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Cotton leaf curl disease (CLCuD), caused by cotton leaf curl viruses (CLCuVs), is among the most devastating diseases in cotton. While the widely cultivated cotton species  Gossypium hirsutum  is generally susceptible, the diploid species  G. arboreum  is a natural source for resistance against CLCuD. However, the influence of CLCuD on the  G. arboreum  transcriptome and the interaction of CLCuD with  G. arboreum  remains to be elucidated. Here we have used an RNA-Seq based study to analyze differential gene expression in  G. arboreum  under CLCuD infestation.  G. arboreum  plants were infested by graft inoculation using a CLCuD infected scion of  G. hirsutum . CLCuD infested asymptomatic and symptomatic plants were analyzed with RNA-seq using an Illumina HiSeq. 2500. Data analysis revealed 1062 differentially expressed genes (DEGs) in  G. arboreum . We selected 17 genes for qPCR to validate RNA-Seq data. We identified several genes involved in disease resistance and pathogen defense. Furthermore, a weighted gene co-expression network was constructed from the RNA-Seq dataset that indicated 50 hub genes, most of which are involved in transport processes and might have a role in the defense response of  G. arboreum  against CLCuD. This fundamental study will improve the understanding of virus-host interaction and identification of important genes involved in  G. arboreum  tolerance against CLCuD.

Transcriptomics reveals multiple resistance mechanisms against cotton leaf curl disease in a naturally immune cotton species, Gossypium arboreum