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bioRxiv2015

The Nicrophorus vespilloides genome and methylome, a beetle with complex social behavior

Testing for conserved and novel mechanisms underlying phenotypic evolution requires a diversity of genomes available for comparison spanning multiple independent lineages. For example, complex social behavior in insects has been investigated primarily with eusocial lineages, nearly all of which are Hymenoptera. If conserved genomic influences on sociality do exist, we need data from a wider range of taxa that also vary in their levels of sociality. Here we present information on the genome of the subsocial beetle Nicrophorus vespilloides, a species long used to investigate evolutionary questions of complex social behavior. We used this genome to address two questions. First, does life history predict overlap in gene models more strongly than phylogenetic groupings? Second, like other insects with highly developed social behavior but unlike other beetles, does N. vespilloides have DNA methylation? We found the overlap in gene models was similar between N. vespilloides and all other insect groups regardless of life history. Unlike previous studies of beetles, we found strong evidence of DNA methylation, which allows this species to be used to address questions about the potential role of methylation in social behavior. The addition of this genome adds a coleopteran resource to answer questions about the evolution and mechanistic basis of sociality.

Genomics↗

bioRxiv2015

Conversion of Genomic DNA to Proxy Constructs Suitable for Accurate Nanopore Sequencing

Nanopore sequencing at single-base resolution is challenging. There are developing technologies to convert DNA molecules to expanded constructs. Such constructs can be sequenced by nanopores in place of the original DNA molecules. We present a novel method for converting genomic DNA to expanded constructs (\"proxies\") with 99.67% accuracy. Our method \"reads\" each base in each DNA fragment and appends an oligonucleotide to the DNA fragment after each base \"reading\". Each appended oligonucleotide represents a specific base type, so that the proxy construct consisting of all the appended oligonucleotides faithfully represents the original DNA sequence. We generated proxies for genomic DNA and confirmed the identities of both the proxies and their corresponding original DNA sequences by performing sequencing using Ion Torrent sequencer.\n\nConversion to proxies had only 0.33% raw error rate. Errors were: 93.96% deletions, 5.29% insertions, and 0.74% substitutions. The longest sequenced proxy was 170 bases, corresponding to a 17-base original DNA sequence. The short length of the detected proxies reflected restrictions imposed by Ion Torrents short reads and was not caused by limitations of our method. The consensus sequence built by using proxies alone (average length: 120 bases; corresponding to original sequences with average length 12 bases) covered 55% of the reference genome with 100% accuracy, and outperformed the Ion Torrent sequencing of the corresponding original DNA fragments in terms of accuracy, coverage and number of aligned sequences. Data and other materials can be found at http://www.vastogen.com/data.html. This proof-of-concept experiment demonstrates highly accurate proxy construction at the whole genome level. To our knowledge, this is the first demonstrated construction of expanded versions of DNA at the whole genome level.

Genomics↗

bioRxiv2015

FecalSeq: methylation-based enrichment for noninvasive population genomics from feces

Obtaining high-quality samples from wild animals is a major obstacle for genomic studies of many taxa, particular at the population level, as collection methods for such samples are typically invasive. DNA from feces is easy to obtain noninvasively, but is dominated by a preponderance of bacterial and other non-host DNA. Because next-generation sequencing technology sequences DNA largely indiscriminately, the high proportion of exogenous DNA drastically reduces the efficiency of high-throughput sequencing for host animal genomics. In order to address this issue, we developed an inexpensive methylation-based capture method for enriching host DNA from noninvasively obtained fecal DNA samples. Our method exploits natural differences in CpG-methylation density between vertebrate and bacterial genomes to preferentially bind and isolate host DNA from majority-bacterial fecal DNA samples. We demonstrate that the enrichment is robust, efficient, and compatible with downstream library preparation methods useful for population studies (e.g., RADseq). Compared to other enrichment strategies, our method is quick and inexpensive, adding only a negligible cost to sample preparation for research that is often severely constrained by budgetary limitations. In combination with downstream methods such as RADseq, our approach allows for cost-effective and customizable genomic-scale genotyping that was previously feasible in practice only with invasive samples. Because feces are widely available and convenient to collect, our method empowers researchers to explore genomic-scale population-level questions in organisms for which invasive sampling is challenging or undesirable.

