. The closest sequences are aligned creating groups of aligned sequences. Then close groups are aligned until all sequences are aligned in one group. The pairwise alignments included in the multiple alignment form a new matrix that is used to produce a hierarchical clustering. If it is different from the first one, iteration of the process can be performed. The method is illustrated by an example: a global alignment of 39 sequences of cytochrome c.
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        ExPASy: SIB bioinformatics resource portal

        ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual resources (databases, web-based and downloadable software tools) are hosted in a ‘decentralized’ way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by different SIB groups and external institutions. The portal features a search function across ‘selected’ resources. Additionally, the availability and usage of resources are monitored. The portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. The new web interface provides, in particular, visual guidance for newcomers to ExPASy.
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          The cornified envelope: a model of cell death in the skin.

          The epidermis functions as a barrier against the environment by means of several layers of terminally differentiated, dead keratinocytes - the cornified layer, which forms the endpoint of epidermal differentiation and death. The cornified envelope replaces the plasma membrane of differentiating keratinocytes and consists of keratins that are enclosed within an insoluble amalgam of proteins, which are crosslinked by transglutaminases and surrounded by a lipid envelope. New insights into the molecular mechanisms and the physiological endpoints of cornification are increasing our understanding of the pathological defects of this unique form of programmed cell death, which is associated with barrier malfunctions and ichthyosis.
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            Author and article information

            Affiliations
            [1 ]Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Austria
            [2 ]Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA), University of Bologna, Italy
            [3 ]Clinical Department for Farm Animals and Herd Management, University of Veterinary Medicine Vienna, Austria
            [4 ]Vienna Zoo, Vienna, Austria
            Author notes

            Associate editor: Dan Graur

            Data deposition: All sequences generated in this study have been deposited at NCBI GenBank under the accession numbers MG243696, MG243697, MG243698.

            Corresponding author: E-mail: leopold.eckhart@ 123456meduniwien.ac.at .
            Journal
            Genome Biol Evol
            Genome Biol Evol
            gbe
            Genome Biology and Evolution
            Oxford University Press
            1759-6653
            February 2018
            12 February 2018
            12 February 2018
            : 10
            : 2
            : 694-704
            29447391 5827346 10.1093/gbe/evy035 evy035
            © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

            This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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            Pages: 11
            Product
            Funding
            Funded by: Austrian Science Fund 10.13039/501100002428
            Award ID: P23801
            Award ID: P28004
            Categories
            Research Article

            Genetics

            feathers, skin, integument, comparative genomics, alligators, crocodiles

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