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Mobile DNA

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https://read.qxmd.com/read/30728866/the-toxic-guardians-multiple-toxin-antitoxin-systems-provide-stability-avoid-deletions-and-maintain-virulence-genes-of-pseudomonas-syringae-virulence-plasmids
#1
Leire Bardaji, Maite Añorga, Myriam Echeverría, Cayo Ramos, Jesús Murillo
Background: Pseudomonas syringae is a γ-proteobacterium causing economically relevant diseases in practically all cultivated plants. Most isolates of this pathogen contain native plasmids collectively carrying many pathogenicity and virulence genes. However, P. syringae is generally an opportunistic pathogen primarily inhabiting environmental reservoirs, which could exert a low selective pressure for virulence plasmids. Additionally, these plasmids usually contain a large proportion of repeated sequences, which could compromise plasmid integrity...
2019: Mobile DNA
https://read.qxmd.com/read/30719103/repetdb-a-unified-resource-for-transposable-element-references
#2
Joëlle Amselem, Guillaume Cornut, Nathalie Choisne, Michael Alaux, Françoise Alfama-Depauw, Véronique Jamilloux, Florian Maumus, Thomas Letellier, Isabelle Luyten, Cyril Pommier, Anne-Françoise Adam-Blondon, Hadi Quesneville
Background: Thanks to their ability to move around and replicate within genomes, transposable elements (TEs) are perhaps the most important contributors to genome plasticity and evolution. Their detection and annotation are considered essential in any genome sequencing project. The number of fully sequenced genomes is rapidly increasing with improvements in high-throughput sequencing technologies. A fully automated de novo annotation process for TEs is therefore required to cope with the deluge of sequence data...
2019: Mobile DNA
https://read.qxmd.com/read/30679961/retrophylogenomics-in-rorquals-indicate-large-ancestral-population-sizes-and-a-rapid-radiation
#3
Fritjof Lammers, Moritz Blumer, Cornelia Rücklé, Maria A Nilsson
Background: Baleen whales (Mysticeti) are the largest animals on earth and their evolutionary history has been studied in detail, but some relationships still remain contentious. In particular, reconstructing the phylogenetic position of the gray whales (Eschrichtiidae) has been complicated by evolutionary processes such as gene flow and incomplete lineage sorting (ILS). Here, whole-genome sequencing data of the extant baleen whale radiation allowed us to identify transposable element (TE) insertions in order to perform phylogenomic analyses and measure germline insertion rates of TEs...
2019: Mobile DNA
https://read.qxmd.com/read/30675192/features-of-a-novel-protein-rusticalin-from-the-ascidian-styela-rustica-reveal-ancestral-horizontal-gene-transfer-event
#4
Maria A Daugavet, Sergey Shabelnikov, Alexander Shumeev, Tatiana Shaposhnikova, Leonid S Adonin, Olga Podgornaya
Background: The transfer of genetic material from non-parent organisms is called horizontal gene transfer (HGT). One of the most conclusive cases of HGT in metazoans was previously described for the cellulose synthase gene in ascidians. Results: In this study we identified a new protein, rusticalin, from the ascidian Styela rustica and presented evidence for its likely origin by HGT. Discernible homologues of rusticalin were found in placozoans, coral, and basal Chordates...
2019: Mobile DNA
https://read.qxmd.com/read/30675191/the-landscape-of-transposable-elements-and-satellite-dnas-in-the-genome-of-a-dioecious-plant-spinach-spinacia-oleracea-l
#5
Shu-Fen Li, Yu-Jiao Guo, Jia-Rong Li, Dong-Xu Zhang, Bing-Xiao Wang, Ning Li, Chuan-Liang Deng, Wu-Jun Gao
Background: Repetitive sequences, including transposable elements (TEs) and satellite DNAs, occupy a considerable portion of plant genomes. Analysis of the repeat fraction benefits the understanding of genome structure and evolution. Spinach ( Spinacia oleracea L.), an important vegetable crop, is also a model dioecious plant species for studying sex determination and sex chromosome evolution. However, the repetitive sequences of the spinach genome have not been fully investigated. Results: We extensively analyzed the repetitive components of draft spinach genome, especially TEs and satellites, by different strategies...
2019: Mobile DNA
https://read.qxmd.com/read/30636978/correction-to-high-performance-gene-expression-and-knockout-tools-using-sleeping-beauty-transposon-system
#6
Kaishun Hu, Yu Li, Wenjing Wu, Hengxing Chen, Zhen Chen, Yin Zhang, Yabin Guo, Dong Yin
[This corrects the article DOI: 10.1186/s13100-018-0139-y.].
2019: Mobile DNA
https://read.qxmd.com/read/30622655/systematic-survey-of-plant-ltr-retrotransposons-elucidates-phylogenetic-relationships-of-their-polyprotein-domains-and-provides-a-reference-for-element-classification
#7
Pavel Neumann, Petr Novák, Nina Hoštáková, Jiří Macas
Background: Plant LTR-retrotransposons are classified into two superfamilies, Ty1/copia and Ty3/gypsy. They are further divided into an enormous number of families which are, due to the high diversity of their nucleotide sequences, usually specific to a single or a group of closely related species. Previous attempts to group these families into broader categories reflecting their phylogenetic relationships were limited either to analyzing a narrow range of plant species or to analyzing a small numbers of elements...
