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Estimates of insertion date and diversity for each MITE family showed that the silkworm MITE families might have experienced burst expansions at different time points of evolution and exhibited various patterns of diversification.
The average divergence for each MITE family was calculated.
The average AT content for each MITE family ranges from 44%to73%3%.
Next, a homology search was used to estimate number of copies for each MITE family in the silkworm genome.
For each MITE group, multiple alignments (including gapped positions) were created from which similarity matrices were calculated using BioEdit software, version 7.0.5.3 (http://www.mbio.ncsu.edu/BioEdit/bioedit.html).html
DNA was prepared for each mite separately, and PCR amplifications using species-specific primer pairs (Additional file 2: Table S1), designed based on each mitochondrial genome sequence, were carried out to test species identity.
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Next, a homology BLAST search was used to scan the silkworm genome sequence with a representative member for estimating copy number of each MITE family.
To check for transcription of MITEs, representatives of each MITE family were used as queries in Blast searches against the grapevine expressed sequence tag (EST) collection at NCBI.
The number of mites in each mite species within each sample was counted, and the percentage of each species relative to the total mite counted for each sample was calculated.
For each P-MITE family, the set of hits were multialigned using ClustalW to deduce a consensus sequence.
Mite density was calculated for each sample as follows: mite density is total number of mites detected/weight of isolated dust (in g).
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