PT  - JOURNAL ARTICLE
AU  - José A. Campoy
AU  - Hequan Sun
AU  - Manish Goel
AU  - Wen-Biao Jiao
AU  - Kat Folz-Donahue
AU  - Nan Wang
AU  - Manuel Rubio
AU  - Chang Liu
AU  - Christian Kukat
AU  - David Ruiz
AU  - Bruno Huettel
AU  - Korbinian Schneeberger
TI  - Chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes
AID  - 10.1101/2020.04.24.060046
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.04.24.060046
4099  - http://biorxiv.org/content/early/2020/09/04/2020.04.24.060046.short
4100  - http://biorxiv.org/content/early/2020/09/04/2020.04.24.060046.full
AB  - 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.Competing Interest StatementThe authors have declared no competing interest.