Genomics↗

bioRxiv2015

No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini

Tardigrades are meiofaunal ecdysozoans that are key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme conditions through cryptobiosis. In a recent paper (Boothby TC et al (2015) Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proc Natl Acad Sci USA 112:15976-15981) the authors concluded that the tardigrade Hypsibius dujardini had an unprecedented proportion (17%) of genes originating through functional horizontal gene transfer (fHGT), and speculated that fHGT was likely formative in the evolution of cryptobiosis. We independently sequenced the genome of H. dujardini. As expected from whole-organism DNA sampling, our raw data contained reads from non-target genomes. Filtering using metagenomics approaches generated a draft H. dujardini genome assembly of 135 Mb with superior assembly metrics to the previously published assembly. Additional microbial contamination likely remains. We found no support for extensive fHGT. Among 23,021 gene predictions we identified 0.2% strong candidates for fHGT from bacteria, and 0.2% strong candidates for fHGT from non-metazoan eukaryotes. Cross-comparison of assemblies showed that the overwhelming majority of HGT candidates in the Boothby et al. genome derived from contaminants. We conclude that fHGT into H. dujardini accounts for at most 1-2% of genes and that the proposal that one sixth of tardigrade genes originate from functional HGT events is an artefact of undetected contamination.

Genomics↗

bioRxiv2015

Clinical Validation of a Non-Invasive Prenatal Test for Genome-Wide Detection of Fetal Copy Number Variants

1.BackgroundCurrent cell-free DNA (cfDNA) assessment of fetal chromosomes does not analyze and report on all chromosomes. Hence, a significant proportion of fetal chromosomal abnormalities are not detectable by current non-invasive methods. Here we report the clinical validation of a novel NIPT designed to detect genome-wide gains and losses of chromosomal material [≥]7 Mb and losses associated with specific deletions <7 Mb.\n\nObjectiveThe objective of this study is to provide a clinical validation of the sensitivity and specificity of a novel NIPT for detection of genome-wide abnormalities.\n\nStudy DesignThis retrospective, blinded study included maternal plasma collected from 1222 study subjects with pregnancies at increased risk for fetal chromosomal abnormalities that were assessed for trisomy 21 (T21), trisomy 18 (T18), trisomy 13 (T13), sex chromosome aneuploidies (SCAs), fetal sex, genome-wide copy number variants (CNVs) 7 Mb and larger, and select deletions smaller than 7 Mb. Performance was assessed by comparing test results with findings from G-band karyotyping, microarray data, or high coverage sequencing.\n\nResultsClinical sensitivity within this study was determined to be 100% for T21, T18, T13, and SCAs, and 97.7% for genome-wide CNVs. Clinical specificity within this study was determined to be 100% for T21, T18, and T13, and 99.9% for SCAs and CNVs. Fetal sex classification had an accuracy of 99.6%.\n\nConclusionThis study has demonstrated that genome-wide non-invasive prenatal testing (NIPT) for fetal chromosomal abnormalities can provide high resolution, sensitive, and specific detection of a wide range of sub-chromosomal and whole chromosomal abnormalities that were previously only detectable by invasive karyotype analysis. In some instances, this NIPT also provided additional clarification about the origin of genetic material that had not been identified by invasive karyotype analysis.

Genomics↗

bioRxiv2016

gEVAL - A web based browser for evaluating genome assemblies

MotivationFor most research approaches, genome analyses are dependent on the existence of a high quality genome reference assembly. However, the local accuracy of an assembly remains difficult to assess and improve. The gEVAL browser allows the user to interrogate an assembly in any region of the genome by comparing it to different datasets and evaluating the concordance. These analyses include: a wide variety of sequence alignments, comparative analyses of multiple genome assemblies, and consistency with optical and other physical maps. gEVAL highlights allelic variations, regions of low complexity, abnormal coverage, and potential sequence and assembly errors, and offers strategies for improvement. While gEVAL focuses primarily on sequence integrity, it can also display arbitrary annotation including Ensembl or TrackHub sources. We provide gEVAL web sites for many human, mouse, zebrafish and chicken assemblies to support the Genome Reference Consortium, and gEVAL is also downloadable to enable its use for any organism and assembly.\n\nAvailabilityWeb Browser: http://geval.sanger.ac.uk, Plugin: http://wchow.github.io/wtsi-geval-plugin.\n\nContactkj2@sanger.ac.uk\n\nSupplementary informationSupplementary data are available at Bioinformatics online.

