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Campoy, Jose A.; Sun, Hequan; Goel, Manish; Jiao, Wen-Biao; Folz-Donahue, Kat; Wang, Nan; Rubio, Manuel; Liu, Chang; Kukat, Christian; Ruiz, David; Huettel, Bruno; Schneeberger, Korbinian (2020): Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes. In: Genome Biology, Vol. 21, No. 1, 306
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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. 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.