Heterozygous genome assembly via binary classification of homologous sequence

Bodily, Paul; Fujimoto, M. Stanley; Ortega, Cameron; Okuda, Nozomu; Price, Joseph; Clement, Mark J.; Snell, Quinn

doi:10.1186/1471-2105-16-s7-s5

Cited by 13 publications

(8 citation statements)

References 31 publications

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“…This shortcoming of the most common assemblers (e.g. ABYSS, Trinity and Velvet) is due to the fact that they were designed to assemble sequences of haploid genomes and they are not optimized for heterozygous sequences or genomes (Bodily et al 2015).…”

Section: Discussionmentioning

confidence: 99%

“…This shortcoming of the most common assemblers (e.g. ABYSS, Trinity and Velvet) is due to the fact that they were designed to assemble haploid sequences and are not optimized for heterozygous sequences or genomes (Bodily et al 2015). Second, not only are allele sequences the more appropriate data type, but phasing sequence capture data also leads to a doubling of the effective sample size, since two sequences are compiled for a diploid individual, in contrast to the single sequence per individual that is recovered when taking the contig approach.…”

Section: Discussionmentioning

confidence: 99%

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Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements

Andermann

Fernandes

Olsson

et al. 2018

Preprint

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Abstract.-Advances in high-throughput sequencing techniques now allow relatively easy 20 and affordable sequencing of large portions of the genome, even for non-model organisms. 21Many phylogenetic studies prefer to reduce costs by focusing their sequencing efforts on a 22 selected set of targeted loci, commonly enriched using sequence capture. The advantage of 23 this approach is that it recovers a consistent set of loci, each with high sequencing depth, 24 which leads to more confidence in the assembly of target sequences. High sequencing depth 25 can also be used to identify phylogenetically informative allelic variation within sequenced 26 individuals, but allele sequences are infrequently assembled in phylogenetic studies. 27Instead, many scientists perform their phylogenetic analyses using contig sequences which 28 result from the de novo assembly of sequencing reads into contigs containing only canonical 29 nucleobases, and this may reduce both statistical power and phylogenetic accuracy. Here, 30we develop an easy-to-use pipeline to recover allele sequences from sequence capture data, 31and we use simulated and empirical data to demonstrate the utility of integrating these 32 allele sequences to analyses performed under the Multispecies Coalescent (MSC) model. 33Our empirical analyses of Ultraconserved Element (UCE) locus data collected from the 34 South American hummingbird genus Topaza demonstrate that phased allele sequences carry 35 sufficient phylogenetic information to infer the genetic structure, lineage divergence, and 36 biogeographic history of a genus that diversified during the last three million years, support 37 the recognition of two species, and suggest a high rate of gene flow across large distances of 38 rainforest habitats but rare admixture across the Amazon River. Our simulations show 39 that analyzing allele sequences leads to more accurate estimates of tree topology and 40 divergence times than the more common approach of using contig sequences. We conclude 41 that allele phasing may be the most appropriate processing scheme for phylogenetic 42 analyses of UCE data in particular, and sequence capture data, more generally. (Fig. 4). Hereafter, we use "contigs" and "contig 61 sequences" to refer to the sequences that are output by de novo assemblers. 62One alternative approach to generating contig sequences uses the depth of 29, 2018; estimation of gene trees, species trees, and divergence times (Garrick et al. 2010; Potts 72 et al. 2014; Lischer et al. 2014). The common practice of neglecting allelic information in 73 phylogenetic studies possibly results from historical inertia and a lack of computational 74 pipelines to prepare allele sequences for phylogenetic analysis using MPS data. CC-BY-ND4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/255752 doi: bioRxiv preprint first posted online Jan. 75In addition to the problems of determining allelic se...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements

Andermann

Fernandes

Olsson

et al. 2018

Preprint

View full text Add to dashboard Cite

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“…The presence of duplicated genes and polyploidy split the assembly, thus leading to shorter scaffolds and contigs. 18 , 19 …”

Section: Introductionmentioning

confidence: 99%

Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop

et al. 2017

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Finger millet (Eleusine coracana (L.) Gaertn) is an important crop for food security because of its tolerance to drought, which is expected to be exacerbated by global climate changes. Nevertheless, it is often classified as an orphan/underutilized crop because of the paucity of scientific attention. Among several small millets, finger millet is considered as an excellent source of essential nutrient elements, such as iron and zinc; hence, it has potential as an alternate coarse cereal. However, high-quality genome sequence data of finger millet are currently not available. One of the major problems encountered in the genome assembly of this species was its polyploidy, which hampers genome assembly compared with a diploid genome. To overcome this problem, we sequenced its genome using diverse technologies with sufficient coverage and assembled it via a novel multiple hybrid assembly workflow that combines next-generation with single-molecule sequencing, followed by whole-genome optical mapping using the Bionano Irys® system. The total number of scaffolds was 1,897 with an N50 length >2.6 Mb and detection of 96% of the universal single-copy orthologs. The majority of the homeologs were assembled separately. This indicates that the proposed workflow is applicable to the assembly of other allotetraploid genomes.

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“…However, assembling a highly heterozygous genotype, accurate phasing, and aligning of Vitis haplotypes is still challenging. With regard to the data on hand and the complexity of this assembly, the application of dedicated scaffolding tools like scaffoldScaffolder (Bodily et al, 2015) or SSPACE (Boetzer et al, 2011) comes at a high risk of generating erroneous connections between contigs. Therefore, we calculated the BoeWGS1.0 assembly with very stringent parameters using the CLC Genomics Workbench toolkit, which contains an implementation of a de Bruijn Graph assembler, and refrained from scaffolding.…”

Section: Genome Sequencingmentioning

confidence: 99%

A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock ‘Börner’ (Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping

et al. 2020

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Grapevine breeding has become highly relevant due to upcoming challenges like climate change, a decrease in the number of available fungicides, increasing public concern about plant protection, and the demand for a sustainable production. Downy mildew caused by Plasmopara viticola is one of the most devastating diseases worldwide of cultivated Vitis vinifera. In modern breeding programs, therefore, genetic marker technologies and genomic data are used to develop new cultivars with defined and stacked resistance loci. Potential sources of resistance are wild species of American or Asian origin. The interspecific hybrid of Vitis riparia Gm 183 x Vitis cinerea Arnold, available as the rootstock cultivar 'Börner,' carries several relevant resistance loci. We applied next-generation sequencing to enable the reliable identification of simple sequence repeats (SSR), and we also generated a draft genome sequence assembly of 'Börner' to access genome-wide sequence variations in a comprehensive and highly reliable way. These data were used to cover the 'Börner' genome with genetic marker positions. A subset of these marker positions was used for targeted mapping of the P. viticola resistance locus, Rpv14, to validate the marker position list. Based on the reference genome sequence PN40024, the position of this resistance locus can be narrowed down to less than 0.5 Mbp on chromosome 5.

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Heterozygous genome assembly via binary classification of homologous sequence

Cited by 13 publications

References 31 publications

Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements

Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements

Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop

A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock ‘Börner’ (Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping

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