Genomics↗

bioRxiv2016

Genome-culture coevolution promotes rapid divergence in the killer whale

The interaction between ecology, culture and genome evolution remains poorly understood. Analysing population genomic data from killer whale ecotypes, which we estimate have globally radiated within less than 250,000 years, we show that genetic structuring including the segregation of potentially functional alleles is associated with socially inherited ecological niche. Reconstruction of ancestral demographic history revealed bottlenecks during founder events, likely promoting ecological divergence and genetic drift resulting in a wide range of genome-wide differentiation between pairs of allopatric and sympatric ecotypes. Functional enrichment analyses provided evidence for regional genomic divergence associated with habitat, dietary preferences and postzygotic reproductive isolation. Our findings are consistent with expansion of small founder groups into novel niches by an initial plastic behavioural response, perpetuated by social learning imposing an altered natural selection regime. The study constitutes an important step toward an understanding of the complex interaction between demographic history, culture, ecological adaptation and evolution at the genomic level.

Genomics↗

bioRxiv2016

Integrating genomics into clinical pediatric oncology using the molecular tumor board at the Memorial Sloan Kettering Cancer Center

BackgroundPediatric oncologists have begun to leverage tumor genetic profiling to match patients with targeted therapies. At the Memorial Sloan Kettering Cancer Center (MSKCC), we developed the Pediatric Molecular Tumor Board (PMTB) to track, integrate, and interpret clinical genomic profiling and potential targeted therapeutic recommendations.\n\nProcedureThis retrospective case series includes all patients reviewed by the MSKCC PMTB from July 2014 to June 2015. Cases were submitted by treating oncologists and potential treatment recommendations were based upon the modified guidelines of the Oxford Centre for Evidence Based Medicine.\n\nResultsThere were 41 presentations of 39 individual patients during the study period. Gliomas, acute myeloid leukemia, and neuroblastoma were the most commonly reviewed cases. Thirty nine (87%) of the 45 molecular sequencing profiles utilized hybrid-capture targeted genome sequencing. In 30 (73%) of the 41 presentations, the PMTB provided therapeutic recommendations, of which 19 (46%) were implemented. Twenty-one (70%) of the recommendations involved targeted therapies. Three (14%) targeted therapy recommendations had published evidence to support the proposed recommendations (evidence levels 1-2), 8 (36%) recommendations had preclinical evidence (level 3), and 11 (50%) recommendations were based upon hypothetical biological rationales (level 4).\n\nConclusionsThe MSKCC PMTB enabled a clinically relevant interpretation of genomic profiling. Effective use of clinical genomics is anticipated to require new and improved tools to ascribe pathogenic significance and therapeutic actionability. Development of specific rule-driven clinical protocols will be needed for the incorporation and evaluation of genomic and molecular profiling in interventional prospective clinical trials.

Genomics↗

bioRxiv2016

Whole-genome characterization in pedigreed non-human primates using Genotyping-By-Sequencing and imputation.

BackgroundRhesus macaques are widely used in biomedical research, but the application of genomic information in this species to better understand human disease is still undeveloped. Whole-genome sequence (WGS) data in pedigreed macaque colonies could provide substantial experimental power, but the collection of WGS data in large cohorts remains a formidable expense. Here, we describe a cost-effective approach that selects the most informative macaques in a pedigree for whole-genome sequencing, and imputes these dense marker data into all remaining individuals having sparse marker data, obtained using Genotyping-By-Sequencing (GBS).\n\nResultsWe developed GBS for the macaque genome using a single digest with PstI, followed by sequencing to 30X coverage. From GBS sequence data collected on all individuals in a 16-member pedigree, we characterized an optimal 22,455 sparse markers spaced ~125 kb apart. To characterize dense markers for imputation, we performed WGS at 30X coverage on 9 of the 16 individuals, yielding ~10.2 million high-confidence variants. Using the approach of \"Genotype Imputation Given Inheritance\" (GIGI), we imputed alleles at an optimized dense set of 4,920 variants on chromosome 19, using 490 sparse markers from GBS. We assessed changes in accuracy of imputed alleles, 1) across 3 different strategies for selecting individuals for WGS, i.e., a) using \"GIGI-Pick\" to select informative individuals, b) sequencing the most recent generation, or c) sequencing founders only; and 2) when using from 1-9 WGS individuals for imputation. We found that accuracy of imputed alleles was highest using the GIGI-Pick selection strategy (median 92%), and improved very little when using >4 individuals with WGS for imputation. We used this ratio of 4 WGS to 12 GBS individuals to impute an expanded set of ~14.4 million variants across all 20 macaque autosomes, achieving ~85-88% accuracy per chromosome.\n\nConclusionsWe conclude that an optimal tradeoff exists at the ratio of 1 individual selected for WGS using the GIGI-Pick algorithm, per 3-5 relatives selected for GBS, a cost savings of ~67-83% over WGS of all individuals. This approach makes feasible the collection of accurate, dense genome-wide sequence data in large pedigreed macaque cohorts without the need for expensive WGS data on all individuals.

