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Journal Article

Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes

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Folz-Donahue,  K.
FACS & Imaging, Core Facilities, Max Planck Institute for Biology of Ageing, Max Planck Society;

/persons/resource/persons129360

Kukat,  C.
FACS & Imaging, Core Facilities, Max Planck Institute for Biology of Ageing, Max Planck Society;

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https://www.ncbi.nlm.nih.gov/pubmed/33372615
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Citation

Campoy, J. A., Sun, H., Goel, M., Jiao, W. B., Folz-Donahue, K., Wang, N., et al. (2020). Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes. Genome Biol, 21(1), 306. doi:10.1186/s13059-020-02235-5.


Cite as: https://hdl.handle.net/21.11116/0000-000B-3090-B
Abstract
Generating chromosome-level, haplotype-resolved assemblies of heterozygous genomes remains challenging. To address this, we developed gamete binning, a method based on single-cell sequencing of haploid gametes enabling separation of the whole-genome sequencing reads into haplotype-specific reads sets. After assembling the reads of each haplotype, the contigs are scaffolded to chromosome level using a genetic map derived from the gametes. We assemble the two genomes of a diploid apricot tree based on whole-genome sequencing of 445 individual pollen grains. The two haplotype assemblies (N50: 25.5 and 25.8 Mb) feature a haplotyping precision of greater than 99% and are accurately scaffolded to chromosome-level.