Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes.
De novo assembly
Haplotype-resolved assembly
Haplotyping
Phasing
Single-cell sequencing
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
29 12 2020
29 12 2020
Historique:
received:
15
05
2020
accepted:
11
12
2020
entrez:
29
12
2020
pubmed:
30
12
2020
medline:
1
12
2021
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 33372615
doi: 10.1186/s13059-020-02235-5
pii: 10.1186/s13059-020-02235-5
pmc: PMC7771071
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
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