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bioRxiv · 10.1101/2020.04.24.060046

Chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes

Campoy, J. A.·Sun, H.·Goel, M.·Jiao, W.-B. A.·Folz-Donahue, K.·Kukat, C.·Rubio, M.·Ruiz, D.·Huettel, B.·Schneeberger, K.
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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. As a proof-of-concept, we assembled 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) featured a haplotyping precision of >99% and were accurately scaffolded to chromosome-level.

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Campoy, J. A., Sun, H., Goel, M., Jiao, W.-B. A., Folz-Donahue, K., Kukat, C., Rubio, M., Ruiz, D., Huettel, B., Schneeberger, K.. 2020-04-25. Chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes. https://doi.org/10.1101/2020.04.24.060046

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