Open Access Research article

The salmonid myostatin gene family: a novel model for investigating mechanisms that influence duplicate gene fate

Casey B Lawson13, Takumu Niino13, Russell A Hermansen4, Vera Brok-Volchanskaya4, Melissa F Jackson23, Dilip K Garikipati13, David A Liberles4* and Buel D Rodgers123*

Author Affiliations

1 Department of Animal Sciences, Washington State University, Pullman, WA 99164, USA

2 School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA

3 Washington Center for Muscle Biology, Washington State University, Pullman, WA, 9916, USA

4 Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA

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BMC Evolutionary Biology 2012, 12:202  doi:10.1186/1471-2148-12-202

Published: 8 October 2012

Additional files

Additional file 1:

MSTN-1a, -1b amino acid phylogeny. This phylogeny was created using an amino acid alignment of MSTN-1a and 1b. Introns were excised from the amino acid sequences by the programs GENSCAN and GeneMark-E. The alignments were then made using MAFFT, and the phylogeny was constructed through PhyML 3.0 [45,46], with a 1000 bootstrap analysis.

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Additional file 2:

MSTN-2a, -2b amino acid phylogeny. This phylogeny was created using an amino acid alignment of MSTN-2a and 2b. Introns were excised from the amino acid sequences by the programs GENSCAN and GeneMark-E. The alignments were then made using MAFFT, and the phylogeny was constructed through PhyML 3.0 [45,46], with a 1000 bootstrap anlaysis.

Format: GIF Size: 17KB Download file

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Additional file 3:

(A) Bayesian Phylogeny of Myostatin proteins (MSTN-1a/1b and MSTN-2a/2b). The topology was generated using all available myostatin proteins from all for myostatin groups MSTN-1a/1b, and MSTN-2a/2b. The phylogeny was constructed using MrBayes 3.2 [47] with posterior probabilities indicated on the internal nodes of the tree. The tree was rooted with R. retropinna as the outgroup. (B) Maximum Likelihood Phylogeny of Myostatin proteins (MSTN-1a/1b and MSTN-2a/2b). The topology was generated using all available myostatin proteins from all for myostatin groups MSTN-1a/1b, and MSTN-2a/2b. The phylogeny was constructed using Phyml 3.0 [45,46] with 1,000 bootstraps indicated on the internal nodes of the tree. The tree was rooted with R. retropinna as the outgroup. (C) Bayesian Phylogeny of Myostatin genes (mstn1a/1b and mstn2a/2b). The topology was generated using all available myostatin genes from all for myostatin groups mstn1a/1b, and mstn2a/2b. The phylogeny was constructed using MrBayes 3.2 [47] with posterior probabilities indicated on the internal nodes of the tree. The tree was rooted with R. retropinna as the outgroup.

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Additional file 4:

BEB analysis of MSTN-1a/1b and MSTN-2a/2b. The amino acid letter represents the amino acid for that position in the first sequence of the alignment used to for the analysis (O. kisutch for MSTN-1a/1b and C. clupeaformis for MSTN-2a/2b). An * indicates there was a gap in the alignment at that position for the first sequence in the alignment. Only sites with probabilities greater than 95% are listed.

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