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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Detalles Bibliográficos
Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7771071/
https://www.ncbi.nlm.nih.gov/pubmed/33372615
http://dx.doi.org/10.1186/s13059-020-02235-5
Descripción
Sumario: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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