scholarly journals Genomic structural variation in ‘Nebbiolo’ grapevines at the individual, clonal and cultivar levels

2020 ◽  
Author(s):  
Simone Maestri ◽  
Giorgio Gambino ◽  
Andrea Minio ◽  
Irene Perrone ◽  
Emanuela Cosentino ◽  
...  
Keyword(s):  
Structural Variation ◽  
Reference Genome ◽  
Red Wines ◽  
Structural Variants ◽  
Genomic Structural Variation ◽  
Grapevine Cultivar ◽  
Long Reads ◽  
Genomic Environment ◽  
The Individual ◽  
North Western

AbstractStructural Variants (SVs) are a widely unexplored source of genetic variation, both due to methodological limitations and because they are generally associated to deleterious effects. However, with the advent of long-range genomic platforms, it has become easier to directly detect SVs. In the same direction, clonally propagated crops provide a unique opportunity to study SVs, offering a suitable genomic environment for their accumulation in heterozygosis. In particular, it has been reported that SVs generate drastic levels of heterozygosity in grapevines. ‘Nebbiolo’ (Vitis vinifera L.) is a grapevine cultivar typical of north-western Italy, appreciated for its use in producing high-quality red wines. Here, we aimed to analyze the frequency of SVs in ‘Nebbiolo’, at three different organizational levels. For this purpose, we generated genomic data based on long-reads, linked-reads and optical mapping. We assembled a reference genome for this cultivar and compared two different clones, including V. vinifera reference genome (PN40024) in our comparisons. Our results indicate that SVs differentially occurring between ‘Nebbiolo’ clones might be rare, while SVs differentiating haplotypes of the same individual are as abundant as those that occur differentially between cultivars.

scholarly journals stLFRsv: A Germline Structural Variant Analysis Pipeline Using Co-barcoded Reads

2021 ◽  
Vol 12 ◽  
Author(s):  
Junfu Guo ◽  
Chang Shi ◽  
Xi Chen ◽  
Ou Wang ◽  
Ping Liu ◽  
...  
Keyword(s):  
Structural Variation ◽  
Signal To Noise Ratio ◽  
Recall Rate ◽  
Structural Variants ◽  
Analysis Pipeline ◽  
Haplotype Phasing ◽  
Base Level ◽  
Long Reads ◽  
Variant Analysis ◽  
Complex Structural

Co-barcoded reads originating from long DNA fragments (mean length >30 kbp) maintain both single base level accuracy and long-range genomic information. We propose a pipeline, stLFRsv, to detect structural variation using co-barcoded reads. stLFRsv identifies abnormal large gaps between co-barcoded reads to detect potential breakpoints and reconstruct complex structural variants (SVs). Haplotype phasing by co-barcoded reads increases the signal to noise ratio, and barcode sharing profiles are used to filter out false positives. We integrate the short read SV caller smoove for smaller variants with stLFRsv. The integrated pipeline was evaluated on the well-characterized genome HG002/NA24385, and 74.5% precision and a 22.4% recall rate were obtained for deletions. stLFRsv revealed some large variants not included in the benchmark set that were verified by long reads or assembly. For the HG001/NA12878 genome, stLFRsv also achieved the best performance for both resource usage and the detection of large variants. Our work indicates that co-barcoded read technology has the potential to improve genome completeness.

scholarly journals Long-read-based Human Genomic Structural Variation Detection with cuteSV

2019 ◽  
Author(s):  
Tao Jiang ◽  
Bo Liu ◽  
Yue Jiang ◽  
Junyi Li ◽  
Yan Gao ◽  
...  
Keyword(s):  
Structural Variation ◽  
High Sensitivity ◽  
Structural Variations ◽  
Genomic Structural Variation ◽  
Long Reads ◽  
Detection Approach ◽  
Refinement Method ◽  
Long Read ◽  
Human Genomic ◽  
And Performance

AbstractLong-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real PacBio and ONT datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. cuteSV is available at https://github.com/tjiangHIT/cuteSV.

scholarly journals Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double-stranded DNA viruses

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Vincent Loiseau ◽  
Elisabeth A Herniou ◽  
Yannis Moreau ◽  
Nicolas Lévêque ◽  
Carine Meignin ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Structural Variation ◽  
Negative Impact ◽  
Wide Spectrum ◽  
Low Frequency ◽  
Beet Armyworm ◽  
Dna Viruses ◽  
Genomic Structural Variation ◽  
Long Reads ◽  
Long Read

