Open Access Highly Accessed Research article

Deep sequencing of New World screw-worm transcripts to discover genes involved in insecticide resistance

Renato A Carvalho12, Ana Maria L Azeredo-Espin12 and Tatiana T Torres13*

Author Affiliations

1 Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil

2 Departamento de Genética e Evolução, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil

3 Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, SP, Brazil

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BMC Genomics 2010, 11:695  doi:10.1186/1471-2164-11-695

Published: 8 December 2010

Additional files

Additional file 1:

Insect databases used for functional annotation of C. hominivorax unigenes. The table contains the source of the databases we used to annotate C. hominivorax unigenes as well as how many sequences were mapped to each database.

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Additional file 2:

Transcripts with different representation between the larval library and the combined adult libraries. To calculate the fold difference in the representation of unigenes in our libraries, we used the number of reads from each library normalized by the library size (in number of reads) as a measure of the transcript abundance. Of the 645 unigenes differently represented, 356 had no read in one of the libraries and the fold change was calculated assuming a value of 1. Positive and negative values represent a highest number of reads in the adult and larva libraries, respectively. Only unigenes represented by at least 20 reads were included.

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Additional file 3:

Transcripts with different representation between male and female libraries. To calculate the fold difference in the representation of unigenes between the two libraries, we used the number of reads from each library normalized by the library size (in number of reads) as a measure of the transcript abundance. Of the 101 unigenes differently represented, 57 was either male or female specific and the fold change was calculated assuming a value of 1 in the library with no reads. Positive and negative values represent a highest number of reads in the female and male libraries, respectively. Only unigenes represented by at least 20 reads were included.

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Additional file 4:

Gene expression levels of NWS candidate genes measured via qRT-PCR. Averaged cycle threshold (CT) and Relative Quantification (RQ) for the 18 candidate genes involved in secondary metabolism. The fold difference in the gene expression was calculated between the control (C) and resistant group (R1). The only gene (CYP6G1) presenting a difference in level of expression more than 2-fold between these groups was re-analyzed in a biological replicate, a second resistant group (R2).

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Additional file 5:

Primer pairs used for the gene expression analysis using qRT-PCR. Annotated NWS unigenes with a possible role in insecticide resistance were selected for the comparison of the gene expression levels. Primer pairs for each unigene were designed using the Primer3 software [64].

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