Toward high‐quality genomes: Standards, challenges, and strategies for assembly and annotation

Abstract

Abstract Genomes provide the fundamental basis for understanding biological systems. Owing to rapid advances in sequencing technologies and assembly methods, the number of sequenced genomes has increased substantially. A high‐quality genome should have high continuity, completeness, and accuracy in its assembly, along with comprehensive and precise annotations of protein‐coding genes and other functional genomic elements. However, it is still difficult to fully achieve these standards due to technical limitations and the inherent genome complexity, especially for plant genomes. This review summarizes current major sequencing technologies and strategies for genome assembly and annotation, elucidates the major challenges encountered in the pursuit of truly high‐quality genomes, and provides practical strategies for meeting high‐quality genome standards. Finally, we highlight several emerging opportunities and promising research directions across the genomic landscape.