Abstract Our knowledge of the diversity and frequency of genomic structural variation segregating in populations of large double-stranded (ds) DNA viruses is limited. Here, we sequenced the genome of a baculovirus (Autographa californica multiple nucleopolyhedrovirus [AcMNPV]) purified from beet armyworm (Spodoptera exigua) larvae at depths >195,000× using both short- (Illumina) and long-read (PacBio) technologies. Using a pipeline relying on hierarchical clustering of structural variants (SVs) detected in individual short- and long-reads by six variant callers, we identified a total of 1,141 SVs in AcMNPV, including 464 deletions, 443 inversions, 160 duplications, and 74 insertions. These variants are considered robust and unlikely to result from technical artifacts because they were independently detected in at least three long reads as well as at least three short reads. SVs are distributed along the entire AcMNPV genome and may involve large genomic regions (30,496 bp on average). We show that no less than 39.9 per cent of genomes carry at least one SV in AcMNPV populations, that the vast majority of SVs (75%) segregate at very low frequency (<0.01%) and that very few SVs persist after ten replication cycles, consistent with a negative impact of most SVs on AcMNPV fitness. Using short-read sequencing datasets, we then show that populations of two iridoviruses and one herpesvirus are also full of SVs, as they contain between 426 and 1,102 SVs carried by 52.4–80.1 per cent of genomes. Finally, AcMNPV long reads allowed us to identify 1,757 transposable elements (TEs) insertions, 895 of which are truncated and occur at one extremity of the reads. This further supports the role of baculoviruses as possible vectors of horizontal transfer of TEs. Altogether, we found that SVs, which evolve mostly under rapid dynamics of gain and loss in viral populations, represent an important feature in the biology of large dsDNA viruses.

scholarly journals Establishment of an eHAP1 Human Haploid Cell Line Hybrid Reference Genome Assembled from Short and Long Reads

2019 ◽  
Author(s):  
William D. Law ◽  
René L. Warren ◽  
Andrew S. McCallion
Keyword(s):  
Cell Line ◽  
Reference Genome ◽  
De Novo ◽  
Open Chromatin ◽  
Haploid Cell ◽  
Structural Variants ◽  
High Quality ◽  
Short Reads ◽  
Long Reads ◽  
Low Coverage

AbstractBackgroundHaploid cell lines are a valuable research tool with broad applicability for genetic assays. As such the fully haploid human cell line, eHAP1, has been used in a wide array of studies. However, the absence of a corresponding reference genome sequence for this cell line has limited the potential for more widespread applications to experiments dependent on available sequence, like capture-clone methodologies.ResultsWe generated ~15x coverage Nanopore long reads from ten GridION flowcells. We utilized this data to assemble a de novo draft genome using minimap and miniasm and subsequently polished using Racon. This assembly was further polished using previously generated, low-coverage, Illumina short reads with Pilon and ntEdit. This resulted in a hybrid eHAP1 assembly with >90% complete BUSCO scores. We further assessed the eHAP1 long read data for structural variants using Sniffles and identify a variety of rearrangements, including a previously established Philadelphia translocation. Finally, we demonstrate how some of these variants overlap open chromatin regions, potentially impacting regulatory regions.ConclusionsBy integrating both long and short reads, we generated a high-quality reference assembly for eHAP1 cells. We identify structural variants using long reads, including some that may impact putative regulatory elements. The union of long and short reads demonstrates the utility in combining sequencing platforms to generate a high-quality reference genome de novo solely from low coverage data. We expect the resulting eHAP1 genome assembly to provide a useful resource to enable novel experimental applications in this important model cell line.

scholarly journals A diploid assembly-based benchmark for variants in the major histocompatibility complex

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Chen-Shan Chin ◽  
Justin Wagner ◽  
Qiandong Zeng ◽  
Erik Garrison ◽  
Shilpa Garg ◽  
...  
Keyword(s):  
Major Histocompatibility Complex ◽  
Performance Assessment ◽  
Reference Genome ◽  
De Novo ◽  
Major Histocompatibility ◽  
Structural Variants ◽  
Histocompatibility Complex ◽  
Human Genomes ◽  
Long Reads ◽  
Complex Variation

