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Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromatin conformation capture data

ABSTRACT: Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromatin capture data

PROVIDER: PRJEB16743 | ENA |

REPOSITORIES: ENA

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	Arabis_alpina.Run-01.bnx.gz	Other
	Arabis_alpina.Run-02.bnx.gz	Other
	Arabis_alpina.Run-03.bnx.gz	Other
	Arabis_alpina.Run-04.bnx.gz	Other

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Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data.

Project description:Long-read sequencing can overcome the weaknesses of short reads in the assembly of eukaryotic genomes; however, at present additional scaffolding is needed to achieve chromosome-level assemblies. We generated Pacific Biosciences (PacBio) long-read data of the genomes of three relatives of the model plant Arabidopsis thaliana and assembled all three genomes into only a few hundred contigs. To improve the contiguities of these assemblies, we generated BioNano Genomics optical mapping and Dovetail Genomics chromosome conformation capture data for genome scaffolding. Despite their technical differences, optical mapping and chromosome conformation capture performed similarly and doubled N50 values. After improving both integration methods, assembly contiguity reached chromosome-arm-levels. We rigorously assessed the quality of contigs and scaffolds using Illumina mate-pair libraries and genetic map information. This showed that PacBio assemblies have high sequence accuracy but can contain several misassemblies, which join unlinked regions of the genome. Most, but not all, of these misjoints were removed during the integration of the optical mapping and chromosome conformation capture data. Even though none of the centromeres were fully assembled, the scaffolds revealed large parts of some centromeric regions, even including some of the heterochromatic regions, which are not present in gold standard reference sequences.

| S-EPMC5411772 | biostudies-literature

Effect of Network-Correcting Molecules

Project description:Effect of Network-Correcting Molecules

| PRJNA635425 | ENA

Long read cassava genome assemblies

Project description:Cassava genomes assembled with single-molecule long reads, optical and Hi-C maps reveal narrow genetic diversity and mono-allelic expression

| PRJEB27129 | ENA

BiSCoT: improving large eukaryotic genome assemblies with optical maps.

Project description:MotivationLong read sequencing and Bionano Genomics optical maps are two techniques that, when used together, make it possible to reconstruct entire chromosome or chromosome arms structure. However, the existing tools are often too conservative and organization of contigs into scaffolds is not always optimal.ResultsWe developed BiSCoT (Bionano SCaffolding COrrection Tool), a tool that post-processes files generated during a Bionano scaffolding in order to produce an assembly of greater contiguity and quality. BiSCoT was tested on a human genome and four publicly available plant genomes sequenced with Nanopore long reads and improved significantly the contiguity and quality of the assemblies. BiSCoT generates a fasta file of the assembly as well as an AGP file which describes the new organization of the input assembly.AvailabilityBiSCoT and improved assemblies are freely available on GitHub at http://www.genoscope.cns.fr/biscot and Pypi at https://pypi.org/project/biscot/.

| S-EPMC7649008 | biostudies-literature

Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies.

Project description:BackgroundIn the metagenomic assembly of a microbial community, abundant species are often thought to assemble well given their deeper sequencing coverage. This conjuncture is rarely tested or evaluated in practice. We often do not know how many abundant species are missing and do not have an approach to recover them.ResultsHere, we propose k-mer based and 16S RNA based methods to measure the completeness of metagenome assembly. We show that even with PacBio high-fidelity (HiFi) reads, abundant species are often not assembled, as high strain diversity may lead to fragmented contigs. We develop a novel reference-free algorithm to recover abundant metagenome-assembled genomes (MAGs) by identifying circular assembly subgraphs. Complemented with a reference-free genome binning heuristics based on dimension reduction, the proposed method rescues many abundant species that would be missing with existing methods and produces competitive results compared to those state-of-the-art binners in terms of total number of near-complete genome bins.ConclusionsOur work emphasizes the importance of metagenome completeness, which has often been overlooked. Our algorithm generates more circular MAGs and moves a step closer to the complete representation of microbial communities.

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Optical Genome Mapping

Project description:Bionano Genomics Optical Genome Mapping Dataset as part of HGSVC3

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Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications.

Project description:Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow. We assembled two high-quality genome references using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical maps (optical map assembly [OM]). A three-way comparison including the published short-read assembly (SR) constructed for the same individual allowed assessing assembly properties and pinpointing misassemblies. By combining information from all three assemblies, we characterized 36 previously unidentified large repetitive regions in the proximity of sequence assembly breakpoints, the majority of which contained complex arrays of a 14-kb satellite repeat or its 1.2-kb subunit. Using whole-genome population resequencing data, we estimated the population-scaled recombination rate (ρ) and found it to be significantly reduced in these regions. These findings are consistent with an effect of low recombination in regions adjacent to centromeric or subtelomeric heterochromatin and add to our understanding of the processes generating widespread heterogeneity in genetic diversity and differentiation along the genome. By combining three different technologies, our results highlight the importance of adding a layer of information on genome structure that is inaccessible to each approach independently.

| S-EPMC5411765 | biostudies-literature

Genome-wide analysis of retinal transcriptome reveals common genetic network underlying perception of contrast and optical defocus detection

Project description:Refractive eye development is regulated by optical defocus in a process of emmetropization. Excessive exposure to negative optical defocus often leads to the development of myopia. However, it is still largely unknown how optical defocus is detected by the retina. Here, we used genome-wide RNA-sequencing (RNA-seq) to conduct analysis of the retinal genetic networks underlying contrast perception and refractive eye development. We report that the genetic network subserving contrast perception plays an important role in optical defocus detection and emmetropization. Our results demonstrate an interaction between contrast perception, the retinal circadian clock pathway and the signaling pathway underlying optical defocus detection. We also observe that the relative majority of genes causing human myopia are involved in the processing of optical defocus. Together, our results support the hypothesis that optical defocus is perceived by the retina using contrast as a proxy and provide new insights into molecular signaling underlying refractive eye development.

2021-06-03 | GSE158732 | GEO

Improving Optical Diagnosis of Colorectal Polyps Using CADx and BASIC.

Project description:Primary, this study aims to develop and validate a computer-aided diagnosis (CADx) system for the characterization of colorectal polyps. Second, this study evaluates the effect of using a clinical classification model Blue Light Imaging Adenoma Serrated International (BASIC) on the diagnostic accuracy of the optical diagnosis of colorectal polyps compared to intuitive optical diagnosis for both expert endoscopists and novices.

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Optical mapping data for 16 cattle

Project description:Bionano optical mapping data for 16 cattle

| PRJEB52551 | ENA