Genomics↗

bioRxiv2016

Wide genome involvement in response to long-term selection for antibody response in an experimental population of White Leghorn chickens

Long-term selection experiments provide a powerful approach to gain empirical insights into adaptation. They allow researchers to uncover the targets of selection and how these contribute to the mode and tempo of adaptation. Here we report results from a pooled genome re-sequencing study to investigate the consequences of 39 generations of bidirectional selection in White Leghorn chickens on a humoral immune trait: antibody response to sheep red blood cells. We observed wide genome involvement in response to this selection regime, with over 200 candidate sweep regions characterised by spans of high genetic differentiation (FST). These sweep signatures, encompassing almost 20% of the chicken genome (208.8 Mb), are primarily the result from bidirectional selection on haplotypes present in the base population. These extensive genomic changes highlight both the extent of standing genetic variation at immune loci available at the onset of selection, as well as how the long-term selection response results from selection on a highly polygenic genetic architecture. Furthermore, we present three examples of strong candidate genes that may have contributed to the profound phenotypic response to selection.\n\nData AvailabilityPooled genome data generated for this study will become available via SRA upon acceptance of manuscript

Genomics↗

bioRxiv2016

Whole genome SNP typing to investigate methicillin-resistant Staphylococcus aureus carriage in a health-care provider as the source of multiple surgical site infections.

BackgroundPrevention of nosocomial transmission of infections is a central responsibility in the healthcare environment, and accurate identification of transmission events presents the first challenge. Phylogenetic analysis based on whole genome sequencing provides a high-resolution approach for accurately relating isolates to one another, allowing precise identification or exclusion of transmission events and sources for nearly all cases. We sequenced 24 methicillin-resistant Staphylococcus aureus (MRSA) genomes to retrospectively investigate a suspected point source of three surgical site infections (SSIs) that occurred over a one-year period. The source of transmission was believed to be a surgical team member colonized with MRSA, involved in all surgeries preceding the SSI cases, who was subsequently decolonized. Genetic relatedness among isolates was determined using whole genome single nucleotide polymorphism (SNP) data.\n\nResultsWhole genome SNP typing (WGST) revealed 283 informative SNPs between the surgical team members isolate and the closest SSI isolate. The second isolate was 286 and the third was thousands of SNPs different, indicating the nasal carriage strain from the surgical team member was not the source of the SSIs. Given the mutation rates estimated for S. aureus, none of the SSI isolates share a common ancestor within the past 14 years, further discounting any common point source for these infections. The decolonization procedures and resources spent on the point source infection control could have been prevented if WGST was performed at the time of the suspected transmission, instead of retrospectively.\n\nConclusionsWhole genome sequence analysis is an ideal method to exclude isolates involved in transmission events and nosocomial outbreaks, and coupling this method with epidemiological data can determine if a transmission event occurred. These methods promise to direct infection control resources more appropriately.