Abstract Most human genomes are characterized by aligning individual reads to the reference genome, but accurate long reads and linked reads now enable us to construct accurate, phased de novo assemblies. We focus on a medically important, highly variable, 5 million base-pair (bp) region where diploid assembly is particularly useful - the Major Histocompatibility Complex (MHC). Here, we develop a human genome benchmark derived from a diploid assembly for the openly-consented Genome in a Bottle sample HG002. We assemble a single contig for each haplotype, align them to the reference, call phased small and structural variants, and define a small variant benchmark for the MHC, covering 94% of the MHC and 22368 variants smaller than 50 bp, 49% more variants than a mapping-based benchmark. This benchmark reliably identifies errors in mapping-based callsets, and enables performance assessment in regions with much denser, complex variation than regions covered by previous benchmarks.

scholarly journals The Polygraph: A Data Structure for Genome Alignment and Variation Detection

10.29007/txxd ◽  
2019 ◽  
Author(s):  
Masaki Fujimoto ◽  
Cole Lyman ◽  
Mark Clement
Keyword(s):  
Data Structure ◽  
Structural Variation ◽  
Genomic Structure ◽  
Genome Alignment ◽  
Graph Structure ◽  
Structural Variants ◽  
De Bruijn Graphs ◽  
Genomic Structural Variation ◽  
Whole Genomes ◽  
Whole Genome Alignment

Comparing whole genomes and finding variation is an important and difficult bioinformatic task. We present the Polygraph, a data structure for reference-free, multiple whole genome alignment that can be used to identify genomic structural variation. This data structure is built from assembled genomes and preserves the genomic structure from the assembly. It avoids the “hairball” graph structure that can occur in other graph methods such as de Bruijn graphs. The Polygraph can easily be visualized and be used for identification of structural variants. We apply the Polygraph to Escherichia coli and Saccharomyces cerevisiae for finding Structural Variants.

Whole genome sequencing of sporadic Burkitt lymphoma in HIV-infected and uninfected patients.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. 8577-8577
Author(s):  
Deborah Ritter ◽  
Kimberly Walker ◽  
Myoung Kwon ◽  
Premal Lulla ◽  
Catherine M. Bollard ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Dna Sequences ◽  
Burkitt Lymphoma ◽  
Structural Variation ◽  
Reference Genome ◽  
Statistical Significance ◽  
Whole Genome ◽  
Average Insert Size ◽  
Structural Variants

8577 Background: Burkitt Lymphoma is defined by canonical translocations between MYC and immunoglobulin IgH, IgK or IgL (8:14, 8:2, 8:22, respectively), and is commonly associated with HIV. The identification of HIV from sequenced samples is critical to understanding HIV-associated Burkitt Lymphoma. While recent novel gene mutations (ID3 and TCF3) have been implicated in functional roles, concomitant genomic structural variants and the interaction of HIV with structural variation is less well defined. Methods: We sequenced the whole genomes of 15 patients with 100bp paired-end reads on Illumina Hi-Seq platform, resulting in an average insert size of 278 (+/- 63) and coverage of 60X tumor and 30X normal. We included 7 HIV-negative, and 8 HIV-positive subjects. Sequencing reads were mapped to the reference genome using BWA. Large-scale structural variation was detected by the BreakDancer and Crest programs. Functional annotation was used to prioritize structural variants for validation. Single nucleotide variants and small insertions and deletions were detected by CARNAC, a somatic variation discovery pipeline. The subset of WGS reads that failed to align to the human reference genome were tested for the presence of HIV sequences by comparing the unmapped reads to a database of viral DNA sequences which included the common subtypes of HIV defined by Los Alamos. Reads matching HIV or EBV with an expectation value of <10-4 were analyzed to determine virus coverage and viral integration sites. Results: Canonical MYC-IgH translocations were identified in 9/15 (60%) tumor samples, with 2 additional subjects harboring either a deletion or an inversion near exon1 of MYC; 4 had no MYC rearrangement. MYC translocations occurred equally in both groups. TP53 and SMARC4 point mutations were observed recurrently in the HIV uninfected group but not in the HIV infected patients. Variable levels of HIV DNA sequence were observed in normal tissue of all HIV infected patients. Conclusions: Whole genome sequencing has identified known somatic variants in HIV infected and uninfected patients. Two genes, TP53 and SMARC4, appear to be differentially mutated, but additional samples are needed to achieve statistical significance.

