期刊
GENOME BIOLOGY
卷 21, 期 1, 页码 -出版社
BMC
DOI: 10.1186/s13059-020-02235-5
关键词
Single-cell sequencing; Haplotype-resolved assembly; Haplotyping; Phasing; De novo assembly
资金
- Humboldt Research Fellowship for Experienced Researchers (Alexander von Humboldt Foundation)
- Marie Sklodowska-Curie Individual Fellowship PrunMut [789673]
- Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) [EXC 2048/1-390686111]
- European Research Council (ERC) [802629]
- Projekt DEAL
- Marie Curie Actions (MSCA) [789673] Funding Source: Marie Curie Actions (MSCA)
- European Research Council (ERC) [802629] Funding Source: European Research Council (ERC)
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.
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