What makes a high-quality genome? Scientists outline standards, challenges, and strategies

BEIJING, China — Genomes provide a fundamental basis for understanding biological systems. Rapid advances in sequencing technologies and assembly algorithms have moved genome research from chromosome-level references toward telomere-to-telomere (T2T) and haplotype-resolved assemblies. Yet a fundamental question remains: What makes a genome truly high quality?

In a new review published in Journal of Systematics and Evolution, researchers from the Institute of Botany, Chinese Academy of Sciences, provide a systematic overview of the standards, challenges, and strategies for achieving high-quality genome assembly and annotation. The review, titled “Toward High-Quality Genomes: Standards, Challenges, and Strategies for Assembly and Annotation,” focuses on three central questions: What defines a high-quality genome? What challenges prevent researchers from reaching these standards? And how can these challenges be overcome?

Defining a high-quality genome

The researchers emphasize that genome quality extends beyond simply assembling long sequences. A high-quality genome assembly should achieve high contiguity, completeness, and correctness, while genome annotation should comprehensively and accurately identify protein-coding genes and other functional genomic elements.

The review summarizes commonly used metrics and approaches for evaluating these dimensions of genome quality, providing researchers with a framework for determining whether a genome assembly and its annotation meet high-quality standards.

Why high-quality genomes remain challenging

Despite major technological advances, producing high-quality genomes remains difficult, particularly for plants. The review highlights several major obstacles, including contamination from exogenous sequences, complex repetitive regions, heterozygosity, polyploidy, and extremely large genome sizes.

These features can complicate sequence assembly, haplotype resolution, and genome annotation, making it difficult to achieve high contiguity, completeness, and correctness simultaneously.

Strategies for achieving high-quality genomes

To address these challenges, the review discusses practical strategies across the major stages of a genome project, from sequencing strategy selection and genome assembly to quality assessment and genome annotation. The authors summarize the strengths and limitations of current sequencing technologies and analytical approaches and discuss how different strategies can be selected according to genome characteristics and research objectives.

Looking ahead, the researchers also highlight emerging opportunities for artificial intelligence, single-cell technologies, and other rapidly developing approaches to advance genome assembly and annotation.

Overall, the review provides a systematic methodological reference for the genomics community. It may be particularly useful for researchers entering the field, helping them make informed decisions about experimental design, sequencing strategies, genome assembly, quality assessment, and annotation.

Original Source:

Kunpeng Li, Xin Yi, Yu Wang, and Yuannian Jiao. 2026. “Toward high-quality genomes: Standards, challenges, and strategies for assembly and annotation.” Journal of Systematics and Evolution. 64: 895-910. https://doi.org/10.1111/jse.70118

Keywords:

genome, high-quality, standards, challenges, strategies

Author’s Institution

The Institute of Botany, Chinese Academy of Sciences (IBCAS), is a comprehensive research institution dedicated to plant science, with research spanning plant diversity and evolution, plant development, ecology, and related fields.

About JSE:

Journal of Systematics and Evolution (JSE) is a peer-reviewed, bi-monthly international English-language journal dedicated to the understanding of biodiversity and evolution. Papers in any of the following and related fields will be considered: systematics and biodiversity conservation, paleobiology and biogeography, adaptation, speciation and domestication, evolutionary genomics and Evo-Devo, theory and methods in evolutionary biology.