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 Structural variations in papaya genomes

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zhenyang Liao ◽  
Xunxiao Zhang ◽  
Shengcheng Zhang ◽  
Zhicong Lin ◽  
Xingtan Zhang ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Enrichment Analysis ◽  
Copy Number Variant ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Structural Variations ◽  
Reproduction Traits ◽  
Depth Study ◽  
Environmental Adaptability ◽  
The Impact

Abstract Background Structural variations (SVs) are a type of mutations that have not been widely detected in plant genomes and studies in animals have shown their role in the process of domestication. An in-depth study of SVs will help us to further understand the impact of SVs on the phenotype and environmental adaptability during papaya domestication and provide genomic resources for the development of molecular markers. Results We detected a total of 8083 SVs, including 5260 deletions, 552 tandem duplications and 2271 insertions with deletion being the predominant, indicating the universality of deletion in the evolution of papaya genome. The distribution of these SVs is non-random in each chromosome. A total of 1794 genes overlaps with SV, of which 1350 genes are expressed in at least one tissue. The weighted correlation network analysis (WGCNA) of these expressed genes reveals co-expression relationship between SVs-genes and different tissues, and functional enrichment analysis shows their role in biological growth and environmental responses. We also identified some domesticated SVs genes related to environmental adaptability, sexual reproduction, and important agronomic traits during the domestication of papaya. Analysis of artificially selected copy number variant genes (CNV-genes) also revealed genes associated with plant growth and environmental stress. Conclusions SVs played an indispensable role in the process of papaya domestication, especially in the reproduction traits of hermaphrodite plants. The detection of genome-wide SVs and CNV-genes between cultivated gynodioecious populations and wild dioecious populations provides a reference for further understanding of the evolution process from male to hermaphrodite in papaya.

scholarly journals 3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome

2020 ◽  
Vol 49 (D1) ◽  
pp. D38-D46
Author(s):  
Kyukwang Kim ◽  
Insu Jang ◽  
Mooyoung Kim ◽  
Jinhyuk Choi ◽  
Min-Seo Kim ◽  
...  
Keyword(s):  
Cell Line ◽  
Large Scale ◽  
Three Dimensional ◽  
Cancer Cell Line ◽  
Cancer Genome ◽  
Structural Variations ◽  
3D Genome ◽  
Tightly Coupled ◽  
Regulatory Effects ◽  
The Impact

Abstract Three-dimensional (3D) genome organization is tightly coupled with gene regulation in various biological processes and diseases. In cancer, various types of large-scale genomic rearrangements can disrupt the 3D genome, leading to oncogenic gene expression. However, unraveling the pathogenicity of the 3D cancer genome remains a challenge since closer examinations have been greatly limited due to the lack of appropriate tools specialized for disorganized higher-order chromatin structure. Here, we updated a 3D-genome Interaction Viewer and database named 3DIV by uniformly processing ∼230 billion raw Hi-C reads to expand our contents to the 3D cancer genome. The updates of 3DIV are listed as follows: (i) the collection of 401 samples including 220 cancer cell line/tumor Hi-C data, 153 normal cell line/tissue Hi-C data, and 28 promoter capture Hi-C data, (ii) the live interactive manipulation of the 3D cancer genome to simulate the impact of structural variations and (iii) the reconstruction of Hi-C contact maps by user-defined chromosome order to investigate the 3D genome of the complex genomic rearrangement. In summary, the updated 3DIV will be the most comprehensive resource to explore the gene regulatory effects of both the normal and cancer 3D genome. ‘3DIV’ is freely available at http://3div.kr.

scholarly journals The Genomic Ecosystem of Transposable Elements in Maize

2019 ◽  
Author(s):  
Michelle C. Stitzer ◽  
Sarah N. Anderson ◽  
Nathan M. Springer ◽  
Jeffrey Ross-Ibarra
Keyword(s):  
Transposable Elements ◽  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Flowering Plant ◽  
Genome Wide ◽  
Family Level ◽  
Genomic Environment ◽  
Single Category ◽  
The Impact

Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. But genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level ecological and evolutionary dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between these attributes of the genomic environment and the survival of TE copies and families. Our analyses reveal a diversity of ecological strategies of TE families, each representing the evolution of a distinct ecological niche allowing survival of the TE family. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences generate a rich ecology of the genome, suggesting families of TEs that coexist in time and space compete and cooperate with each other. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.‘Lumping our beautiful collection of transposons into a single category is a crime’-Michael R. Freeling, Mar. 10, 2017

scholarly journals What is the impact of transposable elements on host genome variability?

