Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19.

Heretofore, little is known about the mechanism underlying the genotype-dependence of embryonic callus (EC) induction, which has severely inhibited the development of maize genetic engineering. Here, we report the genome sequence and annotation of a maize inbred line with high EC induction ratio, A188, which is assembled from single-molecule sequencing and optical genome mapping. We assembled a 2,210 Mb genome with a scaffold N50 size of 11.61 million bases (Mb), compared to those of 9.73 Mb for B73 and 10.2 Mb for Mo17. Comparative analysis revealed that ~30% of the predicted A188 genes had large structural variations to B73, Mo17 and W22 genomes, which caused considerable protein divergence and might lead to phenotypic variations between the four inbred lines. Combining our new A188 genome, previously reported QTLs and RNA sequencing data, we reveal 8 large structural variation genes and 4 differentially expressed genes playing potential roles in EC induction.

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Comprehensive Analysis of Human Subtelomeres by Whole Genome Mapping

10.1101/728519 ◽

2019 ◽

Author(s):

Eleanor Young ◽

Heba Z. Abid ◽

Pui-Yan Kwok ◽

Harold Riethman ◽

Ming Xiao

Keyword(s):

Long Range ◽

Genome Mapping ◽

Subtelomeric Region ◽

Reference Sequence ◽

Segmental Duplications ◽

Structural Variations ◽

Sequence Characterization ◽

Current Reference ◽

Sequencing Technologies ◽

Chromosome Arm

AbstractDetailed comprehensive knowledge of the structures of individual long-range telomere-terminal haplotypes are needed to understand their impact on telomere function, and to delineate the population structure and evolution of subtelomere regions. However, the abundance of large evolutionarily recent segmental duplications and high levels of large structural variations have complicated both the mapping and sequence characterization of human subtelomere regions. Here, we use high throughput optical mapping of large single DNA molecules in nanochannel arrays for 154 human genomes from 26 populations to present a comprehensive look at human subtelomere structure and variation. The results catalog many novel long-range subtelomere haplotypes and determine the frequencies and contexts of specific subtelomeric duplicons on each chromosome arm, helping to clarify the currently ambiguous nature of many specific subtelomere structures as represented in the current reference sequence (HG38). The organization and content of some duplicons in subtelomeres appear to show both chromosome arm and population-specific trends. Based upon these trends we estimate a timeline for the spread of these duplication blocks.Author SummaryThe ends of human chromosomes have caps called telomeres that are essential. These telomeres are influenced by the portions of DNA next to them, a region known as the subtelomere. We need to better understand the subtelomeric region to understand how it impacts the telomeres. This subtelomeric region is not well described in the current references. This is due to large variations in this region and portions that are repeated many times, making current sequencing technologies struggle to capture these regions. Many of these variations are evolutionary recent. Here we use 154 different samples from the 26 geographic regions of the world to gain a better understanding of the variation in these regions. We found many new haplotypes and clarified the haplotypes existing in the current reference. We then examined population and chromosome specific trends.

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Abstract 994: Diagnosing leukemia structural variations via a novel genome mapping approach

10.1158/1538-7445.am2017-994 ◽

2017 ◽

Author(s):

Christopher Pool ◽

Jie Xu ◽

Darrin Bann ◽

David Goldenberg ◽

Arati Sharma ◽

...

Keyword(s):

Genome Mapping ◽

Structural Variations ◽

Mapping Approach

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Crystalloid Inclusions in Hepatocyte Mitochondria and Their Similarity to Cytoplasmic Crystalloids

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100051001 ◽

1974 ◽

Vol 32 ◽

pp. 198-199

Author(s):

Odell T. Minick ◽

Hidejiro Yokoo

Keyword(s):

Liver Disease ◽

Alcoholic Liver Disease ◽

Special Interest ◽

Structural Variations ◽

Mitochondrial Alterations ◽

The Matrix ◽

Crystalloid Inclusions ◽

Liver Biopsies

Mitochondrial alterations were studied in 25 liver biopsies from patients with alcoholic liver disease. Of special interest were the morphologic resemblance of certain fine structural variations in mitochondria and crystalloid inclusions. Four types of alterations within mitochondria were found that seemed to relate to cytoplasmic crystalloids.Type 1 alteration consisted of localized groups of cristae, usually oriented in the long direction of the organelle (Fig. 1A). In this plane they appeared serrated at the periphery with blind endings in the matrix. Other sections revealed a system of equally-spaced diagonal lines lengthwise in the mitochondrion with cristae protruding from both ends (Fig. 1B). Profiles of this inclusion were not unlike tangential cuts of a crystalloid structure frequently seen in enlarged mitochondria described below.

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Stain contamination and embedding in electron microscopy

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100141986 ◽

1986 ◽

Vol 44 ◽

pp. 50-53

Author(s):

Hilton H. Mollenhauer

Keyword(s):

Electron Microscopy ◽

Information Retrieval ◽

Epoxy Resins ◽

Image Contrast ◽

Sample Preservation ◽

Factors Associated ◽

Amount Of Information ◽

Electron Microscopical ◽

Contrast Information

Many factors (e.g., resolution of microscope, type of tissue, and preparation of sample) affect electron microscopical images and alter the amount of information that can be retrieved from a specimen. Of interest in this report are those factors associated with the evaluation of epoxy embedded tissues. In this context, informational retrieval is dependant, in part, on the ability to “see” sample detail (e.g., contrast) and, in part, on tue quality of sample preservation. Two aspects of this problem will be discussed: 1) epoxy resins and their effect on image contrast, information retrieval, and sample preservation; and 2) the interaction between some stains commonly used for enhancing contrast and information retrieval.

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High-resolution nucleic acid sequence mapping via in situ hybridization at the Electron Microscope level

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100140130 ◽

1995 ◽

Vol 53 ◽

pp. 752-753

Author(s):

B.A. Hamkalo ◽

S. Narayanswami ◽

A.P. Kausch

Keyword(s):

Nucleic Acid ◽

Interphase Nucleus ◽

Genome Mapping ◽

Precise Location ◽

Electron Microscope Level ◽

Rna Sequences ◽

Fundamental Interest ◽

Whole Cells ◽

Dna And Rna

The availability of nonradioactive methods to label nucleic acids an the resultant rapid and greater sensitivity of detection has catapulted the technique of in situ hybridization to become the method of choice to locate of specific DNA and RNA sequences on chromosomes and in whole cells in cytological preparations in many areas of biology. It is being applied to problems of fundamental interest to basic cell and molecular biologists such as the organization of the interphase nucleus in the context of putative functional domains; it is making major contributions to genome mapping efforts; and it is being applied to the analysis of clinical specimens. Although fluorescence detection of nucleic acid hybrids is routinely used, certain questions require greater resolution. For example, very closely linked sequences may not be separable using fluorescence; the precise location of sequences with respect to chromosome structures may be below the resolution of light microscopy(LM); and the relative positions of sequences on very small chromosomes may not be feasible.

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