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

Abstract

Background: Cotton (Gossypium hirsutum L.) is a major fiber crop that is grown worldwide; it faces extensive damage from sap-sucking insects, including aphids and whiteflies. Genome-wide transcriptome analysis was performed to understand the molecular details of interaction between Gossypium hirsutum L. and sap-sucking pests, namely Aphis gossypii (Aphid) and Bemisia tabacci (Whiteflies). Roche's GS-Titanium was used to sequence transcriptomes of cotton infested with aphids and whiteflies for 2 h and 24 h.

Results: A total of 100935 contigs were produced with an average length of 529 bp after an assembly in all five selected conditions. The Blastn of the non-redundant (nr) cotton EST database resulted in the identification of 580 novel contigs in the cotton plant. It should be noted that in spite of minimal physical damage caused by the sap-sucking insects, they can change the gene expression of plants in 2 h of infestation; further change in gene expression due to whiteflies is quicker than due to aphids. The impact of the whitefly 24 h after infestation was more or less similar to that of the aphid 2 h after infestation. Aphids and whiteflies affect many genes that are regulated by various phytohormones and in response to microbial infection, indicating the involvement of complex crosstalk between these pathways. The KOBAS analysis of differentially regulated transcripts in response to aphids and whiteflies indicated that both the insects induce the metabolism of amino acids biosynthesis specially in case of whiteflies infestation at later phase. Further we also observed that expression of transcript related to photosynthesis specially carbon fixation were significantly influenced by infestation of Aphids and Whiteflies.

Conclusions: A comparison of different transcriptomes leads to the identification of differentially and temporally regulated transcripts in response to infestation by aphids and whiteflies. Most of these differentially expressed contigs were related to genes involved in biotic, abiotic stresses and enzymatic activities related to hydrolases, transferases, and kinases. The expression of some marker genes such as the overexpressors of cationic peroxidase 3, lipoxygenase I, TGA2, and non-specific lipase, which are involved in phytohormonal-mediated plant resistance development, was suppressed after infestation by aphids and whiteflies, indicating that insects suppressed plant resistance in order to facilitate their infestation. We also concluded that cotton shares several pathways such as phagosomes, RNA transport, and amino acid metabolism with Arabidopsis in response to the infestation by aphids and whiteflies.

Figure 1

Number of differentially expressed genes after aphids and whiteflies, 2 and 24 h of infestation, respectively. Red and blue color bars represent the number of genes induced by the infestation by whiteflies and aphids, respectively.

Figure 2

Genevestigator analysis of differentially expressed genes (A) Phytohormonal-responsive transcripts; (B) Fungal viral, and bacterial-responsive transcripts.

Figure 3

Venn diagram showing the common and unique genes present in the public domain (GSE5525; GSE6516), aphid-induced (A_Chip), and whitefly induced (W_Chip) with aphid-infested transcriptome (A) and whitefly-infested transcriptome (B) of cotton. KOBAS analysis of common genes of aphid (C) whitefly (D) infested public microarray data set and our transcriptomic data.

Figure 4

Venn diagram showing the common and unique genes present in public domain LMPC microarray data (GSE10247) with cotton transcriptomes of aphid-infested (Aphid_diff) (A) and whitefly-infested (Whitefly_diff) (B). KOBAS analysis of common genes of aphid-infested transcriptome (C) and whitefly-infested (D) with phloem cell representing genes. Red represents unique pathways in aphids, green represents unique pathways in whitefly genes, and black represents common pathways.

Figure 5

Validation of transcriptome sequencing data by qRT-PCR of selected induced and suppressed contigs, (A and B) Whitefly 2 h; (C and D) Whitefly 24 h; (E and F) Aphid 2 h; and (G and H) Aphid 24 h of infestation.