In this study, we report evidence of a novel duplication of Melanocortin receptor 1 (Mc1r) in the cavefish genome. This locus was discovered following the observation of excessive allelic diversity in a 820 bp fragment of Mc1r amplified via degenerate PCR from a natural population of Astyanax aeneus fish from Guerrero, Mexico. The cavefish genome reveals the presence of two closely related Mc1r open reading frames separated by a 1.46 kb intergenic region. One open reading frame corresponds to the previously reported Mc1r receptor, and the other open reading frame (duplicate copy) is 975 bp in length, encoding a receptor of 325 amino acids. Sequence similarity analyses position both copies in the syntenic region of the single Mc1r locus in 16 representative craniate genomes spanning bony fish (including Astyanax) to mammals, suggesting we discovered tandem duplicates of this important gene. The two Mc1r copies share 89% sequence similarity and, within Astyanax, are more similar to one another compared to other melanocortin family members. Future studies will inform the precise functional significance of the duplicated Mc1r locus and if this novel copy number variant may have adaptive significance for the Astyanax lineage.
Bibliographical noteFunding Information:
The authors wish to thank members of the Gross Lab for helpful discussions of this project. We also gratefully acknowledge the help of Amanda Powers who assisted with earlier phases of this project. In addition, we are grateful to Marist College undergraduate students enrolled in Genetics (BIOL320) who performed the first direct PCR sequencing of Guerrero fish in 2010. We appreciate the resources provided by the Minnesota Supercomputing Institute, without which this work would not be possible. J.B.G. is supported by grants from the National Science Foundation (DEB-1457630) and the National Institutes of Dental and Craniofacial Research (NIH-DE025033).
J.B.G. is supported by grants from the National Science Foundation (DEB-1457630) and the National Institutes of Dental and Craniofacial Research (NIH-DE025033).
© 2018 Published by NRC Research Press.
- Copy number variation
- brown mutation