Open Access Research article

Molecular cloning of doublesex genes of four cladocera (water flea) species

Kenji Toyota1, Yasuhiko Kato12, Masaru Sato1, Naomi Sugiura13, Shinichi Miyagawa1, Hitoshi Miyakawa1, Hajime Watanabe12, Shigeto Oda1, Yukiko Ogino1, Chizue Hiruta1, Takeshi Mizutani1, Norihisa Tatarazako4, Susanne Paland5, Craig Jackson5, John K Colbourne56 and Taisen Iguchi1*

Author Affiliations

1 Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, and Department of Basic Biology, Faculty of Life Science, Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan

2 Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan

3 Toyota Nishi High School, 14-65 Kosaka, Toyota, Aichi, 471-0035, Japan

4 National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan

5 The Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN, 47405, USA

6 Present address: School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK

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BMC Genomics 2013, 14:239  doi:10.1186/1471-2164-14-239

Published: 10 April 2013

Additional files

Additional file 1:

RT-PCR of oligonucleotides corresponding to highly conserved region of dsx1 (A) and dsx2 (B). The amplified cDNAs were analyzed by agarose gel electrophoresis. Lane M: molecular weight marker. Lane 1 to 10: D. magna (female), D. magna (male), D. pulex (female), D. pulex (male), D. galeata (female), D. galeata (male), C. dubia (female), C. dubia (male), M. macrocopa (female), M. macrocopa (male).

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Additional file 2:

Estimation of evolutionary divergence between the DSX1 except for DM- and oligomerization-domain and COI sequences. The number of amino acid differences per site between sequences are shown. The analysis involved 5 amino acid sequences. All positions containing gaps and missing data were eliminated. There were total of 225 and 208 positions in the final dataset of DSX1 and COI, respectively. Evolutionary analyses were conducted in MEGA5 [45].

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Additional file 3:

Estimation of evolutionary divergence between the DSX2 except for DM- and oligomerization-domain and COI sequences. The number of amino acid differences per site between sequences are shown. The analysis involved 5 amino acid sequences. All positions containing gaps and missing data were eliminated. There were total of 210 and 208 positions in the final dataset of DSX2 and COI, respectively. Evolutionary analyses were conducted in MEGA5 [45].

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Additional file 4:

Gene model annotations on the D. magna and D. pulex genome assembly. (A) D. magna dsx1 and dsx2 gene model annotations on the D. magna genome assembly. (B) D. pulex dsx1 and dsx2 gene model annotations on the D. pulex genome assembly. Figures were created with AnnotationSketch [58].

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Additional file 5:

Nucleotide sequence comparison of dsx1-α promoter regions in D. magna and D. pulex. Pro-Coffee alignment of Dsx1-α 1.0 Kbp upstream promoter region from D. magna and D. pulex.

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Additional file 6:

Nucleotide sequence comparison of dsx1-β promoter regions in D. magna and D. pulex. Pro-Coffee alignment of dsx1-β 1.0 Kbp upstream promoter region from D. magna and D. pulex.

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Additional file 7:

Nucleotide sequence comparison of dsx2 promoter regions in D. magna and D. pulex. Pro-Coffee alignment of dsx2 1.0 Kbp upstream promoter region from D. magna and D. pulex.

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Additional file 8:

dsx1-α TF-map alignment.

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Additional file 9:

dsx1-β TF-map alignments.

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Additional file 10:

dsx2 TF-map alignments.

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Additional file 11:

TF-map alignments unique TFs comparison.

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Additional file 12:

de novo conserved regulatory motifs.

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Additional file 13:

Primer sequences for 5’ and 3’ RACE in D. galeata, C. dubia and M. macrocopa.

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Additional file 14:

Accession numbers of the sequences for phylogenetic analysis.

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Additional file 15:

Primer sequences for quantitative PCR.

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Additional file 16:

DapmaDsx1-α TF-map.

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Additional file 17:

DappuDsx1-α TF-map.

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Additional file 18:

DapmaDsx1-β TF-map.

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Additional file 19:

DappuDsx1-β TF-map.

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Additional file 20:

DapmaDsx2 TF-map.

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Additional file 21:

DappuDsx2 TF-map.

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