Genomics↗

bioRxiv2016

Genomic Prediction of Hybrid Combinations in the Early Stages of a Maize Hybrid Breeding Pipeline

Prediction of single-cross hybrid performance has been a major goal of plant breeders since the beginning of hybrid breeding. Genomic prediction has shown to be a promising approach, but only limited studies have examined the accuracy of predicting single cross performance. Most of the studies rather focused on predicting top cross performance using single tester to determine the inbred parents worth in hybrid combinations. Moreover, no studies have examined the potential of predicting single crosses made among random progenies derived from a series of biparental families, which resembles the structure of germplasm comprising the initial stages of a hybrid maize breeding pipeline. The main objective of this study was to evaluate the potential of genomic prediction for identifying superior single crosses early in the breeding pipeline and optimize its application. To accomplish these objectives, we designed and analyzed a novel population of single-cross hybrids representing the Iowa Stiff Stalk Synthetic/Non-Stiff Stalk heterotic pattern commonly used in the development of North American commercial maize hybrids. The single cross prediction accuracies estimated using cross-validation ranged from 0.40 to 0.74 for grain yield, 0.68 to 0.91 for plant height and 0.54 to 0.94 for staygreen depending on the number of tested parents of the single crosses. The genomic estimated general and specific combining abilities showed a clear advantage over the use of genomic covariances among single crosses, especially when one or both parents of the single cross were untested in hybrid combinations. Overall, our results suggest that genomic prediction of the performance of single crosses made using random progenies from the early stages of the breeding pipeline holds great potential to re-design hybrid breeding and increase its efficiency.

Genomics↗

bioRxiv2016

Forward genetic screen of human transposase genomic rearrangements

Background. Numerous human genes encode potentially active DNA transposases or recombinases, but our understanding of their functions remains limited due to shortage of methods to profile their activities on endogenous genomic substrates. Results. To enable functional analysis of human transposase-derived genes, we combined forward chemical genetic hypoxanthine-guanine phosphoribosyltransferase 1 (HPRT1) screening with massively parallel paired-end DNA sequencing and structural variant genome assembly and analysis. Here, we report the HPRT1 mutational spectrum induced by the human transposase PGBD5, including PGBD5-specific signal sequences (PSS) that serve as potential genomic rearrangement substrates. Conclusions. The discovered PSS motifs and high-throughput forward chemical genomic screening approach should prove useful for the elucidation of endogenous genome remodeling activities of PGBD5 and other domesticated human DNA transposases and recombinases.

Genomics↗

bioRxiv2016

Regions of very low H3K27me3 partition the Drosophila genome into topological domains

BackgroundIt is now well established that eukaryote genomes have a common architectural organization into topologically associated domains (TADs) and evidence is accumulating that this organization plays an important role in gene regulation. However, the mechanisms that partition the genome into TADs and the nature of domain boundaries are still poorly understood.\n\nResultsWe have investigated boundary regions in the Drosophila genome and find that they can be identified as domains of very low H3K27me3. The genome-wide H3K27me3 profile partitions into two states; very low H3K27me3 identifies Depleted (D) domains that contain housekeeping genes and their regulators such as the histone acetyltransferase-containing NSL complex, whereas domains containing mid-to-high levels of H3K27me3 (Enriched or E domains) are associated with regulated genes, irrespective of whether they are active or inactive. The D domains correlate with the boundaries of TADs and are enriched in a subset of architectural proteins, particularly Chromator, BEAF-32, and Z4/Putzig. However, rather than being clustered at the borders of these domains, these proteins bind throughout the H3K27me3-depleted regions and are much more strongly associated with the transcription start sites of housekeeping genes than with the H3K27me3 domain boundaries.\n\nConclusionsWe suggest that the D domain chromatin state, characterised by very low H3K27me3 and established by housekeeping gene regulators, acts to separate topological domains thereby setting up the domain architecture of the genome.

Genomics↗

bioRxiv2016

Chironomus riparius (Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence

Active transposable elements (TEs) may result in divergent genomic insertion and abundance patterns among conspecific populations. Upon secondary contact, such divergent genetic backgrounds can theoretically give rise to classical Dobzhansky-Muller incompatibilities (DMI), a way how TEs can contribute to the evolution of endogenous genetic barriers and eventually population divergence. We investigated whether differential TE activity created endogenous selection pressures among conspecific populations of the non-biting midge Chironomus riparius, focussing on a Chironomus-specific TE, the minisatellite-like Cla-element, whose activity is associated with speciation in the genus. Using an improved and annotated draft genome for a genomic study with five natural C. riparius populations, we found highly population-specific TE insertion patterns with many private insertions. A highly significant correlation of pairwise population FST from genome-wide SNPs with the FST estimated from TEs suggests drift as the major force driving TE population differentiation. However, the significantly higher Cla-element FST level due to a high proportion of differentially fixed Cla-element insertions indicates that segregating, i.e. heterozygous insertions are selected against. With reciprocal crossing experiments and fluorescent in-situ hybridisation of Cla-elements to polytene chromosomes, we documented phenotypic effects on female fertility and chromosomal mispairings that might be linked to DMI in hybrids. We propose that the inferred negative selection on heterozygous Cla-element insertions causes endogenous genetic barriers and therefore acts as DMI among C. riparius populations. The intrinsic genomic turnover exerted by TEs, thus, may have a direct impact on population divergence that is operationally different from drift and local adaptation.

