Genetic polyploid phasing from low-depth progeny samples.
Bioinformatics
Genomics
Sequence analysis
Journal
iScience
ISSN: 2589-0042
Titre abrégé: iScience
Pays: United States
ID NLM: 101724038
Informations de publication
Date de publication:
17 Jun 2022
17 Jun 2022
Historique:
received:
11
02
2022
revised:
20
04
2022
accepted:
16
05
2022
entrez:
13
6
2022
pubmed:
14
6
2022
medline:
14
6
2022
Statut:
epublish
Résumé
An important challenge in genome assembly is haplotype phasing, that is, to reconstruct the different haplotype sequences of an individual genome. Phasing becomes considerably more difficult with increasing ploidy, which makes polyploid phasing a notoriously hard computational problem. We present a novel genetic phasing method for plant breeding with the aim to phase two deep-sequenced parental samples with the help of a large number of progeny samples sequenced at low depth. The key ideas underlying our approach are to (i) integrate the individually weak Mendelian progeny signals with a Bayesian log-likelihood model, (ii) cluster alleles according to their likelihood of co-occurrence, and (iii) assign them to haplotypes via an interval scheduling approach. We show on two deep-sequenced parental and 193 low-depth progeny potato samples that our approach computes high-quality sparse phasings and that it scales to whole genomes.
Identifiants
pubmed: 35692633
doi: 10.1016/j.isci.2022.104461
pii: S2589-0042(22)00732-5
pmc: PMC9184567
doi:
Types de publication
Journal Article
Langues
eng
Pagination
104461Informations de copyright
© 2022 The Authors.
Déclaration de conflit d'intérêts
The authors declare no competing interests.
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