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Open Access Research article

Comprehensive microarray-based analysis for stage-specific larval camouflage pattern-associated genes in the swallowtail butterfly, Papilio xuthus

Ryo Futahashi12, Hiroko Shirataki1, Takanori Narita34, Kazuei Mita5 and Haruhiko Fujiwara1*

Author Affiliations

1 Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan

2 Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan

3 National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan

4 Nihon University College of Bioresource Sciences, Fujisawa, Kanagawa 252-0880, Japan

5 National Institute of Agrobiological Sciences, Owashi, Tsukuba, Ibaraki 305-8634, Japan

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BMC Biology 2012, 10:46  doi:10.1186/1741-7007-10-46

Published: 31 May 2012

Additional files

Additional file 1:

List of 3,341 nonredundant P. xuthus genes. cluster nr: indexing identity number for each cluster; Total ESTs: number of ESTs in each cluster; sequence: 'majority rule' consensus sequence (with N masking regions of low complexity); length: length of consensus sequence; member: list of all individual EST names in the cluster; peptide sequence: predicted peptide sequence; SignalP: putative signal peptide sequence predicted by SignalP 3.0 program; DmGene: best hit from BLASTP analysis to Drosophila melanogaster peptides (Flybase v. 5.42); DmCG: CG number of best hit from BLASTP analysis to D. melanogaster peptides; DmE-value: Evalue of best hit from BLASTP analysis to D. melanogaster peptides; BmGene: best hit from BLASTP analysis to Bombyx mori peptides; BmE-value: Evalue of best hit from BLASTP analysis to B. mori peptides; DpGene: best hit from BLASTP analysis to Danaus plexippus peptides; DpE-value: Evalue of best hit from BLASTP analysis to D. plexippus peptides; Remarks: gene name of each cluster; accession number: GenBank accession number; co-expression cluster: co-expression cluster by microarray analysis (n.d.: not detected: n.e.: not examined); marking specificity: average intensity of mimetic black (mb) vs. mimetic white (mw) and/or cryptic green (CG) vs. cryptic black (CB) over two-fold is indicated.

Format: XLS Size: 5.5MB Download file

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Additional file 2:

List of 1,436 P. polytes nonredundant genes. Explanation of column contents are the same as Additional file 1.

Format: XLS Size: 2.3MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 3:

List of identified putative isoforms or premature transcripts of P. xuthus.

Format: XLS Size: 950KB Download file

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Additional file 4:

List of identified putative isoforms or premature transcripts of P. polytes.

Format: XLS Size: 246KB Download file

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Open Data

Additional file 5:

The Venn diagram of P. xuthus genes. The numbers of homologous genes shared between P. xuthus epidermal expressed sequence tags and other insect genomes are shown (cutoff threshold E values: P < 1e-10 by BLASTP search).

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Additional file 6:

List of 77 additionally cloned P. xuthus genes. Explanation of column contents is the same as Additional file 1.

Format: XLS Size: 144KB Download file

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Additional file 7:

Microarray result of P. xuthus genes. Probe sequences, normalized signal intensity of each sample, sum of signal intensity, and relative expression level of each sample are shown.

Format: XLS Size: 7.4MB Download file

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Additional file 8:

Heat map of the relative expression level of 78 ribosomal protein genes in P. xuthus. Red indicates positive values and green indicates negative values (color spectrum bar is shown to the right; N.D., not detected). Stage and marking of each sample is shown above. The sage-specific co-expression cluster and marking specificity of each gene are also shown. See also Figures 2 to 4.

Format: JPEG Size: 639KB Download file

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Additional file 9:

Heat map of the relative expression level of the 30 most highly expressed genes in P. xuthus. Stage and marking of each sample is shown above. Red indicates positive values and green indicates negative values (color spectrum bar is shown to the right; N.D., not detected). The stage-specific co-expression cluster and marking specificity of each gene are also shown. See also Figures 2 to 4.

Format: JPEG Size: 471KB Download file

Open Data