RT Journal Article
SR Electronic
T1 Chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.04.24.060046
DO 10.1101/2020.04.24.060046
A1 José A. Campoy
A1 Hequan Sun
A1 Manish Goel
A1 Wen-Biao Jiao
A1 Kat Folz-Donahue
A1 Christian Kukat
A1 Manuel Rubio
A1 David Ruiz
A1 Bruno Huettel
A1 Korbinian Schneeberger
YR 2020
UL http://biorxiv.org/content/early/2020/04/28/2020.04.24.060046.abstract
AB Generating haplotype-resolved, chromosome-level assemblies of heterozygous genomes remains challenging. To address this, we developed gamete binning, a method based on single-cell sequencing of hundreds of haploid gamete genomes, which enables the separation of conventional long sequencing reads into two haplotype-specific read sets. After independently assembling the reads of each haplotype, the contigs are scaffolded to chromosome-level using a genetic map derived from the recombination patterns within the same gamete genomes. As a proof-of-concept, we assembled the two genomes of a diploid apricot tree supported by the analysis of 445 pollen genomes. Both assemblies (N50: 25.5 and 25.8 Mb) featured a haplotyping precision of >99% and were accurately scaffolded to chromosome-level as reflected by high levels of synteny to closely-related species. These two assemblies allowed for first insights into haplotype diversity of apricot and enabled the identification of non-allelic crossover events introducing severe chromosomal anomalies in 1.6% of the pollen genomes.Competing Interest StatementThe authors have declared no competing interest.