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Open Access Research article

Sampling Daphnia's expressed genes: preservation, expansion and invention of crustacean genes with reference to insect genomes

John K Colbourne1*, Brian D Eads1, Joseph Shaw2, Elizabeth Bohuski1, Darren J Bauer3 and Justen Andrews1

Author Affiliations

1 The Center for Genomics and Bioinformatics, and Department of Biology, Indiana University, Bloomington, Indiana 47405, USA

2 Department of Biology, Dartmouth College, Hanover, New Hampshire 03755, USA

3 Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA

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BMC Genomics 2007, 8:217  doi:10.1186/1471-2164-8-217

Published: 6 July 2007

Additional files

Additional file 1:

Characterization of the Daphnia pulex EST sequences.

This file contains the following information about the analysis of EST sequences obtained for the study.

(1) EST information.

(2) Top match from Blastx searches of clustered Daphnia ESTs against the NCBI non-redundant (nr) protein database.

(3) Results using Blast2GO (http://www.blast2go.de/ webcite).

(4) Top match from Blastx searches of clustered Daphnia ESTs against all Drosophila melanogaster predicted gene translations from annotation 4.2.1 – 16 columns describe the results. • Cluster id (Daphnia, this study). • Subject id (D. melanogaster dmel-all-translation-r4.2.1 data).

(5) Differential expression results in 3 microarray experiments.

(6) Top match from Blastx searches of Daphnia ESTs against NCBI non-redundant (nr) protein database – 12 columns describe the results. • Subject id of the best match in the nr database.

Format: XLS Size: 1.8MB Download file

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Additional file 2:

Supplemental Table 1. Daphnia genes annotated as regulators of transcription and translation based on sequence conservation with Drosophila genes with known functions. Scores are reported from results obtained by Blastx against all predicted translations from version 4.2.1 of the D. melanogaster genome annotation. First and second columns under DE show genes that are differentially expressed (+ = yes) in microarray experiments comparing male versus female transcripts and metals versus no metals exposure, respectively. TF = transcription factor; TR = transcriptional regulation; TE = transcript elongation; E = translation elongation; R = translation regulation.

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Additional file 3:

Supplemental Table 2. Daphnia genes annotated as signaling proteins and other regulators based on sequence conservation with Drosophila genes with known functions. Scores are reported from results obtained by Blastx against all predicted translations from version 4.2.1 of the D. melanogaster genome annotation. First and second columns under DE show genes that are differentially expressed (+ = yes) in microarray experiments comparing male versus female transcripts and metals versus no metals exposure, respectively.

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Additional file 4:

Supplemental Table 4. Daphnia genes annotated as candidates for gametogenesis based on sequence conservation with Drosophila genes with known functions. Processes include: SP = spermatogenesis; OO = oogenesis; FCD = follicle cell development; GCD = germ cell development; GT = gametogenesis. Two assembled sequences matched CG4027 and two other sequences matched CG2168.

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Additional file 5:

Supplemental Table 4. Daphnia genes annotated as genes associated with exoskeletal function and molting. These include: CP = structural cuticle proteins; PM = peritrophic membrane; CM = cuticle metabolism; CA = chitinase; M = molting; CB = cuticle binding. Assignments are to proteins based on sequence conservation with Drosophila genes with known functions.

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