Distribution, systematics and nomenclature of the three taxa of Common Stonechats (Aves, Passeriformes, Muscicapidae, Saxicola) that breed in the Caucasian region

2020 ◽  
Vol 29 (1) ◽  
pp. 33-57
Author(s):  
V.M. Loskot ◽  
G.B. Bakhtadze
Keyword(s):  
Geographic Distribution ◽  
Habitat Preferences ◽  
Junior Synonym ◽  
Type Locality ◽  
Diagnostic Features ◽  
Western Turkey ◽  
Geographical Variations ◽  
History Of ◽  
The Individual ◽  
North Western

Geographic distribution and habitat preferences of Saxicola rubicola rubicola (Linnaeus, 1766), S. maurus variegatus (S.G. Gmelin, 1774), and S. m. armenicus (Stegman, 1935) inhabiting the Caucasian Isthmus and adjacent areas are described in detail. We examined the individual, sexual, age, seasonal and geographical variations of seven main diagnostic features of both plumage and morphometrics (exactly, the length of wing and tail) using 381 skin specimens. Substantially improved diagnoses of S. m. variegatus and S. m. armenicus are provided. After a thorough examination of the materials and history of the expedition of Samuel Gmelin in 1768–1774, and his description of Parus variegatus, it was concluded that the type locality of this taxon was the vicinity of Shamakhi in Azerbaijan not Enzeli in North-Western Turkey. It is also shown the fallacy of the recently proposed attribution of the holotype of the northern subspecies S. m. variegatus to the southern taxon S. m. armenicus and synonymisation of these names, as well as the replacement of the name S. m. variegatus by its junior synonym S. m. hemrichii Ehrenberg, 1833 for the northern subspecies.

Individual psychological characteristics of employees of criminal investigation departments in transport due to the risk of professional deformation

2020 ◽  
Vol 2020 (4) ◽  
pp. 220-230
Author(s):  
Yuliya Novikova ◽  
Alexander Shakhmatov ◽  
Maria Salyah
Keyword(s):  
Police Officers ◽  
Social Intelligence ◽  
Federal District ◽  
Psychological Characteristics ◽  
Criminal Investigation ◽  
Professional Burnout ◽  
The North ◽  
The Individual ◽  
North Western ◽  
Learn Behavior

The relevance of the study of individual psychological characteristics of employees of criminal investigation departments in transport in the North-Western Federal district of the Ministry of Internal Affairs of Russia (hereinafter referred to as the NWFD) in relation to indicators of professional deformation is due to the specific features of their official activities. Despite a significant amount of research on the phenomenon of professional deformity of police officers, there are few thoroughly developed and completed works on the prevention of professional deformities of police officers. The purpose of our research was to study the individual psychological characteristics of employees of criminal investigation departments in connection with the risk of professional deformation. The results of the empirical study were processed by correlation and factor analysis (49 parameters). The results of the initial analysis showed that the overall assessment of job satisfaction among employees of the studied departments is average with a downward trend. The results of the study on «professional burnout» revealed that a number of employees surveyed are close to emotional exhaustion. It is established that empathic abilities, social intelligence, and constructive coping strategies play an important role in the structure of individual psychological characteristics of police officers. Low ability of employees to learn behavior determines non-constructive strategies and models for coping with stressful situations, which leads to deformation of relationships with other people, i.e. to professional deformation. The obtained data can be used as the basis for the program of psychoprophylaxis of professional deformation of criminal investigation units in transport in the northwestern Federal district.

scholarly journals Between Pleasure and Resistance: The Role of Substance Consumption in an Italian Working-Class Subculture

Societies ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 58
Author(s):  
Placido
Keyword(s):  
Working Class ◽  
Cultural Practices ◽  
Critical Criminology ◽  
Ethnographic Case Study ◽  
Youth Cultures ◽  
The Individual ◽  
Substance Consumption ◽  
North Western

In this article I discuss how illegal substance consumption can act as a tool of resistance and as an identity signifier for young people through a covert ethnographic case study of a working-class subculture in Genoa, North-Western Italy. I develop my argument through a coupled reading of the work of the Centre for Contemporary Cultural Studies (CCCS) and more recent post-structural developments in the fields of youth studies and cultural critical criminology. I discuss how these apparently contrasting lines of inquiry, when jointly used, shed light on different aspects of the cultural practices of specific subcultures contributing to reflect on the study of youth cultures and subcultures in today’s society and overcoming some of the ‘dead ends’ of the opposition between the scholarly categories of subculture and post-subculture. In fact, through an analysis of the sites, socialization processes, and hedonistic ethos of the subculture, I show how within a single subculture there could be a coexistence of: resistance practices and subversive styles of expression as the CCCS research program posits; and signs of fragmentary and partial aesthetic engagements devoid of political contents and instead primarily oriented towards the affirmation of the individual, as argued by the adherents of the post-subcultural position.

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