In plants, alternative splicing is a crucial mechanism for regulating gene expression at the post-transcriptional level, which leads to diverse proteins by generating multiple mature mRNA isoforms and diversify the gene regulation. Due to the complexity and variability of this process, accurate identification of splicing events is a vital step in studying alternative splicing. This article presents the application of alternative splicing algorithms with or without reference genomes in plants, as well as the integration of advanced deep learning techniques for improved detection accuracy. In addition, we also discuss alternative splicing studies in the pan-genomic background and the usefulness of integrated strategies for fully profiling alternative splicing.

Adoxophyes orana (Lepidoptera: Tortricidae) is a significant polyphagous leafroller that damages trees and shrubs in Rosaceae and other families. However, the molecular mechanisms by which this pest recognizes sex pheromones and host plant volatiles remain largely unknown. Tissue expression profiles indicated that two general odorant-binding proteins (AoraGOBP1 and AoraGOBP2) were more abundant in the antennae and wings of both sexes, with AoraGOBP1 being rich in the female head and abdomen. Temporal expression profiles showed that AoraGOBP1 was expressed at the highest level in 5 day-nmated adults, while AoraGOBP2 exhibited high expression in 5 day-unmated, 7 day-unmated, and mated female adults. Fluorescence competitive binding assays of heterologous expressed AoraGOBPs demonstrated that AoraGOBP2 strongly bound to the primary sex pheromone Z9-14:Ac, and two minor sex pheromones Z9-14:OH and Z11-14:OH, whereas AoraGOBP1 only showed a high binding affinity to Z9-14:Ac. What is more, AoraGOBP1 exhibited a broader binding spectrum for host plant volatiles than AoraGOBP2. Molecular dockings, molecular dynamic simulations, and per-residue binding free decompositions indicated that the van der Waals interaction was the predominant contributor to the binding free energy. Electrostatic interactions between aldehydes, or alcohols and AoraGOBPs stabilized the conformational structures. Phe12 from AoraGOBP1, and Phe13 from AoraGOBP2 were identified as the most important residues that contributed to bind free energy. Our findings provide a comprehensive insight into the molecular mechanisms of olfactory recognition in A. orana, facilitating the development of chemical ecology-based approaches for the control.

Although sugars and acids have a substantial influence on the taste of apple fruits, the genetic and regulatory networks underlying their metabolism in fruit remain insufficiently determined. To fully decipher the genetic basis of the accumulation of sugars and acids in apple fruits, we adopted an integrated strategy that included time-course RNA-seq, QTL mapping, and whole-genome sequencing to examine two typical cultivars (‘HanFu’ and ‘Huahong’) characterized by distinctive flavors. Whole-genome sequencing revealed substantial genetic variation between the two cultivars, thereby providing an indication of the genetic basis of the distinct phenotypes. Constructed co-expression networks yielded information regarding the intra-relationships among the accumulation of different types of metabolites, and also revealed key regulatory nodes associated with the accumulation of sugars and acids, including the genes MdEF2, MdPILS5, and MdGUN8. Additionally, on the basis of QTL mapping using a high-density genetic map, we identified a series of QTLs and functional genes underlying vital traits, including sugar and acid contents. Collectively, our methodology and observations will provide an important reference for further studies focusing on the flavor of apples.

Stone and pome fruit trees play a significant role in fruit production and consumption in China. As an economic fruit tree variety in Shaanxi Province, the cultivation area of Malus ‘Jinxiu’ has been gradually expanding. Brown rot, caused by several species of the genus Monilinia, can result in flower blight and fruit rot, leading to serious economic losses. In September 2025, brown rot symptoms were observed on Malus ‘Jinxiu’ fruits in orchards in Shaanxi Province, China. A total of 90 isolates recovered from symptomatic fruits were identified based on morphological characteristics, pathogenicity, and multi-locus sequence analyses of the internal transcribed spacer of ribosomal DNA (rDNA-ITS), β-tubulin gene (tub2), and laccase genes (lcc2). The results showed that the causal agent of Malus ‘Jinxiu’ brown rot in Shaanxi Province is Monilinia yunnanensis. Furthermore, upon artificial inoculation, M. yunnanensis isolates from both Malus ‘Jinxiu’ and ‘Fuji’ apple hosts can cross-infect and cause brown rot symptoms. At the same time, a M. yunnanensis isolate from Malus ‘Jinxiu’ showed similar virulence on five other local cultivated apple varieties. To our knowledge, this is the first report of M. yunnanensis infecting Malus ‘Jinxiu’. This study provides a basis for developing field diagnosis and integrated control measures for brown rot disease of Malus ‘Jinxiu’ in Shaanxi Province, China.

Introduction: Alternative splicing (AS) is a major source of transcriptome diversity in plants, but short-read RNA sequencing (RNA-seq) has limited power for resolving full-length transcripts and complex AS patterns, particularly in perennial crops. Methods: We integrated Oxford Nanopore Technology (ONT) long-read cDNA sequencing with Illumina RNA-seq to characterize the full-length transcriptome across seven apple ( Malus domestica ) tissues, including vegetative organs and three fruit developmental stages. Gene- and transcript-level expression were quantified, and AS variation was assessed using percent spliced in (PSI) and differential splicing analyses. Results: We identified 56,809 genes and 100,911 transcript isoforms and constructed an AS atlas comprising 29,842 events across seven AS types, involving 17,659 genes and 73,067 transcript isoforms. These analyses revealed extensive tissue-associated transcriptional and post-transcriptional regulation, including large sets of tissue-specific genes, transcript isoforms, and AS events, as well as widespread differential splicing between tissue pairs. Discussion: Together, our results show that integrating ONT long reads for isoform discovery with Illumina short reads for quantitative support improves apple transcriptome annotation and enables systematic characterization of tissue-resolved transcript and AS variation. The resulting full-length transcriptome, unified transcript annotation, and AS atlas provide a valuable resource for studies of post-transcriptional regulation, trait-associated transcript variation, and genetic improvement in apple.

Laccase (LAC) genes play important roles in plant lignin biosynthesis, cell wall formation, growth and development, and responses to biotic and abiotic str