Open Access Highly Accessed Research article

Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes

Christine E Schnitzler1, Kevin Pang2, Meghan L Powers3, Adam M Reitzel4, Joseph F Ryan2, David Simmons5, Takashi Tada6, Morgan Park7, Jyoti Gupta7, Shelise Y Brooks7, Robert W Blakesley17, Shozo Yokoyama6, Steven HD Haddock3, Mark Q Martindale5 and Andreas D Baxevanis1*

Author Affiliations

1 Genome Technology Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Bethesda, MD 20892, USA

2 Sars International Centre for Marine Molecular Biology, Thormøhlensgt. 55, N-5008, Bergen Norway

3 Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA

4 Department of Biology, University of North Carolina at Charlotte, 9210 University City Boulevard, Charlotte, NC 28223, USA

5 Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawaii at Manoa, 41 Ahui Street, Honolulu, HI 96813, USA

6 Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA

7 NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, 5625 Fishers Lane, Rockville, MD 20852, USA

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BMC Biology 2012, 10:107  doi:10.1186/1741-7007-10-107

Published: 21 December 2012

Additional files

Additional file 1:

Overall pairwise photoprotein percent amino acid identity comparisons for a subset of photoproteins and photoprotein-like sequences.

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Additional file 2:

Predicted molecular weight (kDa) and isoelectric point (pH) values and averages for the 10 Mnemiopsis photoproteins.

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Additional file 3:

Global analysis results for sequence pairs with evidence for recombination from GENECONV for the Mnemiopsis photoproteins.

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Additional file 4:

Alignment of EF-hand domains I, III, and IV of select photoprotein and photoprotein-like sequences. Important calcium ligand residues in the 12-residue calcium binding loops within each EF-hand domain are indicated with black triangles. Columns of residues are shaded as in Figure 2. Species are abbreviated as follows: Ac = Aequorea coerulescens; Aque = Amphimedon queenslandica; Cg = Clytia gregarium; Mc = Mitrocoma cellularia; Mlei = Mnemiopsis leidyi; Nvec = Nematostella vectensis; Og = Obelia geniculata.

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Additional file 5:

In situ hybridizations showing mRNA expression patterns for two photoprotein-like genes from Nematostella. (A) NvecPP2: Panels A-C and E-H are lateral views, with the oral pole to the left. Panel D is an oral view. Expression is first detected in the early polyp stage (A-D) in the endoderm, particularly in the mesenteries. There is also an additional expression in the apical tuft (B). In older polyp stages (E-H), the expression in the mesenteries decreases, while the apical tuft expression remains. There is also an additional expression domain in the tips of newly forming tentacles (F, H). (B) NvecPP1: Panels A-C and E-H are lateral views, with the oral pole to the left and Panel D is an oral view. Expression of NvecPP1 is detected in the late planula stages (A), in small patches in the endoderm towards the oral pole. In early polyp stages (B-D), the expression continues and forms a ring in the endoderm, although expression is highest in the areas between where the tentacles grow. In older polyp stages (E-H), the endodermal expression slowly decreases. In these stages, there is also endodermal expression in the tips of newly forming tentacles (F-H). Format: TIF

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Additional file 6:

Opsin seven-transmembrane pairwise comparisons of percent amino acid identity (top right) and similarity (bottom left) for a subset of opsin sequences. Species are abbreviated as follows: Hs = Homo sapiens; Nv = Nematostella vectensis; Mlei = Mnemiopsis leidyi; Ppil = Pleurobrachia pileus.

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Additional file 7:

Alignment of the seven-transmembrane region of select opsin sequences. Columns of residues are shaded by similarity group conservation (defined by GeneDoc and the BLOSUM62 matrix) where black shows 100%, dark grey shows ≥80%, and light grey shows ≥60% similar residues in a column. Gene name abbreviations: MWS = medium-wavelength sensitive; RGR = retinal G protein-coupled receptor. Conserved sites of chromophore linkage at Lys296 (black circle), disulfide bridge formation at Cys110-Cys187 (black stars) and signal propagation at Glu134-Arg35-Tyr136 (black square) are indicated. Sites corresponding to the acidic counterion in the vertebrate pigments (Glu113) and the counterion in other species (Glu181) are also indicated (black triangles). Species are abbreviated as follows: Dm = Drosophila melanogaster; Es = Euprymna scolopes; Hs = Homo sapiens; Mlei = Mnemiopsis leidyi; Nv = Nematostella vectensis.

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Additional file 8:

Fifty percent majority rule consensus tree of photoprotein genes.

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Additional file 9:

Fifty percent majority rule consensus tree of opsin genes.

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Additional file 10:

Fifty percent majority rule consensus tree of opsin genes minus MleiOpsin3.

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Additional file 11:

RACE primers used for 5'- and 3'-RACE-PCR confirmation of Mnemiopsis photoprotein genes.

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Additional file 12:

Photoprotein multiple sequence alignment in FASTA format. Species abbreviations as in Figure 3.

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Additional file 13:

Opsin seven-transmembrane multiple sequence alignment in FASTA format.

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Additional file 14:

Primers used for cloning a subset of Mnemiopsis photoproteins for expression experiments. A first set of PCR primers was used to clone the full-length proteins; a second set of expression cloning primers was used to add restriction sites for cloning proteins into an expression vector. For = forward; Rev = reverse.

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