Genome-wide screening and characterization of transposable elements and their distribution analysis in the silkworm, Bombyx mori

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Abstract

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.

Introduction

In eukaryotes, mobile elements or transposable elements (TEs) constitute a large fraction of the genome (Kazazian, 2004). TEs have been divided into two classes based on their transposition intermediate (Capy et al., 1997). Class I elements use an RNA-mediated mode of transposition and encode a reverse transcriptase (RT). They are further divided into two subclasses, the elements that are characterized by direct, long terminal repeats (LTR retrotransposons), and the elements that lack terminal repeats (non-LTR retrotransposons). Autonomous non-LTR retrotransposons are also called LINEs (long interspersed nuclear elements) and are thought to be responsible for mobilization of non-autonomous short interspersed nuclear elements (SINEs). On the other hand, class II elements (transposons) use a DNA-mediated mode of ‘cut and paste’ transposition. In the silkworm (Bombyx mori), many TEs have been identified [e.g. Pao (Xiong et al., 1993), Kamikaze and Yamato (Abe et al., 2001), BMC1 (Ogura et al., 1994), L1Bm (Ichimura et al., 1997), R1Bm (Xiong and Eickbush, 1988), R2Bm (Burke et al., 1987), SART1 (Takahashi et al., 1997), TRAS1 (Okazaki et al., 1995), Bm1 (Adams et al., 1986) and mariner (Robertson and Asplund, 1996, Tomita et al., 1997)].

With a recent availability of genomic sequences in many species, it has been suggested that TEs have a major impact upon genome evolution in various scales e.g. genome size, genome rearrangement and deletion/insertion of a single nucleotide (Kazazian, 2004, Kidwell, 2002, Petrov, 2001). Although the elucidation of interaction of TEs with their host genome is undoubtedly an important work, it had been impracticable in the silkworm genome due to the lack of a sufficient genomic resource. However, the currently available silkworm genomic resource (ISGSC, in preparation), e.g. the new genome assembly by integrating two independent whole genome shotgun sequences data (Mita et al., 2004, Xia et al., 2004) and comprehensive catalogue of silkworm repetitive sequences, provides powerful new opportunities for rigorous analysis of TEs distribution in the genome. The preliminary analysis revealed that TEs make up about 35% of the silkworm genome, and that SINEs and non-LTR retrotransposons constitute about 75% of the TEs-derived sequences (ISGSC, in preparation). This tendency contrasts the genomic structure of B. mori with that of insects such as Drosophila melanogaster (Bergman et al., 2006), Anopheles gambiae (Holt et al., 2002) and Apis mellifera (HGSC, 2006), but similar to Aedes aegypti in which TEs share about 47% of the genome (Nene et al., 2007), and also to the human genome, in which L1 non-LTR retrotransposon and an SINE named Alu make up more than 27% of the genome (IHGSC, 2001).

In this paper, we aimed at detailed characterization of TEs, especially non-LTR retrotransposons, and their distribution in the silkworm genome in order to clarify their contribution to the genome structure and evolution.

Section snippets

Bombyx genomic sequence and transposable elements

We used silkworm scaffold build2 (ISGSC, in preparation) as genomic sequences data. The total length of all scaffolds with and without gaps amounted to 480.78 and 431.76 Mb, respectively. Total length of scaffolds mapped onto chromosomes with and without gaps (Ns) amounted to 419.98 and 377.18 Mb, respectively. The GC% of scaffolds in total was 37.7. The library of the silkworm TEs was same as used in the related paper (ISGSC, in preparation). To state briefly, to analyze the share of

Fraction and classes of TE-derived sequences in Bombyx genome

Table 1 summarizes the number of copies and fraction of genome for each TE classes. As mentioned above, the TEs constitute about 35% of the silkworm genome. Compared to other insects in which genomic sequences have been released, the silkworm genome was found to be second repetitive. The most TE-rich insect is A. aegypti, in which TEs share 47% of the genome (Nene et al., 2007). The TE content in D. melanogaster euchromatin is about 5.5% (Bergman et al., 2006), and about 77% including other

Conclusion

The genome-wide screening and characterization of the silkworm TEs revealed that a large amount of the silkworm genome is due to TEs, especially non-LTRs and SINEs. From the distribution analysis, it was shown that the silkworm TEs have positive correlations with regional GC content and recombination rate, indicating that TEs have greatly marked the genomic structure of the silkworm genome. These data are valuable in considering how TEs contribute to genome evolution.

Acknowledgements

This work was supported in part by grants in aid for scientific research from the Ministry of Education, Science, and Culture of Japan (to HF), the Insect Technology Program of MAFF (to KM), PROBRAIN, the Basic Research Program (to KM and HF), and Research Fellowship of Japan Society for the Promotion of Science for Young Scientists (to MO). We thank Kazutoshi Yoshitake for helping with the data analysis.

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