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Open Access Highly Accessed Research article

Genomic organization and molecular phylogenies of the beta (β) keratin multigene family in the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata): implications for feather evolution

Matthew J Greenwold and Roger H Sawyer*

Author Affiliations

Department of Biological Sciences, University of South Carolina, Columbia, SC 29205, USA

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BMC Evolutionary Biology 2010, 10:148  doi:10.1186/1471-2148-10-148

Published: 18 May 2010

Additional files

Additional file 1:

Annotation of β-keratins resulting from BLAST Searches of the Gallus gallus and Taeniopygia guttata Genomes. List of all sequences used in this study that resulted from a BLAST search of the G. gallus and T. guttata genomes [7,8]. Annotation of each sequence used in this study, its position on its respective chromosome, and strand orientation is indicated by a lowercase c (complement) if it was found on the complementary strand. Additionally, the Ensembl Gene identification numbers were listed for every β-keratin sequence that was annotated by Ensembl, and was not eliminated from this study by criteria described in the Methods section.

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Additional file 2:

PAML Analysis of all Feather β-keratin Loci that Resulted in Positively Selected Sites: The six models are listed in the first column with a brief description, and the values obtained from each analysis are listed in their respective rows. The dN/dS ratios are the average of the sum of all branches. All positively selected sites above 95% are listed, with those reaching 99% shown in bold. The Naïve Empirical Bayes (NEB) and Bayes Empirical Bayes (BEB) are shown when appropriate. The M3 model only uses the NEB analysis [61]. Additionally, the tables for the likelihood ratio test (LRT) results for each locus are included (see Methods).

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Additional file 3:

Expressed Sequence Tag BLAST results. List of all β-keratin sequences in the genomes of G. gallus and T. guttata that had at least an E-value score of 1e-160 and 1e-150, respectably, for an expressed sequence tag (EST). EST database was downloaded via NCBI for each species. The GI number for each EST, region of the EST matching the coding region of the β-keratin, the 5' region outside of the coding region for each matching EST, the 3' region outside of the coding region for each matching EST, the tissue source of the EST, the developmental stage of the collected EST source and the sex are listed.

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Additional file 4:

Two-dimensional Gels of β-keratin Expression in Chick Epidermal Appendages. Reprint of Figure 2 in Shames et al [19]. Two-dimensional gels of protein extracted from 19-20 day embryonic chick (A) scutate scale epidermis, (B) cornified beak, (C) egg tooth, (D) periderm, and (E) claw. The acidic (Ac) and basic (Ba) ends of the gel and the molecular weight markers are indicated for the second dimension. The protein spots labeled 1 and 2, 3 are scale β-keratins identified by hybrid-selection using a scale specific oligonucleotide probe [65].

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Additional file 5:

Tree Reconstruction of all β-keratin genes found in the Gallus gallus and Taeniopygia guttata Genomes. Neighbor-Joining tree reconstruction of the 219 β-keratin nucleotide sequences from both avian genomes and the three nile crocodile sequences as the outgroup. The subfamilies are colored with the following scheme: GGA25_Keratinocyte = red, scale β-keratin genes = blue, claw β-keratin genes = yellow, feather β-keratin genes = green and feather-like β-keratin genes = magenta. The taxa nomenclature and methodology is detailed in the Methods section. Only bootstrap values from the Neighbor-Joining method are listed.

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Additional file 6:

Tree Reconstruction of all β-keratin genes found in the Gallus gallus and Taeniopygia guttata Genomes. Maximum Likelihood tree reconstruction of the 219 β-keratin nucleotide sequences from both avian genomes and the three nile crocodile sequences as the outgroup. The subfamilies are colored with the following scheme: GGA25_Keratinocyte = red, scale β-keratin genes = blue, claw β-keratin genes = yellow, feather β-keratin genes = green and feather-like β-keratin genes = magenta. The taxa nomenclature and methodology is detailed in the Methods section. Only bootstrap values from the Maximum Likelihood method are listed.

Format: PDF Size: 13KB Download file

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