MOTIVATION: Trimmomatic is a widely adopted tool for preprocessing high-throughput sequencing data, particularly from Illumina platforms. Since its original publication in 2014, the volume and complexity of sequencing data have increased dramatically, necessitating continuous tool evolution. RESULTS: We present the substantial updates to Trimmomatic over the past decade. Key enhancements include a robust multithreading model for high-performance parallel processing, parallel GZIP/BZIP2 compression, and a suite of new trimming and filtering steps to provide users with more flexible quality control. Usability has been significantly improved through automatic PHRED encoding detection and simplified file handling. The codebase has also been modernized including Maven support, and continuous integration to ensure long-term sustainability and community contributions. These updates solidify Trimmomatic's role as an efficient, flexible, and essential tool in modern bioinformatics pipelines. AVAILABILITY: Trimmomatic remains open-source under the GPL V3 license, with the latest version available at https://github.com/usadellab/Trimmomatic and also on our website https://www.plabipd.de/trimmomatic_main.html (DOI: https://doi.org/10.5281/zenodo.18678155).

Next-generation sequencing has triggered an explosion of available genomic and transcriptomic resources in the plant sciences. Although genome and transcriptome sequencing has become orders of magnitudes cheaper and more efficient, often the functional annotation process is lagging behind. This might be hampered by the lack of a comprehensive enumeration of simple-to-use tools available to the plant researcher. In this comprehensive review, we present (i) typical ontologies to be used in the plant sciences, (ii) useful databases and resources used for functional annotation, (iii) what to expect from an annotated plant genome, (iv) an automated annotation pipeline and (v) a recipe and reference chart outlining typical steps used to annotate plant genomes/transcriptomes using publicly available resources.