Open Access Highly Accessed Research article

Comparative genomics of parasitic silkworm microsporidia reveal an association between genome expansion and host adaptation

Guoqing Pan1, Jinshan Xu23, Tian Li1, Qingyou Xia1, Shao-Lun Liu3, Guojie Zhang4, Songgang Li4, Chunfeng Li1, Handeng Liu1, Liu Yang1, Tie Liu1, Xi Zhang2, Zhengli Wu1, Wei Fan4, Xiaoqun Dang1, Heng Xiang1, Meilin Tao1, Yanhong Li1, Junhua Hu1, Zhi Li12, Lipeng Lin1, Jie Luo1, Lina Geng1, LinLing Wang2, Mengxian Long1, Yongji Wan1, Ningjia He1, Ze Zhang1, Cheng Lu1, Patrick J Keeling3, Jun Wang4, Zhonghuai Xiang1 and Zeyang Zhou12*

Author Affiliations

1 State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China

2 College of Life Sciences, Chongqing Normal University, Chongqing, 400047, China

3 Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada

4 Beijing Genomics Institute at Shenzhen, Shenzhen, 518000, China

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BMC Genomics 2013, 14:186  doi:10.1186/1471-2164-14-186

Published: 16 March 2013

Additional files

Additional file 1:

Summary of reads data production in N. bombycis.

Format: DOCX Size: 12KB Download file

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Additional file 2:

Statistics of genome assembly in N. bombycis.

Format: DOCX Size: 11KB Download file

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Additional file 3:

The calculation of genomic size of N. antheraeae based on the frequency distribution of 15-mers depth of reads.

Format: TIFF Size: 144KB Download file

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Additional file 4:

Gene ontology classification of three microsporidian Nosema. Y axis: Log 10 (the proportion of gene numbers in certain sort occupied on the total Go-annotated gene numbers).

Format: TIFF Size: 1.6MB Download file

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Additional file 5:

Comparison of average length of homologous gene among five different microsporidian species.

Format: TIFF Size: 763KB Download file

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Additional file 6:

List of main transposable elements among three Nosema species.

Format: DOCX Size: 12KB Download file

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Additional file 7:

The potential transposition of DNA sequences by Piggybac element.

Format: DOCX Size: 13KB Download file

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Additional file 8:

Complete list of the annotation genes from genomes, and some lists of genetic position/names of identified element in text.

Format: XLSX Size: 367KB Download file

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Additional file 9:

Diagram showing the Piggybac transposon-mediated exogenous DNA sequence in the collinear region of N. bombycis. TTAA indicates the recognition site of the Piggybac transposon.

Format: TIFF Size: 414KB Download file

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Additional file 10:

Summary of 55 horizontally transferred genes in the N. bombycis genome.

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Additional file 11:

Figure showing phosphomevalonate kinase that horizontal transfer from bacteria integrates the mevalonate pathway of N. bombycis.

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Additional file 12:

The location of segmental duplications in Nosema bombycis genome.

Format: XLS Size: 126KB Download file

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Additional file 13:

Cumulative plot and statistics of the dN/dS values for CPG and COG genes in N. bombycis.

Format: TIFF Size: 354KB Download file

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Additional file 14:

The numbers of EST tags for positively selected CPG genes.

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Additional file 15:

Table of parameter estimates for all positively selected CPGs.

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Additional file 16:

Supplementary materials for library construction and genomic assembly.

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