2019: Mobile DNA
https://read.qxmd.com/read/30574213/carbapenemases-on-the-move-it-s-good-to-be-on-ices
#8
João Botelho, Adam P Roberts, Ricardo León-Sampedro, Filipa Grosso, Luísa Peixe
Background: The evolution and spread of antibiotic resistance is often mediated by mobile genetic elements. Integrative and conjugative elements (ICEs) are the most abundant conjugative elements among prokaryotes. However, the contribution of ICEs to horizontal gene transfer of antibiotic resistance has been largely unexplored. Results: Here we report that ICEs belonging to mating-pair formation (MPF) classes G and T are highly prevalent among the opportunistic pathogen Pseudomonas aeruginosa , contributing to the spread of carbapenemase-encoding genes (CEGs)...
2018: Mobile DNA
https://read.qxmd.com/read/30568734/variation-in-proviral-content-among-human-genomes-mediated-by-ltr-recombination
#9
Jainy Thomas, Hervé Perron, Cédric Feschotte
Background: Human endogenous retroviruses (HERVs) occupy a substantial fraction of the genome and impact cellular function with both beneficial and deleterious consequences. The vast majority of HERV sequences descend from ancient retroviral families no longer capable of infection or genomic propagation. In fact, most are no longer represented by full-length proviruses but by solitary long terminal repeats (solo LTRs) that arose via non-allelic recombination events between the two LTRs of a proviral insertion...
2018: Mobile DNA
https://read.qxmd.com/read/30564290/properties-of-line-1-proteins-and-repeat-element-expression-in-the-context-of-amyotrophic-lateral-sclerosis
#10
Gavin C Pereira, Laura Sanchez, Paul M Schaughency, Alejandro Rubio-Roldán, Jungbin A Choi, Evarist Planet, Ranjan Batra, Priscilla Turelli, Didier Trono, Lyle W Ostrow, John Ravits, Haig H Kazazian, Sarah J Wheelan, Sara R Heras, Jens Mayer, Jose Luis García-Pérez, John L Goodier
Background: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease involving loss of motor neurons and having no known cure and uncertain etiology. Several studies have drawn connections between altered retrotransposon expression and ALS. Certain features of the LINE-1 (L1) retrotransposon-encoded ORF1 protein (ORF1p) are analogous to those of neurodegeneration-associated RNA-binding proteins, including formation of cytoplasmic aggregates. In this study we explore these features and consider possible links between L1 expression and ALS...
2018: Mobile DNA
https://read.qxmd.com/read/30534207/high-performance-gene-expression-and-knockout-tools-using-sleeping-beauty-transposon-system
#11
Kaishun Hu, Yu Li, Wenjing Wu, Hengxing Chen, Zhen Chen, Yin Zhang, Yabin Guo, Yin Dong
Background: Similar to retro-/lenti- virus system, DNA transposons are useful tools for stable expression of exogenous genes in mammalian cells. Sleeping Beauty (SB) transposon has adopted for integrating genes into host genomes in recent studies. However, SB-derived vector system for proteins purifying/tracking and gene knockout are still not available. Results: In this study, we generated a series of vectors (termed as pSB vectors) containing Sleeping Beauty IRDR-L/R that can be transposed by SB transposase...
2018: Mobile DNA
https://read.qxmd.com/read/30455747/can-sine-dynamics-in-the-giant-panda-and-three-other-caniformia-genomes
#12
Changjun Peng, Lili Niu, Jiabo Deng, Jianqiu Yu, Xueyan Zhang, Chuang Zhou, Jinchuan Xing, Jing Li
Background: Although repeat sequences constitute about 37% of carnivore genomes, the characteristics and distribution of repeat sequences among carnivore genomes have not been fully investigated. Based on the updated Repbase library, we re-annotated transposable elements (TEs) in four Caniformia genomes (giant panda, polar bear, domestic dog, and domestic ferret) and performed a systematic, genome-wide comparison focusing on the Carnivora-specific SINE family, Can-SINEs. Results: We found the majority of young recently integrated transposable elements are LINEs and SINEs in carnivore genomes...
2018: Mobile DNA
https://read.qxmd.com/read/30450130/an-advanced-enrichment-method-for-rare-somatic-retroelement-insertions-sequencing
#13
Alexander Y Komkov, Anastasia A Minervina, Gaiaz A Nugmanov, Mariia V Saliutina, Konstantin V Khodosevich, Yuri B Lebedev, Ilgar Z Mamedov
Background: There is increasing evidence that the transpositional activity of retroelements (REs) is not limited to germ line cells, but often occurs in tumor and normal somatic cells. Somatic transpositions were found in several human tissues and are especially typical for the brain. Several computational and experimental approaches for detection of somatic retroelement insertions was developed in the past few years. These approaches were successfully applied to detect somatic insertions in clonally expanded tumor cells...
