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Sunday, July 7, 2019

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies.

Many tools have been developed for haplotype assembly-the reconstruction of individual haplotypes using reads mapped to a reference genome sequence. Due to increasing interest in obtaining haplotype-resolved human genomes, a range of new sequencing protocols and technologies have been developed to enable the reconstruction of whole-genome haplotypes. However, existing computational methods designed to handle specific technologies do not scale well on data from different protocols. We describe a new algorithm, HapCUT2, that extends our previous method (HapCUT) to handle multiple sequencing technologies. Using simulations and whole-genome sequencing (WGS) data from multiple different data types-dilution pool sequencing, linked-read sequencing, single molecule…

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Sunday, July 7, 2019

Untangling heteroplasmy, structure, and evolution of an atypical mitochondrial genome by PacBio Sequencing.

The highly compact mitochondrial (mt) genome of terrestrial isopods (Oniscidae) presents two unusual features. First, several loci can individually encode two tRNAs, thanks to single nucleotide polymorphisms at anticodon sites. Within-individual variation (heteroplasmy) at these loci is thought to have been maintained for millions of years because individuals that do not carry all tRNA genes die, resulting in strong balancing selection. Second, the oniscid mtDNA genome comes in two conformations: a ~14 kb linear monomer and a ~28 kb circular dimer comprising two monomer units fused in palindrome. We hypothesized that heteroplasmy actually results from two genome units of the same dimeric…

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Sunday, July 7, 2019

The genetic basis of resistance and matching-allele interactions of a host-parasite system: The Daphnia magna-Pasteuria ramosa model.

Negative frequency-dependent selection (NFDS) is an evolutionary mechanism suggested to govern host-parasite coevolution and the maintenance of genetic diversity at host resistance loci, such as the vertebrate MHC and R-genes in plants. Matching-allele interactions of hosts and parasites that prevent the emergence of host and parasite genotypes that are universally resistant and infective are a genetic mechanism predicted to underpin NFDS. The underlying genetics of matching-allele interactions are unknown even in host-parasite systems with empirical support for coevolution by NFDS, as is the case for the planktonic crustacean Daphnia magna and the bacterial pathogen Pasteuria ramosa. We fine-map one locus…

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Sunday, July 7, 2019

Morphological and genetic analyses of the invasive forest pathogen Phytophthora austrocedri reveal two clonal lineages colonised Britain and Argentina from a common ancestral population.

Phytophthora austrocedri is causing widespread mortality of Austrocedrus chilensis in Argentina and Juniperus communis in Britain. The pathogen has also been isolated from J. horizontalis in Germany. Isolates from Britain, Argentina and Germany are homothallic with no clear differences in the dimensions of sporangia, oogonia or oospores. Argentinian and German isolates grew faster than British isolates across a range of media and had a higher temperature tolerance although most isolates regardless of origin grew best at 15°C and all isolates were killed at 25°C. Argentinian and British isolates caused lesions on both hosts when inoculated onto A. chilensis and J.…

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Sunday, July 7, 2019

Dense and accurate whole-chromosome haplotyping of individual genomes.

The diploid nature of the human genome is neglected in many analyses done today, where a genome is perceived as a set of unphased variants with respect to a reference genome. This lack of haplotype-level analyses can be explained by a lack of methods that can produce dense and accurate chromosome-length haplotypes at reasonable costs. Here we introduce an integrative phasing strategy that combines global, but sparse haplotypes obtained from strand-specific single-cell sequencing (Strand-seq) with dense, yet local, haplotype information available through long-read or linked-read sequencing. We provide comprehensive guidance on the required sequencing depths and reliably assign more than…

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Sunday, July 7, 2019

Ultraaccurate genome sequencing and haplotyping of single human cells.

Accurate detection of variants and long-range haplotypes in genomes of single human cells remains very challenging. Common approaches require extensive in vitro amplification of genomes of individual cells using DNA polymerases and high-throughput short-read DNA sequencing. These approaches have two notable drawbacks. First, polymerase replication errors could generate tens of thousands of false-positive calls per genome. Second, relatively short sequence reads contain little to no haplotype information. Here we report a method, which is dubbed SISSOR (single-stranded sequencing using microfluidic reactors), for accurate single-cell genome sequencing and haplotyping. A microfluidic processor is used to separate the Watson and Crick strands…

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Sunday, July 7, 2019

Estimating fitness of viral quasispecies from next-generation sequencing data.

The quasispecies model is ubiquitous in the study of viruses. While having lead to a number of insights that have stood the test of time, the quasispecies model has mostly been discussed in a theoretical fashion with little support of data. With next-generation sequencing (NGS), this situation is changing and a wealth of data can now be produced in a time- and cost-efficient manner. NGS can, after removal of technical errors, yield an exceedingly detailed picture of the viral population structure. The widespread availability of cross-sectional data can be used to study fitness landscapes of viral populations in the quasispecies…

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Sunday, July 7, 2019

HapCol: accurate and memory-efficient haplotype assembly from long reads.

