scholarly journals Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats

2020 ◽  
Vol 11 ◽  
Author(s):  
Romain De Oliveira ◽  
Hélène Rimbert ◽  
François Balfourier ◽  
Jonathan Kitt ◽  
Emeric Dynomant ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Structural Variations ◽  
Chromosome 3B

scholarly journals CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259540
Author(s):  
Morad M. Mokhtar ◽  
Alsamman M. Alsamman ◽  
Haytham M. Abd-Elhalim ◽  
Achraf El Allali
Keyword(s):  
Transposable Elements ◽  
Crop Improvement ◽  
Draft Genome ◽  
Structural Variations ◽  
Web Based ◽  
Cicer Echinospermum ◽  
Genome Wide ◽  
Cicer Species ◽  
Trait Improvement ◽  
Made In

Recently, Cicer species have experienced increased research interest due to their economic importance, especially in genetics, genomics, and crop improvement. The Cicer arietinum, Cicer reticulatum, and Cicer echinospermum genomes have been sequenced and provide valuable resources for trait improvement. Since the publication of the chickpea draft genome, progress has been made in genome assembly, functional annotation, and identification of polymorphic markers. However, work is still needed to identify transposable elements (TEs) and make them available for researchers. In this paper, we present CicerSpTEdb, a comprehensive TE database for Cicer species that aims to improve our understanding of the organization and structural variations of the chickpea genome. Using structure and homology-based methods, 3942 C. echinospermum, 3579 C. reticulatum, and 2240 C. arietinum TEs were identified. Comparisons between Cicer species indicate that C. echinospermum has the highest number of LTR-RT and hAT TEs. C. reticulatum has more Mutator, PIF Harbinger, Tc1 Mariner, and CACTA TEs, while C. arietinum has the highest number of Helitron. CicerSpTEdb enables users to search and visualize TEs by location and download their results. The database will provide a powerful resource that can assist in developing TE target markers for molecular breeding and answer related biological questions. Database URL: http://cicersptedb.easyomics.org/index.php

scholarly journals Organization and evolution of transposable elements along the bread wheat chromosome 3B

2014 ◽  
Vol 15 (12) ◽  
Author(s):  
Josquin Daron ◽  
Natasha Glover ◽  
Lise Pingault ◽  
Sébastien Theil ◽  
Véronique Jamilloux ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Bread Wheat ◽  
Wheat Chromosome ◽  
Evolution Of Transposable Elements ◽  
Chromosome 3B

The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations

genesis ◽  
2020 ◽  
Vol 58 (12) ◽  
Author(s):  
Marco Fambrini ◽  
Gabriele Usai ◽  
Alberto Vangelisti ◽  
Flavia Mascagni ◽  
Claudio Pugliesi
Keyword(s):  
Transposable Elements ◽  
Structural Variations ◽  
The Impact ◽  
Plastic Genome

scholarly journals Chromosomal rearrangements but no change of genes and transposable elements repertoires in an invasive forest-pathogenic fungus

2021 ◽  
Author(s):  
Arthur Demené ◽  
Benoît Laurent ◽  
Sandrine Cros-Arteil ◽  
Christophe Boury ◽  
Cyril Dutech
Keyword(s):  
Transposable Elements ◽  
Fungal Pathogen ◽  
De Novo ◽  
Pathogenic Fungus ◽  
Chromosomal Rearrangements ◽  
Low Complexity ◽  
Cryphonectria Parasitica ◽  
Genome Comparison ◽  
Structural Variations ◽  
High Quality

AbstractChromosomal rearrangements have been largely described among eukaryotes, and may have important consequences on evolution of species. High genome plasticity have been often reported in Fungi, which may explain their apparent ability to quickly adapt to new environments.Cryphonectria parasitica, causing the Chestnut blight disease, is an invasive fungal pathogen species associated with several recent host shifts during its successive introductions from Asia to North America and Europe. Previous cytological karyotyping and genomic studies suggested several chromosomal rearrangements which remains to be described in details for this species. A serious limitation for valid genome comparisons is the access to robust genome assemblies that usually contain genomic regions of low complexity.We present a new de-novo whole-genome assembly obtained from a high quality DNA extraction and long reads sequencing Nanopore technology obtained from an isolate sampled in the native Japanese area of the species. The comparison with a recently published reference genome showed no significant variations in gene and transposable elements (TEs) repertoires. We also showed that theC. parasiticagenome is lowly compartmentalized, with a poor association between TEs and some specific genes, such as those potentially involved in host interactions (i.e. genes coding for small secreted proteins or for secondary metabolites). This genome comparison, however, detected several large chromosomal rearrangements that may have important consequences in gene regulations and sexual mating in this invasive species. This study opens the way for more comparisons of high-quality assembled genomes, and questions the role of structural variations on the invasive success of this fungal pathogen species.

Crystalloid Inclusions in Hepatocyte Mitochondria and Their Similarity to Cytoplasmic Crystalloids

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.

Survey of transposable elements from rice genomic sequences

2001 ◽  
Vol 25 (2) ◽  
pp. 169-179 ◽  
Author(s):  
Kime Turcotte ◽  
Sujatha Srinivasan ◽  
Thomas Bureau
Keyword(s):  
Transposable Elements ◽  
Genomic Sequences

Direct Read and Quantify Damage Nucleotide from an Oligonucleotide Using a Single Molecule Interface

2019 ◽  
Author(s):  
Jiajun Wang ◽  
Meng-Yin Li ◽  
Jie Yang ◽  
Ya-Qian Wang ◽  
Xue-Yuan Wu ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Single Molecule ◽  
Genetic Diseases ◽  
High Sensitivity ◽  
Dna Lesions ◽  
Lesion Detection ◽  
The Novel ◽  
Structural Variations ◽  
Dna Lesion ◽  
Base Lesion

DNA lesion such as metholcytosine(<sup>m</sup>C), 8-OXO-guanine(<sup>O</sup>G), inosine(I) <i>etc</i> could cause the genetic diseases. Identification of the varieties of lesion bases are usually beyond the capability of conventional DNA sequencing which is mainly designed to discriminate four bases only. Therefore, lesion detection remain challenge due to the massive varieties and less distinguishable readouts for minor structural variations. Moreover, standard amplification and labelling hardly works in DNA lesions detection. Herein, we designed a single molecule interface from the mutant K238Q Aerolysin, whose confined sensing region shows the high compatible to capture and then directly convert each base lesion into distinguishable current readouts. Compared with previous single molecule sensing interface, the resolution of the K238Q Aerolysin nanopore is enhanced by 2-order. The novel K238Q could direct discriminate at least 3 types (<sup>m</sup>C, <sup>O</sup>G, I) lesions without lableing and quantify modification sites under mixed hetero-composition condition of oligonucleotide. Such nanopore could be further applied to diagnose genetic diseases at high sensitivity.

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