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Evolution of Hox Clusters in Salmonidae: A Comparative Analysis Between Atlantic Salmon (Salmo salar) and Rainbow Trout (Oncorhynchus mykiss)

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Abstract

We studied the genomic organization of Hox genes in Atlantic salmon (Salmo salar) and made comparisons to that in rainbow trout (Oncorhynchus mykiss), another member of the family Salmonidae. We used these two species to test the hypothesis that the Hox genes would provide evidence for a fourth round of duplication (4R) of this gene family given the recent polyploid ancestry of the salmonid fish. Thirteen putative Hox clusters were identified and 10 of these complexes were localized to the current Atlantic salmon genetic map. Syntenic regions with the rainbow trout linkage map were detected and further homologies and homeologies are suggested. We propose that the common ancestor of Atlantic salmon and rainbow trout possessed at least 14 clusters of Hox genes, and additional clusters cannot be ruled out. Salmonid Hox cluster complements seem to be more similar to those of zebrafish (Danio rerio) than medaka (Oryzias latipes) or pufferfish (Sphoeroides nephelus and Takifugu rubripes), as both Atlantic salmon and rainbow trout have retained HoxCb ortholog, which has been lost in medaka and pufferfish but not in zebrafish. However, our data suggest that phylogenetically, the homologous genes within each cluster express mosaic relationships among the teleosts tested and, thus, leave unresolved the interfamilial relationships among these taxa.

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Acknowledgments

This research was supported by AquaNet, Canada’s Network of Centers of Excellence in aquaculture, and the Natural Sciences and Engineering Research Council of Canada (NSERC). We also wish to thank Dr. Teresa Crease and the JME reviewers for their constructive comments on the manuscript and Xia Yue and Karim Gharbi for their laboratory assistance and technical advice.

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Authors and Affiliations

  1. Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada

    Hooman K. Moghadam, Moira M. Ferguson & Roy G. Danzmann

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  1. Hooman K. Moghadam
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  2. Moira M. Ferguson
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  3. Roy G. Danzmann
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Correspondence to Roy G. Danzmann.

Additional information

Sequence data from this article have been deposited within the EMBL/GenBank Data Libraries under the following accession numbers: AY677341, AY677342, AY677343, AY677344, AY677345, AY677346, AY677347, AY677348, AY677349, AY677350, AY677351, AY677352, AY677353, AY677354, AY677355, AY677356, AY677357, AY677358, AY677359, AY677360, AY677361, AY677362, AY677363, AY677364 and AY677365.

[Reviewing Editor: Dr. Axel Meyer]

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Moghadam, H.K., Ferguson, M.M. & Danzmann, R.G. Evolution of Hox Clusters in Salmonidae: A Comparative Analysis Between Atlantic Salmon (Salmo salar) and Rainbow Trout (Oncorhynchus mykiss). J Mol Evol 61, 636–649 (2005). https://doi.org/10.1007/s00239-004-0338-7

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