Plants activated their immune systems upon pathogens infected. Extensive research revealed tremendous details about how plants response to pathogen attacks. Damage to the chloroplast and inhibition of photosynthesis, global downregulation of photosynthesis related genes were the pivotal steps in virus successful infection. However, it was unclear why virus infected leaves retain green or chlorosis. A naturally occurring leaf variegated plant of pecan was obtained and infected with a novel badnavirus named pecan mosaic virus (PMV). It was encouraging that the leaf variegated plants are half green leaves and half yellow leaves when develop pinnately compound leaf. PMV infection trigged PTI and ETI, inhibited the IPA pathway (Tryptophan-IPA-IAD-IAA) of IAA biosynthesis, restrained the biosynthesis of fatty acid, oleic acid (C18:1) and VLCFA in PMV infected green and yellow leaves. And reduced the level of C18:1 promoted JA biosynthesis and transduction. PMV infection damaged chloroplast structure, inhibited photosynthesis, restrained cytokines and SA biosynthesis, led to dramatic changes in carbohydrate partitioning, were the major reasons for leave chlorosis. In green leaves, chloroplast clusting, strengthened remarkably of cytokinin biosynthesis and signaling transductions, establish a strong antiviral immunity system. Moreover, disturbance of the ribosome biogenesis activating plant immune responses maybe lead to leaves stay green.
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