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Abstract Intron retention (IR) is the most common alternative splicing event in Arabidopsis. An increasing number of studies have demonstrated the major role of IR in gene expression regulation. The impacts of IR on plant growth and development and response to environments remain underexplored. Here, we found that IR functions directly in gene expression regulation on a genome-wide scale through the detainment of intron-retained transcripts (IRTs) in the nucleus. Nuclear-retained IRTs can be kept away from translation through this mechanism. COP1-dependent light modulation of the IRTs of light signaling genes, such as PIF4, RVE1, and ABA3, contribute to seedling morphological development in response to changing light conditions. Furthermore, light-induced IR changes are under the control of the spliceosome, and in part through COP1-dependent ubiquitination and degradation of DCS1, a plant-specific spliceosomal component. Our data suggest that light regulates the activity of the spliceosome and the consequent IRT nucleus detainment to modulate photomorphogenesis through COP1.

Abstract Abiotic stresses are major factors constraining the growth, development and productivity of tomato (Solanum lycopersicum), the most cultivated vegetable crop worldwide. Uridine diphosphate glycosyltransferases (UDPGTs or UGTs) are essential enzymes that utilize 5-uridine diphosphate as a glycosyl donor molecule to facilitate the catalysis of glycosylation reactions across diverse substrates, thereby playing a pivotal role in conferring abiotic stress tolerance. Currently, there is a limited understanding of the structure and functions of the UDPGT gene family in tomato. In this work, 106 members of the SlUDPGT gene family were identified through in silico analysis, besides, their protein sequence properties, phylogenetic relationships, gene structure, chromosomal distribution, cis-acting elements, tissue expression and hormone- and stress-induced expression were comprehensively investigated. The expression of representative SlUDPGTs under abiotic stress and exogenous hormone treatments, including salt, polyethylene glycol, methyl viologen, gibberellic acid, jasmonic acid, abscisic acid and brassinolide, was investigated through qRT‒PCR analysis. Numerous cis-acting elements linked to stress and hormone signaling were present in the promoter regions of SlUDPGTs. According to microarray data, most SlUDPGT genes were responsive to hormones and abiotic stresses, while certain SlUDPGTs were specifically differentially expressed under Botrytis cinerea and tomato spotted wilt virus infection. Additionally, diverse expression profiles of SlUDPGTs were observed in various tissues and developmental stages. Furthermore, CRISPR/Cas9-mediated knockout of SlUDPGT52 led to enhanced drought tolerance due to enhanced reactive oxygen species (ROS) scavenging. These findings lay the foundations for the future functional characterization of specific UDPGT gene family members, assisting the biotechnology-mediated improvement of tomato and other horticultural crops.

The fruit development and ripening process involve a series of changes regulated by fine-tune gene expression at the transcriptional level. Acetylation levels of histones on lysine residues are dynamically regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), which play an essential role in the control of gene expression. However, their role in regulating fruit development and ripening process, especially in pepper (Capsicum annuum), a typical non-climacteric fruit, remains to understand. Herein, we performed genome-wide analyses of the HDAC and HAT family in the pepper, including phylogenetic analysis, gene structure, encoding protein conserved domain, and expression assays. A total of 30 HAT and 15 HDAC were identified from the pepper genome and the number of gene differentiation among species. The sequence and phylogenetic analysis of CaHDACs and CaHATs compared with other plant HDAC and HAT proteins revealed gene conserved and potential genus-specialized genes. Furthermore, fruit developmental trajectory expression profiles showed that CaHDAC and CaHAT genes were differentially expressed, suggesting that some are functionally divergent. The integrative analysis allowed us to propose CaHDAC and CaHAT candidates to be regulating fruit development and ripening-related phytohormone metabolism and signaling, which also accompanied capsaicinoid and carotenoid biosynthesis. This study provides new insights into the role of histone modification mediate development and ripening in non-climacteric fruits.

Retroduplication variation (RDV), a type of retrocopy polymorphism, is considered to have essential biological significance, but its effect on gene function and species phenotype is still poorly understood. To this end, we analyzed the retrocopies and RDVs in 3,010 rice genomes. We calculated the RDV frequencies in the genome of each rice population; detected the mutated, ancestral and expressed retrogenes in rice genomes; and analyzed their RDV influence on rice phenotypic traits. Collectively, 73 RDVs were identified, and 14 RDVs in ancestral retrogenes can significantly affect rice phenotypes. Our research reveals that RDV plays an important role in rice migration, domestication and evolution. We think that RDV is a good molecular breeding marker candidate. To our knowledge, this is the first study on the relationship between retrogene function, expression, RDV and species phenotype.

Retrocopies, which are considered “junk genes,” are occasionally formed via the insertion of reverse-transcribed mRNAs at new positions in the genome. However, an increasing number of recent studies have shown that some retrocopies exhibit new biological functions and may contribute to genome evolution. Hence, the identification of retrocopies has become very meaningful for studying gene duplication and new gene generation. Current pipelines identify retrocopies through complex operations using alignment programs and filter scripts in a step-by-step manner. Therefore, there is an urgent need for a simple and convenient retrocopy annotation tool. Here, we report the development of RetroScan, a publicly available and easy-to-use tool for scanning, annotating and displaying retrocopies, consisting of two components: an analysis pipeline and a visual interface. The pipeline integrates a series of bioinformatics software programs and scripts for identifying retrocopies in just one line of command. Compared with previous methods, RetroScan increases accuracy and reduces false-positive results. We also provide a Shiny app for visualization. It displays information on retrocopies and their parental genes that can be used for the study of retrocopy structure and evolution. RetroScan is available at https://github.com/Vicky123wzy/RetroScan.