Nucleosome patterns in four plant pathogenic fungi with contrasted genome structures by Clairet, Colin, Lapalu, Nicolas, Simon, Adeline, Soyer, Jessica L., Viaud, Muriel, Zehraoui, Enric, Dalmais, Berengère, Fudal, Isabelle, Ponts, Nadia

“…Genomes of phytopathogenic fungi are often compartmentalized: the core genome contains housekeeping genes whereas the fast-evolving genome mainly contains transposable elements and species-specific genes. In this study, we analysed nucleosome landscapes of four phytopathogenic fungi with contrasted genome organizations to describe and compare nucleosome repartition patterns in relation with genome structure and gene expression level. …”
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Comparative Genomic In Situ Hybridization and the Possible Role of Retroelements in the Karyotypic Evolution of Three Akodontini Species by Naiara Pereira Araújo, Gustavo Campos Silva Kuhn, Flávia Nunes Vieira, Thaís Queiroz Morcatty, Adriano Pereira Paglia, Marta Svartman

“…The results led us to infer that transposable elements have played an important role in the enormous chromosome variation found in Akodontini.…”
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MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication by Jonathan Cahn, Michael Regulski, Jason Lynn, Evan Ernst, Cristiane de Santis Alves, Srividya Ramakrishnan, Kapeel Chougule, Sharon Wei, Zhenyuan Lu, Xiaosa Xu, Umamaheswari Ramu, Jorg Drenkow, Melissa Kramer, Arun Seetharam, Matthew B. Hufford, W. Richard McCombie, Doreen Ware, David Jackson, Michael C. Schatz, Thomas R. Gingeras, Robert A. Martienssen

“…Furthermore, the morphological traits selected during domestication are recapitulated, both in gene expression and within regulatory regions containing enhancer RNAs, while highlighting the conflict between enhancer activity and silencing of the neighboring transposable elements.…”
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Structural Variation of Element and Human Disease by Songmi Kim, Chun-Sung Cho, Kyudong Han, Jungnam Lee

“…Transposable elements are one of major sources to cause genomic instability through various mechanisms including de novo insertion, insertion-mediated genomic deletion, and recombination-associated genomic deletion. …”
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The relationship of lamins with epigenetic factors during aging by R. N. Mustafin, E. K. Khusnutdinova

“…This may be due to the role of lamins in protection from both viruses and transposons, since viruses and transposons are evolutionarily related. Transposable elements and lamins are secondary messengers of environmental stressors that can serve as triggers for aging and carcinogenesis. …”
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Adaptive Evolution Coupled with Retrotransposon Exaptation Allowed for the Generation of a Human-Protein-Specific Coding Gene That Promotes Cancer Cell Proliferation and Metastasis... by Spyros I. Papamichos, Dimitrios Margaritis, Ioannis Kotsianidis

“…Second, we demonstrate the precious impact of exonized transposable elements on the creation of MYEOV gene structure. …”
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A High-Quality Phased Genome Assembly of Stinging Nettle (<i>Urtica dioica</i> ssp. <i>dioica</i>) by Kaede Hirabayashi, Christopher R. Dumigan, Matúš Kučka, Diana M. Percy, Gea Guerriero, Quentin Cronk, Michael K. Deyholos, Marco Todesco

“…Despite its relatively small size, the nettle genome displays very high levels of repetitiveness, with transposable elements comprising more than 60% of the genome, as well as considerable structural variation. …”
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The chromatin remodeling factor OsINO80 promotes H3K27me3 and H3K9me2 deposition and maintains TE silencing in rice by Kangxi Du, Jiabing Wu, Jiachen Wang, Wenhao Xie, Liufan Yin, Xiang Li, Chao Li, Aiwu Dong

“…Here, we characterize the regulatory effects of OsINO80 on protein-coding genes and transposable elements (TEs) in rice. Upon OsINO80 overexpression in rice, we found three types of OsINO80-occupied regions with different chromatin signatures: type I (enriched with H2A.Z), type II (enriched with H3K9me2), and type III (deficient in H2A.Z/H3K9me2). …”
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Molecular genetics of idiopathic pulmonary fibrosis by R. N. Mustafin

