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Open Access Research article

Annotation, phylogenetics, and expression of the nuclear receptors in Daphnia pulex

Susanne A Thomson1, William S Baldwin2, Ying H Wang1, Gwijun Kwon1 and Gerald A LeBlanc1*

Author Affiliations

1 Department of Environmental and Molecular Toxicology, North Carolina State University, Raleigh, North Carolina, USA

2 Environmental Toxicology Program and Biological Sciences Department, Clemson University, Pendleton, South Carolina, USA

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BMC Genomics 2009, 10:500  doi:10.1186/1471-2164-10-500

Published: 28 October 2009

Additional files

Additional file 1:

Sequence identification of nuclear receptors. NCBI accession numbers of all D. melanogaster, H. sapiens, and C. elegans nuclear receptors used for the alignments and phylogenetic analysis are listed.

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Additional file 2:

Detailed summary of each NR sequence, including its position in the D. pulex Dappu v1.1 draft genome assembly, annotated open reading frames and corresponding amino acid sequences. An Excel workbook (xls) table of each of the NR genes and found in the Daphnia pulex genome, their nucleotide and amino acid sequences, links to their scaffold position, manual protein identifying number, and presence of an expressed sequence tag (EST) within the "chosen one".

Format: XLS Size: 180KB Download file

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Open Data

Additional file 3:

Expandable pdf file of the nuclear receptor phylogenetic tree provided as Figure 2. Phylogenetic relationship of nuclear receptors in D. pulex, D. melanogaster, C. elegans, and H. sapiens. The nuclear receptors from four different species were subjected to phylogenetic comparisons using Bayesian Inference, Maximum Parsimony, and Neighbor-Joining. The Bayesian tree is shown with posterior probabilities from the Bayesian tree, and bootstrap support values (frequency of occurrence) from the Maximum Parsimony and Neighbour-Joining trees provided in order from left to right, respectively. The probability values are separated by forward slashes at each corresponding node; an X indicates an area of disagreement from the Bayesian tree. Notations Dp, Dm, Hp, and Ce in association with receptor names denote sequences from D. pulex, D. melanogaster, H. sapiens, and C. elegans, respectively.

Format: PDF Size: 72KB Download file

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Open Data

Additional file 4:

Phylogenetic tree of full length nuclear receptors. Phylogenetic relationship of full length nuclear receptors in D. pulex, D. melanogaster, C. elegans, and H. sapiens. The nuclear receptors from four different species were subjected to phylogenetic comparisons using Bayesian Inference, Maximum Parsimony, and Neighbor-Joining. The Bayesian tree is shown with posterior probabilities from the Bayesian tree, and bootstrap support values (frequency of occurrence) from the Maximum Parsimony and Neighbor-Joining (Distance) trees provided in order from left to right, respectively. The probability values are separated by forward slashes at each corresponding node; an X indicates an area of disagreement from the Bayesian tree. The non-Bayesian trees were not able to distinguish separate subfamilies. The phylogenetic comparisons were done as described for the LBD/DBD trees, except the burnin was 10,000 for the full length Bayesian Inference analysis. Notations Dp, Dm, Hp, and Ce in association with receptor names denote sequences from D. pulex, D. melanogaster, H. sapiens, and C. elegans, respectively.

Format: PDF Size: 61KB Download file

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Open Data

Additional file 5:

Nucleotide sequences of nuclear receptor RT-PCR products. Nucleotide sequences of RT-PCR products depicted in Figure 3. The sequences confirmed expression and contributed to the manual annotation of the nuclear receptors. Result present the consensus sequence of both DNA forward and reverse strands unless indicated otherwise with 'forward' or 'reverse' indicating the strand sequenced.

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