1999 ◽  
Vol 266 (1429) ◽  
pp. 1677-1683 ◽  
Author(s):  
P. T. J. Emery ◽  
T. E. Robinson ◽  
R. Duddington ◽  
J. F. Y. Brookfield
Keyword(s):  
Transposable Elements ◽  
Host Genome ◽  
Genome Variability ◽  
The Impact

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 The impact of transposable elements on mammalian development

Development ◽  
2016 ◽  
Vol 143 (22) ◽  
pp. 4101-4114 ◽  
Author(s):  
Jose L. Garcia-Perez ◽  
Thomas J. Widmann ◽  
Ian R. Adams
Keyword(s):  
Transposable Elements ◽  
Mammalian Development ◽  
The Impact

scholarly journals The impact of transposable elements on tomato diversity

2020 ◽  
Author(s):  
Marisol Domínguez ◽  
Elise Dugas ◽  
Médine Benchouaia ◽  
Basile Leduque ◽  
José Jimenez-Gomez ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Agronomic Traits ◽  
Association Studies ◽  
Low Frequency ◽  
Genome Wide Association Studies ◽  
Environmental Response ◽  
Whole Genome Resequencing ◽  
Wild Accessions ◽  
Genetic Pool ◽  
The Impact

ABSTRACTTomatoes come in a multitude of shapes and flavors despite a narrow genetic pool. Here, we leveraged whole-genome resequencing data available for 602 cultivated and wild accessions to determine the contribution of transposable elements (TEs) to tomato diversity. We identified 6,906 TE insertions polymorphisms (TIPs), which result from the mobilization of 337 distinct TE families. Most TIPs are low frequency variants and disproportionately located within or adjacent to genes involved in environmental response. In addition, we show that genic TE insertions tend to have strong transcriptional effects and can notably lead to the generation of multiple transcript isoforms. We also uncovered through genome-wide association studies (GWAS) ~180 TIPs associated with extreme variations in major agronomic traits or secondary metabolites. Importantly, these TIPs tend to affect loci that are distinct from those tagged by SNPs. Collectively, our findings suggest a unique and important role for TE mobilization in tomato diversification, with important implications for future breeding.

scholarly journals Hidden biases in germline structural variant detection

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Michael M. Khayat ◽  
Sayed Mohammad Ebrahim Sahraeian ◽  
Samantha Zarate ◽  
Andrew Carroll ◽  
Huixiao Hong ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
False Negative ◽  
False Negative Rate ◽  
Next Generation Sequencing Data ◽  
Chinese Family ◽  
Next Generation ◽  
Sequencing Data ◽  
Structural Variations ◽  
The Impact ◽  
Generation Sequencing

Abstract Background Genomic structural variations (SV) are important determinants of genotypic and phenotypic changes in many organisms. However, the detection of SV from next-generation sequencing data remains challenging. Results In this study, DNA from a Chinese family quartet is sequenced at three different sequencing centers in triplicate. A total of 288 derivative data sets are generated utilizing different analysis pipelines and compared to identify sources of analytical variability. Mapping methods provide the major contribution to variability, followed by sequencing centers and replicates. Interestingly, SV supported by only one center or replicate often represent true positives with 47.02% and 45.44% overlapping the long-read SV call set, respectively. This is consistent with an overall higher false negative rate for SV calling in centers and replicates compared to mappers (15.72%). Finally, we observe that the SV calling variability also persists in a genotyping approach, indicating the impact of the underlying sequencing and preparation approaches. Conclusions This study provides the first detailed insights into the sources of variability in SV identification from next-generation sequencing and highlights remaining challenges in SV calling for large cohorts. We further give recommendations on how to reduce SV calling variability and the choice of alignment methodology.

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

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