Abstract
BackgroundFor translational genomics, a roadmap is needed to know the molecular similarities or differences between species, such as model species and crop species. This knowledge is invaluable for the selection of target genes and pathways to alter downstream in response to the same stimuli. Here, the transcriptomic responses to six treatments including hormones (abscisic acid - ABA and salicylic acid - SA); treatments that cause oxidative stress (3-amino-1,2,4-triazole - 3AT, methyl viologen - MV); inhibit respiration (antimycin A - AA) or induce genetic damage (ultraviolet radiation -UV) were analysed and compared between Arabidopsis (Arabidopsis thaliana), barley (Hordeum vulgare) and rice (Oryza sativa).ResultsCommon and opposite responses were identified between species, with the number of differentially expressed genes (DEGs) varying greatly between treatments and species. At least 70% of DEGs overlapped with at least one other treatment within a species, indicating overlapping response networks. Remarkably, 15 to 34% of orthologous DEGs showed opposite responses between species, indicating diversity in responses, despite orthology. Orthologous DEGs with common responses to multiple treatments across the three species were correlated with experimental data showing the functional importance of these genes in biotic/abiotic stress responses. The mitochondrial dysfunction response was revealed to be highly conserved in all three species in terms of responsive genes and regulation via the mitochondrial dysfunction element.ConclusionsThe orthologous DEGs that showed a common response between species indicate conserved transcriptomic responses of these pathways between species. However, many genes, including prominent salt-stress responsive genes, were oppositely responsive in multiple-stresses, highlighting fundamental differences in the responses and regulation of these genes between species. This work provides a resource for translation of knowledge or functions between species.
Highlights
For translational genomics, a roadmap is needed to know the molecular similarities or differences between species, such as model species and crop species
Dynamic expression responses to stress in Arabidopsis, rice and barley The transcriptome responses of a model species (Arabidopsis) and two crop species to six treatments designed to mimic stress responses were analysed by using either hormones; treatments that cause oxidative stress (3-amino-1,2,4-triazole - 3AT, methyl viologen - Methyl viologen (MV)); inhibit respiration or induce genetic damage (Table 1)
The induction of various marker genes was 16-fold or greater at 3 h in all species and treatments, except in barley, abscisic acid (ABA) treatment for the marker gene Beta-glucosidase 31 was > than 8-fold, and with the induction of AOX1a with ABA treatment in barley similar to that seen in rice and Arabidopsis this was considered sufficient
Summary
A roadmap is needed to know the molecular similarities or differences between species, such as model species and crop species This knowledge is invaluable for the selection of target genes and pathways to alter downstream in response to the same stimuli. The transcriptomic responses to six treatments including hormones (abscisic acid - ABA and salicylic acid - SA); treatments that cause oxidative stress (3-amino-1,2,4-triazole - 3AT, methyl viologen - MV); inhibit respiration (antimycin A - AA) or induce genetic damage (ultraviolet radiation -UV) were analysed and compared between Arabidopsis (Arabidopsis thaliana), barley (Hordeum vulgare) and rice (Oryza sativa) Throughout their lifecycle, plants are exposed to a variety of non-optimal growth conditions lasting from hours and days to seasons. As plants are exposed to multiple abiotic and biotic stimuli, along with variations in the environment; from soil to beneficial microbial interactions, integration of these various signals is required throughout development to optimise growth [6]
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