Journal
INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY
Volume 38, Issue 12, Pages 1046-1057Publisher
PERGAMON-ELSEVIER SCIENCE LTD
DOI: 10.1016/j.ibmb.2008.05.012
Keywords
Silkworm; Bombyx mori; Genome; Transposable elements; GC content; Recombination; Retrotransposon; Evolution
Categories
Funding
- Ministry of Education, Science, and Culture of Japan
- Insect Technology Program of MAFF
- PROBRAIN, the Basic Research Program
- Japan Society for the Promotion of Science for Young Scientists
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To elucidate the contribution of transposable elements (TEs) to the silkworm genome structure and evolution, we have conducted genome-wide analysis of TEs using the newly released genome assembly. The TEs made up 35% of the genome and contributed greatly to the genome size. Non-long terminal repeat retrotransposons (non-LTRs) and short interspersed nuclear elements (SINEs) were the predominant TE classes. From characterization of the TE distribution in the genome, it was revealed that non-LTRs, especially R1 clade elements, are frequently inserted into GC-rich regions. The GC content of non-LTRs themselves was over 40%, which indicate their contribution to the GC content of the insertion region. TEs accumulated in regions with low gene density, and there were relatively strong positive correlations between TE density and chromosomal recombination rate, We also characterized the clade distribution of the non-LTRs. The silkworm non-LTRs represented 10 of the 16 previously defined clades, which had the most variety than that reported for other genomes. Two partial CRE clade elements were found, which is one of the most ancient lineages of non-LTRs, and have been only found in Trypanosoma and fungi before. This analysis suggests that Bombyx genome is influenced by numerous amounts and variety of TEs. (C) 2008 Elsevier Ltd. All rights reserved.
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