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

José A CampoyHequan SunManish GoelWen-Biao JiaoKat Folz-DonahueNan WangManuel RubioChang LiuChristian KukatDavid RuizBruno HuettelKorbinian Schneeberger
Published in: Genome biology (2020)
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.
Keyphrases
  • single cell
  • high throughput
  • rna seq
  • copy number
  • machine learning
  • genome wide
  • dna methylation
  • gene expression
  • deep learning
  • liquid chromatography
  • high density