Open Access Research article

Burst expansion, distribution and diversification of MITEs in the silkworm genome

Min-Jin Han1, Yi-Hong Shen1, Ying-Hui Gao1, Li-Yong Chen2*, Zhong-Huai Xiang1 and Ze Zhang13*

Author Affiliations

1 The Key Sericultural Laboratory of Agricultural Ministry, Southwest University, Chongqing 400715, China

2 Department of Anesthesiology, Research Institute of Surgery and Daping Hospital, Third Medical University, Chongqing, 400042, China

3 The Institute of Agricultural and Life Sciences, Chongqing University, Chongqing 400044, China

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BMC Genomics 2010, 11:520  doi:10.1186/1471-2164-11-520

Published: 27 September 2010

Additional files

Additional file 1:

The examples for Pseudo-MITEs: (A) undetermined fragments (designated as Ns in scaffolds), (B) solely composed of simple repeats, and (C) nested in repeats, arrow represents TSD and underline represents TIR.

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Additional file 2:

The information about insertion sites of the MITEs into scaffolds.

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Additional file 3:

The secondary structures of silkworm MITEs predicted by the program of UNADOLD: 1: BmMITE-1,2-16: BmMITE-3-17, respectively.

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Additional file 4:

Primers for PCR verification of BmMITE-2;

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Additional file 5:

The results for PCR verification of predicted BmMITE-2.

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Additional file 6:

Sequencing result of PCR products for the presence or absence of BmMITE-2 at insertion site 3. "DXTZ", "SSHB" represent DaXianTuZhong and ShangSanHuBan strains, respectively. The box represents the sequence of BmMITE-2.

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Additional file 7:

Nucleotide variation (π) along MITE sequence for each family. Nucleotide diversity π and its standard deviation were calculated by the program of DnaSP version 5.10. Then, the same program was used to define conserved and variable of the MITE sequences by sliding window analysis with both window size and step size 20 nucleotides. Windows with diversity equal or higher than average sequence diversity (π) + 2SD were defined as variable. Those with diversity less than average sequence diversity (π) - 2SD were considered as conserved.

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Additional file 8:

Distribution of the silkworm MITEs on the 28 chromosomes. The observed distribution is significantly different from the expected one based on the total length of 28 chromosomes (Chi-square = 297, df = 27, P < 0.01). *The chromosomes that show the observed copies more than expected.

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Additional file 9:

MITE distances to the nearest genes.

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Additional file 10:

The annotation of the closest genes using WEGO.

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