Open Access Highly Accessed Research article

Divergence in cis-regulatory sequences surrounding the opsin gene arrays of African cichlid fishes

Kelly E O'Quin1, Daniel Smith1, Zan Naseer1, Jane Schulte1, Samuel D Engel1, Yong-Hwee E Loh2, J Todd Streelman2, Jeffrey L Boore34 and Karen L Carleton1*

  • * Corresponding author: Karen L Carleton kcarleto@umd.edu

  • † Equal contributors

Author Affiliations

1 Department of Biology, University of Maryland, College Park, MD 20742, USA

2 School of Biology, Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332 USA

3 Genome Project Solutions, Hercules, CA 94547, USA

4 Department of Integrative Biology, University of California, Berkeley, CA 94720, USA

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BMC Evolutionary Biology 2011, 11:120  doi:10.1186/1471-2148-11-120

Published: 9 May 2011

Additional files

Additional file 1:

Synteny (Pip plots) of O. niloticus and M. zebra opsin-containing BAC sequences.

Format: PDF Size: 693KB Download file

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Additional file 2:

Synteny (Pip plots) of O. niloticus opsin-containing BACs against the genome assemblies of five teleost species.

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Additional file 3:

Opsin gene content of five teleost genomes. Phylogeny of the teleost taxa is recreated from [118].

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Additional file 4:

Orthology of RH2 and SWS2 opsin paralogs from five teleost fish genomes. A) RH2 phylogeny. B) SWS2 phylogeny. In both cases, broken lines indicate branches leading from the outgroup that were shortened to fit each tree into the figure; these do not represent missing or incomplete branch length information.

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Additional file 5:

FASTA file of 20 conserved non-coding elements (CNEs), promoter sequences, 3-UTRs, and seven non-opsin promoters from O. niloticus and M. zebra (80 sequences total).

Format: FAS Size: 42KB Download file

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Additional file 6:

Complete transcription factor binding site profiles for 20 CNEs in O. niloticus and M. zebra.

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Additional file 7:

Complete list of miRNA target sites identified within the 3'-UTR of each opsin in O. niloticus and M. zebra.

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Additional file 8:

Names, opsin expression values, and polymorphisms found within the proximal promoters of 18 Lake Malawi cichlid species.

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Additional file 9:

Length and Dxy scores between O. niloticus and M. zebra for each coding and non-coding region examined.

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Additional file 10:

Identification of opsin-containing BACs from Finger Printed Contigs. A-C) BACs fingerprinted contig containing the SWS2A-SWS2B-LWS (A) RH2 (B) and SWS1 (C) genes. Arrows indicate PCR products successfully amplified using primers designed to BAC end sequences for clones whose names are shown in the corresponding color. Colored circles are the approximate locates of each gene.

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Additional file 11:

GenBank accession numbers for all sequences generated in this study.

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Additional file 12:

Primers used to amplify and sequence the proximal promoter regions and 3'-UTR of several opsins from 18 Lake Malawi cichlid species.

Format: XLS Size: 17KB Download file

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