Genome-wide identification of the Dicer-like family in cotton and analysis of the DCL expression modulation in response to biotic stress in two contrasting commercial cultivars

Abstract Background Dicer-like proteins (DCLs) are fundamental players in RNA-silencing mechanisms acting in gene regulation via miRNAs and in antiviral protection in plants, in addition to being related to other biotic and abiotic stresses. Despite be identified in some crops, cotton DCLs weren't characterized until now. Here we characterize the DCLs of three cotton species and analyzed their expression profiles during biotic stress. Results We identified 11 DCLs in the allotetraploid cotton Gossypium hirsutum and 7 and 6 in the diploid G. arboreum and G. raimondii, respectively. Among some DCL duplication observed in these genomes, we observe the presence of an extra DCL3 in the three cotton species, not found in others eudicots until now. All the DCL types identified by in silico analysis in the allotetraploid cotton genome were able to generate transcripts, as observed by gene expression analysis in distinct tissues. Based on the importance of DCLs for plant virus defense, responses of cotton DCLs to virus infection and/or herbivore attack using two commercial cotton cultivars (cv.), one susceptible (Fibermax 966) and another resistant (Delta Opal) to polerovirus CLRDV infection were analyzed. Both cvs. responded differently to virus infection. At the initial stages, 24dpi, the resistant cv. showed strong induction of DCL2a and b, while the susceptible cv. showed a down-regulation of these genes, wherever DCL4 expression was highly induced. Herbivore attack did not induce contrasting profiles between cotton DCLs transcripts in either cotton cv. Conclusions The allotetraploide cotton G. hirsutum has almost all DCLs found in their diploid relative and duplication of DCL2 and DCL3 were found in the three species. All the four classes of DCL respond to aphid attack and virus infection in G. hirsutum, however, remarkable differences in DCL initial responses against the virus itself may be responsible for the virus susceptible and/or resistant phenotype of the contrasting cotton cv. studied.