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

José Antonio Campoy; Hequan Sun; Manish Goel; Wen‐Biao Jiao; Kat Folz‐Donahue; Nan Wang; Manuel Rubio; Chang Liu; Christian Kukat; David Ruiz; Bruno Hüettel; Korbinian Schneeberger

doi:10.1186/s13059-020-02235-5

GenomicsGenome biologyDec 1, 2020

Peer-reviewed journal article

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

José Antonio Campoy iD, Hequan Sun iD, Manish Goel iD, Wen‐Biao Jiao iD, Kat Folz‐Donahue, Nan Wang iD, Manuel Rubio iD, Chang Liu iD, Christian Kukat iD, David Ruiz iD, Bruno Hüettel iD, Korbinian Schneeberger iD

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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