2019
DOI: 10.1101/737171
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Chromosome-length haplotigs for yak and cattle from trio binning assembly of an F1 hybrid

Abstract: words max)Background Assemblies of diploid genomes are generally unphased, pseudo-haploid representations that do not correctly reconstruct the two parental haplotypes present in the individual sequenced. Instead, the assembly alternates between parental haplotypes and may contain duplications in regions where the parental haplotypes are sufficiently different. Trio binning is an approach to genome assembly that uses short reads from both parents to classify long reads from the offspring according to maternal … Show more

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Cited by 7 publications
(12 citation statements)
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“…Long read sequencing and sophisticated genome assembly methods enabled spectacular improvements in the quality of linear reference sequences particularly for species with gigabase-sized genomes [2]. Recently generated de novo assemblies exceed in quality and continuity all current reference sequences [3,4]. However, modifications and amendments to existing linear reference sequences causes shifts in their coordinates that require large efforts from the genomics community to make data compatible with updated reference sequences [5].…”
Section: Introductionmentioning
confidence: 99%
“…Long read sequencing and sophisticated genome assembly methods enabled spectacular improvements in the quality of linear reference sequences particularly for species with gigabase-sized genomes [2]. Recently generated de novo assemblies exceed in quality and continuity all current reference sequences [3,4]. However, modifications and amendments to existing linear reference sequences causes shifts in their coordinates that require large efforts from the genomics community to make data compatible with updated reference sequences [5].…”
Section: Introductionmentioning
confidence: 99%
“…Using GenomeScope, we estimated the F1 offspring haploid genome size to be 590Mb with a repeat fraction of 27% ( Supplementary Figure 3). Successful haplotype separation was possible due to the high estimated heterozygosity (~1.9%) of the F1 offspring genome ( Supplementary Figure 3), with greater levels of heterozygosity achieved through our same-species A. plantaginis cross than previously achieved through an inter-species cross between yak (Bos grunniens) and cattle (Bos taurus), which gave an F1 heterozygosity of ~1.2% [7].…”
Section: Resultsmentioning
confidence: 82%
“…Using a family trio with same-species A. plantaginis parents, 99.98% of offspring reads were successfully binned into parental haplotypes. This was possible due to the high heterozygosity of the A. plantaginis genome; heterozygosity of the F1 offspring was estimated to be ~1.9%, exceeding levels (~1.2%) obtained when crossing different bovid species [7]. Both resulting haploid assemblies are highly contiguous and complete, strongly supporting trio binning as an effective strategy for de novo assembly of heterozygous genomes.…”
Section: Data Description Backgroundmentioning
confidence: 99%
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