More Efficient Genome Analysis: New Method Developed for Sequencing Plant Gamete Cells
21 February 2025
An international research team from China and Germany, including researchers from Forschungszentrum Jülich’s Institute of Bio- and Geosciences – Bioinformatics, has described a new protocol for a method of analysing plant genomes based on sequencing the DNA of sperm cells (gametes). This sequencing, i.e. the decoding of DNA, enables genetic differences and structures in a plant’s chromosomes to be precisely recorded and assigned to a parent. This represents a significant step in the characterization of plant species and their evolutionary history, and may contribute to the development of more robust and adaptable crops. The results of this research were published in the journal Nature Protocols.
The method in question is called haplotype phasing . Haplotypes are groups of alleles (different variants of a gene) that are inherited together from one parent and serve as central units of genetic information. Detailed analysis of these genes has already provided a deeper understanding of how plant species develop and how genetic traits such as disease resistance or increased yields evolve in crops such as tomatoes, potatoes, or tea. The new method can help to obtain a more complete and differentiated picture of genetic diversity, which can contribute to the development of more robust and adaptable crops.
Traditional genome sequencing methods often construct a “consensus genome” that can overlook unique genetic variations, especially in species with complex genetic structures, such as plants. To avoid this, the research team focused on sequencing gametes – i.e. haploid cells such as sperm and egg cells. These cells have only a single set of chromosomes, which means that the complex assignment of genetic information to a specific parent is no longer necessary – which greatly simplifies the process of haplotype phasing. This enables the researchers to identify crossover events – referring to the exchange of genetic material between chromosomes during cell division – and to record genetic diversity more precisely. Key benefits at a glance:
- Haplotype phasing: This method makes it possible to precisely characterize genomes at chromosome level using isolated plant gametes and to accurately localize genetic variations.
- Haplotype phasing: This method makes it possible to precisely characterize genomes at chromosome level using isolated plant gametes and to accurately localize genetic variations.
- Efficiency: The entire process, from the isolation of the gamete cells to data analysis, can be completed within a day.
The Institute of Bio- and Geosciences – Bioinformatics was primarily involved in developing the bioinformatics workflow and provides the software in the form of a container (Docker image) that scientists worldwide can use to apply the method in their own projects. A Docker image is a pre-built, portable, and immutable template that contains all the necessary files, dependencies, and configurations to run an application in an isolated environment (container). This enables consistent execution and analysis of the data on any computer system. This innovation not only contributes to basic research, but also promotes global collaboration in genome research.
Original publication
Zhang, W., Tariq, A., Jia, X., Yan, J., Fernie, A. R., Usadel, B., & Wen, W. (2024). Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points. Nature Protocols, DOI: 10.1038/s41596-024-01063-2.
Weitere relevante Publikationen
Zhang W., Zhang Y., Qiu H., Guo Y., Wan H., Zhang X., Scossa F., Alseekh S., Zhang Q., Wang P., Xu L., Schmidt M. H., Jia X., Li D., Zhu A., Guo F., Chen W., Ni D., Usadel B., Fernie A. R., & Wen W. (2020) Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties. Nature Communications, 11(1):3719. DOI: 10.1038/s41467-020-17498-6.
Tariq, A., Meng, M., Jiang, X., Bolger, A., Beier, S., Buchmann, J. P., Fernie, A. R., Wen, W., Usadel, B. (2024). In‐depth exploration of the genomic diversity in tea varieties based on a newly constructed pangenome of Camellia sinensis. The Plant Journal. DOI: 10.1111/tpj.16874
Qiu, H., Zhang, X., Zhang, Y., Jiang, X., Ren, Y., Gao, D., Zhu, X., Usadel, B., Fernie, A. R., Wen, W. (2024). Depicting the genetic and metabolic panorama of chemical diversity in the tea plant. Plant Biotechnology Journal, 22(4), 1001-1016. DOI: 10.1111/pbi.14241
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