“…Analysis of the MDTE database (miRNAs derived from Transposable Elements) allowed the detection of 12 different miRNAs derived in evolution from transposons and associated with IPF (miR-31, miR-302, miR-326, miR-335, miR-340, miR-374, miR-487, miR-493, miR-495, miR-630, miR-708, miR-1343). …”
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Comparative Genomics of the First and Complete Genome of “Actinobacillus porcitonsillarum” Supports the Novel Species Hypothesis by Valentina Donà, Vincent Perreten

“…The four strains showed distinct and shared transposable elements, CRISPR/Cas systems, and integrated prophages. …”
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Multiple Roles of the Y Chromosome in the Biology of Drosophila melanogaster by Roberto Piergentili

“…This is due to the intrinsic nature of this genetic element, namely, (1) its molecular composition (mainly transposable elements and satellite DNA), (2) its genetic inertia (lack of recombination due to its heterochromatic nature), (3) the absence of homology with the X (with the only exception of the nucleolar organizer), (4) the lack of visible phenotypes when it is missing (indeed, except for their sterility, X0 flies are normal males), and (5) its low density as for protein-coding sequences (to date, only 13 genes out of approximately 14,000 have been mapped on this chromosome in D. melanogaster, i.e., ~0.1% of the total). …”
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Chromosome‐scale genome assembly of Poa trivialis and population genomics reveal widespread gene flow in a cool‐season grass seed production system by Caio A. C. G. Brunharo, Christopher W. Benson, David R. Huff, Jesse R. Lasky

“…The genome assembly resulted in 1.35 Gb of DNA sequence distributed among seven chromosome‐scale scaffolds, revealing a high content of transposable elements, conserved synteny with Poa annua, and a close relationship with other C3 grasses. …”
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Exogenous Janus Kinase 617 Codon Influences Small Noncoding RNAs and Gene Expression in Ba/F3 Cells by Yi-Yang Chen, Ying-Hsuan Wang, Chih-Cheng Chen, Cih-En Huang, Chia-Chen Hsu, Shu-Huei Hsiao, Yu-Wei Leu

“…The differently expressed variations contained enriched transposable elements and piRNAs, indicating a rearranged epigenome. …”
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Comparative genomics of Botryosphaeria dothidea and B. kuwatsukai, causal agents of apple ring rot, reveals both species expansion of pathogenicity-related genes and variations in... by Bo Wang, Xiaofei Liang, Mark L. Gleason, Rong Zhang, Guangyu Sun

“…Botryosphaeria kuwatsukai contained significantly more transposable elements and higher value of repeat induced point (RIP) index than B. dothidea. …”
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Domestication of different varieties in the cheese-making fungus Geotrichum candidum by Bennetot, Bastien, Vernadet, Jean-Philippe, Perkins, Vincent, Hautefeuille, Sophie, Rodríguez de la Vega, Ricardo C., O’Donnell, Samuel, Snirc, Alodie, Grondin, Cécile, Lessard, Marie-Hélène, Peron, Anne-Claire, Labrie, Steve, Landaud, Sophie, Giraud, Tatiana, Ropars, Jeanne

“…Cheese populations lacked two beta lactamase-like genes present in the wild clade, involved in xenobiotic clearance, and displayed higher contents of transposable elements, likely due to relaxed selection. Our findings suggest the existence of genuine domestication in G. candidum, which led to diversification into different varieties with contrasted phenotypes. …”
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Genome assembly of an endemic butterfly (Minois aurata) shed light on the genetic mechanisms underlying ecological adaptation to arid valley habitat by Wenqian Hu, Yi Wang, Xiaoxiao Chen, Jialong Huang, Jingge Kuang, Lei Wang, Kangshan Mao, Liang Dou

“…The expansion of transposable elements (TEs) accounts for the relatively large genome size of M. aurata, potentially aiding its adaptation to environmental conditions. …”
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