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

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.

SUBMITTER: Campoy JA

PROVIDER: S-EPMC7771071 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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

Campoy José A JA Sun Hequan H Goel Manish M Jiao Wen-Biao WB Folz-Donahue Kat K Wang Nan N Rubio Manuel M Liu Chang C Kukat Christian C Ruiz David D Huettel Bruno B Schneeberger Korbinian K

Genome biology 20201229 1

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 base ...[more]

PMID: 33372615

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