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Abstract Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment of critical sequence depth and read length is important for allocating limited resources. To this end, we have generated eight assemblies for the complex genome of the maize inbred line NC358 using PacBio datasets ranging from 20 to 75 × genomic depth and with N50 subread lengths of 11–21 kb. Assemblies with ≤30 × depth and N50 subread length of 11 kb are highly fragmented, with even low-copy genic regions showing degradation at 20 × depth. Distinct sequence-quality thresholds are observed for complete assembly of genes, transposable elements, and highly repetitive genomic features such as telomeres, heterochromatic knobs, and centromeres. In addition, we show high-quality optical maps can dramatically improve contiguity in even our most fragmented base assembly. This study provides a useful resource allocation reference to the community as long-read technologies continue to mature.
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This content will become publicly available on January 15, 2026
Guidelines for gene and genome assembly nomenclature
Abstract The rapid increase in the number of reference-quality genome assemblies presents significant new opportunities for genomic research. However, the absence of standardized naming conventions for genome assemblies and annotations across datasets creates substantial challenges. Inconsistent naming hinders the identification of correct assemblies, complicates the integration of bioinformatics pipelines, and makes it difficult to link assemblies across multiple resources. To address this, we developed a specification for standardizing the naming of reference genome assemblies, to improve consistency across datasets and facilitate interoperability. This specification was created with FAIR (Findable, Accessible, Interoperable, and Reusable) practices in mind, ensuring that reference assemblies are easier to locate, access, and reuse across research communities. Additionally, it has been designed to comply with primary genomic data repositories, including members of the International Nucleotide Sequence Database Collaboration consortium, ensuring compatibility with widely used databases. While initially tailored to the agricultural genomics community, the specification is adaptable for use across different taxa. Widespread adoption of this standardized nomenclature would streamline assembly management, better enable cross-species analyses, and improve the reproducibility of research. It would also enhance natural language processing applications that depend on consistent reference assembly names in genomic literature, promoting greater integration and automated analysis of genomic data. This is a good time to consider more consistent genomic data nomenclature as many research communities and data resources are now finding themselves juggling multiple datasets from multiple data providers.
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- Award ID(s):
- 2126334
- PAR ID:
- 10584718
- Editor(s):
- Harris, T
- Publisher / Repository:
- Genetics Society of America
- Date Published:
- Journal Name:
- GENETICS
- Volume:
- 229
- Issue:
- 3
- ISSN:
- 1943-2631
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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