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Abstract BackgroundAlternative splicing of precursor mRNAs serves as a crucial mechanism to enhance gene expression plasticity for organismal adaptation. However, the precise regulation and function of alternative splicing in plant immune gene regulation remain elusive. ResultsHere, by deploying in-depth transcriptome profiling with deep genome coverage coupled with differential expression, differential alternative splicing, and differential transcript usage analysis, we reveal profound and dynamic changes in alternative splicing following treatment with microbial pattern flg22 peptides inArabidopsis. Our findings highlight RNA polymerase II C-terminal domain phosphatase-like 3 (CPL3) as a key regulator of alternative splicing, preferentially influencing the splicing patterns of defense genes rather than their expression levels. CPL3 mediates the production of a flg22-induced alternative splicing variant, diacylglycerol kinase 5α (DGK5α), which differs from the canonical DGK5β in its interaction with the upstream kinase BIK1 and subsequent phosphorylation, resulting in reduced flg22-triggered production of phosphatidic acid and reactive oxygen species. Furthermore, our functional analysis suggests that DGK5β, but not DGK5α, contributes to plant resistance against virulent and avirulent bacterial infections. ConclusionsThese findings underscore the role of CPL3 in modulating alternative splicing dynamics of defense genes and DGK5 isoform-mediated phosphatidic acid homeostasis, shedding light on the intricate mechanisms underlying plant immune gene regulation. 

A bstract In this work, we use Ising chain and Kitaev chain to check the validity of an earlier proposal in arXiv:2011.02859 that enriched fusion (higher) categories provide a unified categorical description of all gapped/gapless quantum liquid phases, including symmetry-breaking phases, topological orders, SPT/SET orders and CFT-type gapless quantum phases. In particular, we show explicitly that, in each gapped phase realized by these two models, the spacetime observables form a fusion category enriched in a braided fusion category such that its monoidal center is trivial. We also study the categorical descriptions of the boundaries of these models. In the end, we obtain a classification of and the categorical descriptions of all 1-dimensional (spatial dimension) gapped quantum phases with a bosonic/fermionic finite onsite symmetry. 

A bstract We develop a mathematical theory of symmetry protected trivial (SPT) orders and anomaly-free symmetry enriched topological (SET) orders in all dimensions via two different approaches with an emphasis on the second approach. The first approach is to gauge the symmetry in the same dimension by adding topological excitations as it was done in the 2d case, in which the gauging process is mathematically described by the minimal modular extensions of unitary braided fusion 1-categories. This 2d result immediately generalizes to all dimensions except in 1d, which is treated with special care. The second approach is to use the 1-dimensional higher bulk of the SPT/SET order and the boundary-bulk relation. This approach also leads us to a precise mathematical description and a classification of SPT/SET orders in all dimensions. The equivalence of these two approaches, together with known physical results, provides us with many precise mathematical predictions.