Open Access Highly Accessed Research article

Comparative transcriptome analysis of Gossypium hirsutum L. in response to sap sucking insects: aphid and whitefly

Neeraj Kumar Dubey1, Ridhi Goel1, Alok Ranjan1, Asif Idris1, Sunil Kumar Singh1, Sumit K Bag1, Krishnappa Chandrashekar1, Kapil Deo Pandey2, Pradhyumna Kumar Singh1 and Samir V Sawant1*

Author Affiliations

1 CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India

2 Department of Botany, Banaras Hindu University, Varanasi 221005, India

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BMC Genomics 2013, 14:241  doi:10.1186/1471-2164-14-241

Published: 11 April 2013

Additional files

Additional file 1:

Contigs size distribution. JEPG file showed contigs size distribution of assembled reads obtained from transcriptome sequencing at different time points of infestation with aphids and whiteflies.

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Additional file 2:

Singletons size distribution. JEPG file showed size distribution of singletons obtained at different time points of infestation by aphids and whiteflies.

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Additional file 3:

Size distributions (in base pair) of generated contigs of common data set. JEPG file showed size distribution of generated contigs of common data set.

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Additional file 4:

Differentially up- and down-regulated contigs (≥ 2 fold) expression in TPM in comparison to the control. Excel file containing the list of contigs that are more than 2 fold up- and down-regulated in different sets of aphid- and whitefly-infested experiments.

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Additional file 5:

Average fold change of aphid and whitefly infestation mediated differentially expressed transcript. Excel file containing the average fold-change expression of cotton transcriptomes after infestation by aphids and whiteflies.

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Additional file 6:

Expression pattern of biological replicate in microarray experiment for Control condition. Figure of expression pattern of biological triplicate in microarray experiment for Control Condition. Third sample was selected for transcriptome sequencing.

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Additional file 7:

Expression pattern of biological replicate in microarray experiment for Whitefly infestation. Figure of expression pattern of biological triplicate in microarray experiment for Whitefly infestation. Third sample was selected for transcriptome sequencing.

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Additional file 8:

(A) GO annotation of ≥2 fold up- and down-regulated genes represented in molecular functions (F) and biological processes (P). C-A2_up and C-A24_up represent aphid 2 and 24 h infestation’s up-regulated genes; whereas C-A2_down and C-A24_down represent aphid infestation’s down-regulated gene as compared with the control. (B) GO annotation of ≥2 fold up- and down-regulated genes represented in molecular functions (F) and biological processes (P). C-W2_up and C-W24_up represent whitefly 2 and 24 h infestation’s up-regulated genes; whereas C-W2_down and C-W24_down represent whitefly infestation’s down-regulated gene as compared with the control.

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Additional file 9:

List of induced and suppressed defense-related genes. Excel file containing the induced as well as defense-related transcripts and their fold-change expression in experiments depicting infestation by aphids and whiteflies.

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Additional file 10:

Expression pattern of overexpressors of cationic peroxidase 3 and downy mildew resistance 6 gene in response to infestation by aphids and whiteflies with RT-PCR. Figure shows Downy mildew resistance 6 gene (At5g24530) (A) and cationic peroxidase 3 (At5g11270) (B) in response to infestation by aphids and whiteflies with real-time PCR.

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Additional file 11:

Different pathogens that influence the expression pattern of aphid- and whitefly induced genes. JEPG file showing pathogens that also influence the expression of genes which showed differential expression after infestation by aphids and whiteflies in cotton.

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Additional file 12:

Expression pattern by qRT-PCR of selected constant expressive contigs. Validation of transcriptome sequencing data by qRT-PCR of selected contigs that have constant expression throughout the experiment.

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Additional file 13:

Expression profile of developmental, virus multiplication and glucosinolate transporter- related transcripts in TPM during different stages of insect infestation. Excel file containing the comparative TPM of developmental and virus multiplication-related transcripts during infestation by aphids and whiteflies.

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Additional file 14:

Comparative transcript per million (TPM) of generated contigs. Excel file containing the comparative TPM analysis of generated contigs.

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Additional file 15:

TAIR9 Protein Database BLAST Result. Excel file containing the annotation of contigs of common data set with the TAIR9 protein database by the blastx program at the e-value 10-5.

Format: XLS Size: 1.9MB Download file

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Additional file 16:

Cotton EST BLAST Result. Excel file containing the annotation of contigs of common data set with the cotton EST gene list by the blastn program at the e-value 10-5.

Format: XLS Size: 3.9MB Download file

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Additional file 17:

Primer sequences of selected contigs used in qRT-PCR. Excel file containing the selected contigs and their primer sequences used in validation of transcriptomes.

Format: XLS Size: 29KB Download file

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