genomics↗

bioRxiv2016

Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings

Understanding the three-dimensional (3D) architecture of the chromatin and its relation to gene expression and regulation is fundamental to understanding how the genome functions. Advances in Hi-C technology now permit us to have a glimpse into the 3D genome organization and identify topologically associated domains (TADs), but we still lack an understanding of the structural dynamics of chromosomes. The dynamic couplings between regions separated by large genomic distances (> 50 megabases) have yet to be characterized. We adapted a well-established protein-modeling framework, the Gaussian Network Model (GNM), to the task of modeling chromatin dynamics using Hi-C contact data. We show that the GNM can identify structural dynamics at multiple scales: it can quantify the fluctuations in the positions of gene loci, find large genomic compartments and smaller TADs that undergo en-bloc movements, and identify dynamically coupled distal regions along the chromosomes. We show that the predictions of the GNM correlate well with DNase-seq and ATAC-seq measurements on accessibility, the previously identified A and B compartments of chromatin structure, and pairs of interacting loci identified by ChIA-PET. We describe a method to use the GNM to identify novel cross-correlated distal domains (CCDDs) representing regions of long-range dynamic coupling and show that CCDDs are often associated with increased gene coexpression using a large-scale analysis of 212 expression experiments. Together, these results show that GNM provides a mathematically well-founded unified framework for assessing chromatin dynamics and the structural basis of genome-wide observations.

genomics↗

bioRxiv2016

Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample

As part of a study into the molecular genetics of sexually dimorphic complex traits, we used next-generation sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly (Drosophila melanogaster) population. We successfully resequenced the whole genome of 2 females from the Berkeley reference line (BDGP6/dm6), and 220 hemiclonal females that were heterozygous for the same reference line genome, and a unique haplotype from the outbred base population (LHM). The use of a static and known genetic background enabled us to obtain sequences from whole-genome phased haplotypes. We used a BWA-Picard-GATK pipeline for mapping sequence reads to the dm6 reference genome assembly, at a median depth-of coverage of 31X, and have made the resulting data publicly-available in the NCBI Short Read Archive (BioProject PRJNA282591). Haplotype Caller discovered and genotyped 1,726,931 genetic variants (SNPs and indels, <200bp). Additionally, we used GenomeStrip/2.0 to discover and genotype 167 large structural variants (1-100Kb in size). Sequence data and quality-filtered genotype data are publicly-available at NCBI (Short Read Archive, dbSNP and dbVar). We have also released the unfiltered genotype data, and the code and logs for data processing, summary statistics, and graphs, via the research data repository, Zenodo, (https://zenodo.org/, Sussex Drosophila Sequencing community).

genomics↗

bioRxiv2016

The megabase-sized fungal genome of Rhizoctonia solani assembled from nanopore reads only.

The ability to quickly obtain accurate genome sequences of eukaryotic pathogens at low costs provides a tremendous opportunity to identify novel targets for therapeutics, develop pesticides with increased target specificity and breed for resistance in food crops. Here, we present the first report of the ~54 MB eukaryotic genome sequence of Rhizoctonia solani, an important pathogenic fungal species of maize, using nanopore technology. Moreover, we show that optimizing the strategy for wet-lab procedures aimed to isolate high quality and ultra-pure high molecular weight (HMW) DNA results in increased read length distribution and thereby allowing generation of the most contiguous genome assembly for R. solani to date. We further determined sequencing accuracy and compared the assembly to short-read technologies. With the current sequencing technology and bioinformatics tool set, we are able to deliver an eukaryotic fungal genome at low cost within a week. With further improvements of the sequencing technology and increased throughput of the PromethION sequencer we aim to generate near-finished assemblies of large and repetitive plant genomes and cost-efficiently perform de novo sequencing of large collections of microbial pathogens and the microbial communities that surround our crops.

genomics↗