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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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
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author 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
author_facet 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
author_sort Campoy, José A.
collection PubMed
description 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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spelling pubmed-77710712020-12-30 Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes 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 Genome Biol Method 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. BioMed Central 2020-12-29 /pmc/articles/PMC7771071/ /pubmed/33372615 http://dx.doi.org/10.1186/s13059-020-02235-5 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
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
Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes
title Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes
title_full Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes
title_fullStr Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes
title_full_unstemmed Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes
title_short Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes
title_sort gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes
topic Method
url 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
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