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

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 set...

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Bibliographic Details
Published in:Genome Biology 2020-12, Vol.21 (1), p.306-306, Article 306
Main Authors: Campoy, José A, Sun, Hequan, Goel, Manish, Jiao, Wen-Biao, Folz-Donahue, Kat, Wang, Nan, Rubio, Manuel, Liu, Chang, Kukat, Christian, Ruiz, David, Huettel, Bruno, Schneeberger, Korbinian
Format: Article
Language:English
Subjects:
Chromosomes
De novo assembly
Diploids
Diploidy
Gametes
Genome
Genome Size
Genomes
Germ Cells
Haploidy
Haplotype-resolved assembly
Haplotypes
Haplotyping
Heterozygote
High-Throughput Nucleotide Sequencing - methods
Method
Methods
Phasing
Plant Shoots
Pollen
Pollen - genetics
Polymorphism, Single Nucleotide
Sequence Analysis, DNA
Single-cell sequencing
Spain
Whole Genome Sequencing
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Summary: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.
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-020-02235-5