Haplotype assembly is the computational problem of reconstructing haplotypes in diploid organisms and is of fundamental importance for characterizing the effects of single-nucleotide polymorphisms on the expression of phenotypic traits. Haplotype assembly highly benefits from the advent of ‘future-generation’ sequencing technologies and their capability to produce long reads at increasing coverage. Existing methods are not able to deal with such data in a fully satisfactory way, either because accuracy or performances degrade as read length and sequencing coverage increase or because they are based on restrictive assumptions.By exploiting a feature of future-generation technologies-the uniform distribution of sequencing errors-we designed an…

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Sunday, July 7, 2019

Genomic resources and their influence on the detection of the signal of positive selection in genome scans.

Genome scans represent powerful approaches to investigate the action of natural selection on the genetic variation of natural populations and to better understand local adaptation. This is very useful, for example, in the field of conservation biology and evolutionary biology. Thanks to Next Generation Sequencing, genomic resources are growing exponentially, improving genome scan analyses in non-model species. Thousands of SNPs called using Reduced Representation Sequencing are increasingly used in genome scans. Besides, genome sequences are also becoming increasingly available, allowing better processing of short-read data, offering physical localization of variants, and improving haplotype reconstruction and data imputation. Ultimately, genome sequences…

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Sunday, July 7, 2019

Read-based phasing of related individuals.

Read-based phasing deduces the haplotypes of an individual from sequencing reads that cover multiple variants, while genetic phasing takes only genotypes as input and applies the rules of Mendelian inheritance to infer haplotypes within a pedigree of individuals. Combining both into an approach that uses these two independent sources of information-reads and pedigree-has the potential to deliver results better than each individually.We provide a theoretical framework combining read-based phasing with genetic haplotyping, and describe a fixed-parameter algorithm and its implementation for finding an optimal solution. We show that leveraging reads of related individuals jointly in this way yields more phased…

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Sunday, July 7, 2019

Selecting reads for haplotype assembly

Haplotype assembly or read-based phasing is the problem of reconstructing both haplotypes of a diploid genome from next-generation sequencing data. This problem is formalized as the Minimum Error Correction (MEC) problem and can be solved using algorithms such as WhatsHap. The runtime of WhatsHap is exponential in the maximum coverage, which is hence controlled in a pre-processing step that selects reads to be used for phasing. Here, we report on a heuristic algorithm designed to choose beneficial reads for phasing, in particular to increase the connectivity of the phased blocks and the number of correctly phased variants compared to the…

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Sunday, July 7, 2019

Long single-molecule reads can resolve the complexity of the influenza virus composed of rare, closely related mutant variants

As a result of a high rate of mutations and recombination events, an RNA-virus exists as a heterogeneous “swarm” of mutant variants. The long read length offered by single-molecule sequencing technologies allows each mutant variant to be sequenced in a single pass. However, high error rate limits the ability to reconstruct heterogeneous viral population composed of rare, related mutant variants. In this paper, we present 2SNV, a method able to tolerate the high error-rate of the single-molecule protocol and reconstruct mutant variants. 2SNV uses linkage between single nucleotide variations to efficiently distinguish them from read errors. To benchmark the sensitivity…

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Sunday, July 7, 2019

Probabilistic viral quasispecies assembly

Viruses are pathogens that cause infectious diseases. The swarm of virions is subject to the host’s immune pressure and possibly antiviral therapy. It may escape this selective pressure and gain selective advantage by acquiring one or more of the genomic alterations: single-nucleotide variants (SNVs), loss or gain of one or more amino acids, large deletions, for example, due to alternative splicing, or recombination of different strains. Genotypic antiretroviral drug resistance testing is performed via sequencing. Next-generation sequencing (NGS) technologies revolutionized assessing viral genetic diversity experimentally. In viral quasispecies analysis, there are two main goals: the identification of low-frequency variants and…

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Sunday, July 7, 2019

WhatsHap: fast and accurate read-based phasing

Read-based phasing allows to reconstruct the haplotype structure of a sample purely from sequencing reads. While phasing is a required step for answering questions about population genetics, compound heterozygosity, and to aid in clinical decision making, there has been a lack of an accurate, usable and standards-based software. WhatsHap is a production-ready tool for highly accurate read-based phasing. It was designed from the beginning to leverage third-generation sequencing technologies, whose long reads can span many variants and are therefore ideal for phasing. WhatsHap works also well with second-generation data, is easy to use and will phase not only SNVs, but…

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Sunday, July 7, 2019

Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study.

Haplotypes are the units of inheritance in an organism, and many genetic analyses depend on their precise determination. Methods for haplotyping single individuals use the phasing information available in next-generation sequencing reads, by matching overlapping single-nucleotide polymorphisms while penalizing post hoc nucleotide corrections made. Haplotyping diploids is relatively easy, but the complexity of the problem increases drastically for polyploid genomes, which are found in both model organisms and in economically relevant plant and animal species. Although a number of tools are available for haplotyping polyploids, the effects of the genomic makeup and the sequencing strategy followed on the accuracy of…

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