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Exploring systemic RNA interference in insects: a genome-wide survey for RNAi genes in Tribolium

Yoshinori Tomoyasu12*, Sherry C Miller12, Shuichiro Tomita3, Michael Schoppmeier4, Daniela Grossmann5 and Gregor Bucher5

Author Affiliations

1 Division of Biology, Kansas State University, Manhattan, Kansas 66506, USA

2 K-State Arthropod Genomics Center, Kansas State University, Manhattan, Kansas 66506, USA

3 Insect Genome Research Unit, National Institute of Agrobiological Sciences, 1-2, Owashi, Tsukuba, Ibaraki 305-8634, Japan

4 Universitat Erlangen, Institut fur Biologie, Abteilung fur Entwicklungsbiologie, Staudtstr., D-91058 Erlangen, Germany

5 Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Georg-August-Universität Göttingen, Abteilung Entwicklungsbiologie, Justus-von-Liebig-Weg, 37077 Göttingen, Germany

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Genome Biology 2008, 9:R10  doi:10.1186/gb-2008-9-1-r10

Published: 17 January 2008

Additional files

Additional data file 1:

Multiple alignments used for pylogenetic analyses.

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Additional data file 2:

Phylogenetic tree for Eri-1-like nucleases including C. elegans Crn-4.

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Additional data file 3:

sil gene expression profile in Tribolium.

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Additional data file 4:

Blue boxes indicate conserved portions of the amino-terminal extracellular domain shown in Figure 6. Amino acids making up predicted transmembrane regions for each protein are shown in orange, while the 11 predicted transmembrane domains of Tc-SilA protein are denoted with orange bars. The region corresponding to TM2 to TM11 (delimited by green arrows) was used for phylogenetic analysis.

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Additional data file 5:

Dot-matcher alignments of Tc-SilA protein with Sid-1-like proteins from various organisms. Conservation between two proteins is visualized as a diagonal line. Tc-SilA does not show high conservation with Ce-Sid-1 in the amino-terminal extracellular region (A, red box), but shows conservation with Ce-Tag130 (B, red box). Additional conservation is seen in the carboxy-terminal transmembrane domains (B, blue boxes), which is lacking in Ce-Sid-1(A, blue box). These conserved domains are seen in all Sid-1-like proteins examined (B-F), except Ce-Sid-1 (A).

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Additional data file 6:

(A) tag-130 gene exon/intron structure. The regions deleted in tag-130gk245 and tag-130OK1073 are indicated with orange bars. (B) An enlargement of the OK1073 deleted region and schematic diagrams of two mRNA forms detected in tag-130OK1073 mutants. The deleted region is indicated in orange. In isoform OK1073-A, which is the more abundant of the two forms, the remaining portion of intron 13 is not spliced out and is juxtaposed with the remaining portion of exon 17. Intron 13 contains a stop codon in this reading frame, which should cause truncation of the protein. In the other isoform (OK1073-B), the remaining portion of intron 13 is spliced out along with the remaining portion of exon 17 (and intron 17), juxtaposing exon 13 with exon 18. This changes the reading frame in exon 18, and should also result in premature truncation of the protein.

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Additional data file 7:

GLEAN gene number and corresponding gene names.

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Additional data file 8:

RNAi and miRNA components in Tribolium, Drosophila and C. elegans.

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Additional data file 9:

Primers used for dsRNA synthesis.

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