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Open Access Highly Accessed Research article

Adaptive evolution of Toll-like receptor 5 in domesticated mammals

Sarah A Smith1, Oliver C Jann2, David Haig1, George C Russell3, Dirk Werling4, Elizabeth J Glass2 and Richard D Emes1*

Author Affiliations

1 School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington LE12 5RD, UK

2 The Roslin Institute and Royal Dick School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK

3 Royal Veterinary College, University of London, Hawkshead Lane, Hatfield, Herts, AL9 7TA, UK

4 Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK

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BMC Evolutionary Biology 2012, 12:122  doi:10.1186/1471-2148-12-122

Published: 24 July 2012

Additional files

Additional file 1:

Results and parameter estimates of all single branch-sites tests.

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Additional file 2:

Results and parameter estimates of all multiple branch-site analysis.

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Additional file 3:

Positions of detected bovine SNPs. Results of SNP detection across 15 breeds of cattle. W/T refers to wildtype; Mut refers to mutation form. NS = non-synonymous polymorphism; S = synonymous polymorphism. Amino acid one letter code names amino acid by convention. The type of nucleotide for each SNP and each breed is recorded using IUBMB single-letter code for nucleotide bases and ambiguity codes: R = A/G; Y = C/T; M = A/C; W = A/T; S = C/G; K = G/T.

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Additional file 4:

Positions of detected ovine SNPs. Results of SNP detection across 10 breeds of sheep. W/T refers to wildtype; Mut refers to mutation form. NS = non-synonymous polymorphism; S = synonymous polymorphism. Amino acid one letter code names amino acid by convention. The type of nucleotide for each SNP and each breed is recorded using IUBMB single-letter code for nucleotide bases and ambiguity codes: R = A/G; Y = C/T; M = A/C; W = A/T; S = C/G; K = G/T.

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Additional file 5:

Secondary structure sequence predictions (PSI-pred) affecting SNP A659T in cattle TLR5.

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Additional file 6:

Subspecies distribution of SNPs detected in Bovine TLR5. S: = synonymous SNP; NS: = non-synonymous SNP.

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Additional file 7:

Accession numbers of all sequences compared. Accession numbers of TLR5 coding nucleotide sequences used for PAML analysis.

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Additional file 8:

Alignment of all TLR5 genes analysed in Fasta format.

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Additional file 9 :

Phylogenetic tree of all TLR5 genes analysed.

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Additional file 10:

Details of bovine DNA samples. Bovine DNA samples. Sample size and subspecies characterization for each breed is detailed.

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Additional file 11:

Details of ovine DNA samples. Ovine DNA sample set. Sample size for each breed is detailed.

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Additional file 12:

Bovine primer sequences Primers used for the sequencing of the coding sequence of bovine TLR5. Forward primer 1 and Reverse Primer 6 are positioned in the un-translated regions either side of the single exon of TLR5.

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Additional file 13:

Ovine primer sequences. Ovine TLR5 sequencing primers. Forward primer 1 and reverse primer 4 are positioned in the un-translated region either side of the single exon of TLR5.

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