BmTEdb:a Collective Database Of Transposable Elements In The Silkworm (Bombyx Mori)Genome

Repetitive sequences (repeats) represent a significant fraction of the eukaryotic genomes and can be divided into tandem repeats, segmental duplications and interspersed repeats on the basis of their sequence characteristics and of how they are formed. Most interspersed repeats are derived from transposable elements (TEs). TEs can move in the genome and insert into new chromosomal locations and often make duplicate copies of them in this process. According to the intermediate they use to move is RNA or DNA, eukaryotic TEs have been subdivided into two major classes, retrotransposons and DNA transposons. In eukaryotes, TEs constitute a large fraction of a genome, accounting for45%of the human genome,22%of the fruit fly (Drosophila melanogaster) genome and80%of the maize (Zea mays) genome.The transposition and amplification of TEs have had a great impact on the evolution of genes and the stability of genomes. They play important roles in chromosome structure, genome size, genome rearrangement, new gene origination, and gene structure and regulation. Moreover, they are challenges for genome sequencing, assembly and annotation due to the repetitive nature of TEs. However, the identification and classification of TEs are complex and difficult due to the fact that their structure and classification are complex and diverse compared with those of other types of repeats. The identification, classification and annotation of TEs in eukaryote genomes can be broken down into three different steps:(1) assembly of a repeat library,(2) repeat curation and classification,(3) genome annotation. Recently scientists at home and abroad have developed many programs to assist in these three steps. But different computational approaches have both advantages and drawbacks and so far any single tool cannot fulfill the accurate identification, classification and annotation of the TEs in a given genome. To accurately identify, classify and annotate the TEs in eukaryotic genomes requires combined methods. The silkworm, Bombyx mori, is one kind of insect of great economic importance and the derived sericulture industry is an important component of agricultural economy in China. It is a model organism for insect genetics, development and molecular biology owing to the availability of strains and mutants from genetically homogeneous inbred lines. The releases of the draft sequence and fine map have greatly promoted the research for silkworm genomics. Previous studies showed that TEs represent～35%of the whole genome and this figure is larger than those for fruit fly (22%) and Anopheles gambiae (16%) and is less than that for Aedes aegypti (47%). Besides, the silkworm is diverse in the types of TEs. Taken altogether, silkworms can be used a model organism for insect TE biology. TEs are crucial fraction of the silkworm genome and they have great significance to the silkworm organization, evolution and gene regulation. So it is vital to accurately identify, classify and annotate TEs in the silkworm genome.Complete identification and classification of TEs in the silkworm genome was performed using a combination of multiple methods and a comprehensive database for B. mori transposable elements, BmTEdb was constructed. The main contents and results are as follows:1. The construction of B. mori transposable elements database, BmTEdbTo better understand the roles of TEs played during the silkworm domestication and in the organization, structure and evolution of the silkworm genome, a combination of de novo, structure-based and homology-based approaches was used to identify the TEs in the silkworm genome. And reported TEs in Repbase, NCBI nucleotide database and published literature were also included. Redundant and false positive sequences were removed from TEs identified, and then they were classified based on homology and structural characterictics and related tools. A comprehensive database for B. mori transposable elements, BmTEdb was constructed using Linux, Apache, MySQL and PERL. Users are entitled to browse, search and download the sequences in the database. Sequence analyses such as BLAST, HMMER and EMBOSS GetORF were also provided in BmTEdb. To some degree, this database will contribute to the studies for the silkworm genomics, especially to the investigations of the roles TEs played in silkworm domestication and the TE functions in the silkworm genome.2. Characterization, classification and phylogenetic analysis of LTR retrotransposons in the silkworm, B. mori LTR retrotransposons in the domesticated silkworm were identified using structured-based and homology-based approaches and38families were found,6of which were novel. The sequences of these families constitute0.64%of the whole genome, which is much less than that previously reported. We also found that26of38families have EST evidence, implying that they had potential activity. Then RT-PCR was performed to validate the expressions of11families (6families have EST evidence and5families have no EST evidence) and the results showed that these11families were expressed in some tissues, further supporting their transcriptional activities. Based on these results, we speculated that most of LTR retrotransposon families in the silkworm genome have potential activity. We estimated the insertion time of LTR retrotransposons, and found that most of them were recently inserted into the silkworm genome. A comparison of Ty3/Gypsy superfamily in D. melanogaster, A. gambiae and B. mori showed that this superfamily experienced different expansion patterns. Given the importance of LTR retrotransposon activity in the evolution of other genomes, these results provide some insights into the roles of LTR in insect genome evolution.