2018: Mobile DNA
https://read.qxmd.com/read/30237828/phylogenomic-analysis-reveals-splicing-as-a-mechanism-of-parallel-evolution-of-non-canonical-svas-in-hominine-primates
#14
Annette Damert
SVA (SINE-R-VNTR- Alu ) elements are non-autonomous non-LTR (Long Terminal Repeat) retrotransposons. They are found in all hominoid primates but did not amplify to appreciable numbers in gibbons. Recently, phylogenetic networks of hominid (orangutan, gorilla, chimpanzee, human) SVA elements based on comparison of overall sequence identity have been reported. Here I present a detailed phylogeny of SVA_D elements in gorilla, chimpanzee and humans based on sorting of co-segregating substitutions. Complementary comparative genomics analysis revealed that the majority (1763 out of 1826-97%) of SVA_D elements in gorilla represent species-specific insertions - indicating very low activity of the subfamily before the gorilla/chimpanzee-human split...
2018: Mobile DNA
https://read.qxmd.com/read/30211913/meeting-report-mobile-genetic-elements-and-genome-plasticity-2018
#15
John M Abrams, Irina R Arkhipova, Marlene Belfort, Jef D Boeke, M Joan Curcio, Geoffrey J Faulkner, John L Goodier, Ruth Lehmann, Henry L Levin
The Mobile Genetic Elements and Genome Plasticity conference was hosted by Keystone Symposia in Santa Fe, NM USA, February 11-15, 2018. The organizers were Marlene Belfort, Evan Eichler, Henry Levin and Lynn Maquat. The goal of this conference was to bring together scientists from around the world to discuss the function of transposable elements and their impact on host species. Central themes of the meeting included recent innovations in genome analysis and the role of mobile DNA in disease and evolution. The conference included 200 scientists who participated in poster presentations, short talks selected from abstracts, and invited talks...
2018: Mobile DNA
https://read.qxmd.com/read/30181787/insertion-sequence-elements-mediated-structural-variations-in-bacterial-genomes
#16
Etienne Nzabarushimana, Haixu Tang
Mobile genetic elements (MGEs) impact the evolution and stability of their host genomes. Insertion sequence (IS) elements are the most common MGEs in bacterial genomes and play a crucial role in mediating large-scale variations in bacterial genomes. It is understood that IS elements and MGEs in general coexist in a dynamical equilibrium with their respective hosts. Current studies indicate that the spontaneous movement of IS elements does not follow a constant rate in different bacterial genomes. However, due to the paucity and sparsity of the data, these observations are yet to be conclusive...
2018: Mobile DNA
https://read.qxmd.com/read/30147753/impact-of-non-ltr-retrotransposons-in-the-differentiation-and-evolution-of-anatomically-modern-humans
#17
Etienne Guichard, Valentina Peona, Guidantonio Malagoli Tagliazucchi, Lucia Abitante, Evelyn Jagoda, Margherita Musella, Marco Ricci, Alejandro Rubio-Roldán, Stefania Sarno, Donata Luiselli, Davide Pettener, Cristian Taccioli, Luca Pagani, Jose Luis Garcia-Perez, Alessio Boattini
Background: Transposable elements are biologically important components of eukaryote genomes. In particular, non-LTR retrotransposons (N-LTRrs) played a key role in shaping the human genome throughout evolution. In this study, we compared retrotransposon insertions differentially present in the genomes of Anatomically Modern Humans, Neanderthals, Denisovans and Chimpanzees, in order to assess the possible impact of retrotransposition in the differentiation of the human lineage. Results: We first identified species-specific N-LTRrs and established their distribution in present day human populations...
2018: Mobile DNA
https://read.qxmd.com/read/30123327/length-variations-within-the-merle-retrotransposon-of-canine-pmel-correlating-genotype-with-phenotype
#18
Sarah C Murphy, Jacquelyn M Evans, Kate L Tsai, Leigh Anne Clark
Background: The antisense insertion of a canine short interspersed element (SINEC_Cf) in the pigmentation gene PMEL (or SILV ) causes a coat pattern phenotype in dogs termed merle. Merle is a semi-dominant trait characterized by patches of full pigmentation on a diluted background. The oligo(dT) tract of the Merle retrotransposon is long and uninterrupted and is prone to dramatic truncation. Phenotypically wild-type individuals carrying shorter oligo(dT) lengths of the Merle allele have been previously described and termed cryptic merles...
2018: Mobile DNA
https://read.qxmd.com/read/30100927/f-cphi-represents-a-new-homing-endonuclease-family-using-the-endo-vii-catalytic-motif
#19
Xiaoting Fang, YongLiang Jiang, Kim Li, Qinglu Zeng
Background: There are six known families of homing endonucleases, LAGLIDADG, GIY-YIG, HNH, His-Cys box, PD-(D/E)-XK, and EDxHD, which are characterized by their conserved residues. Previously, we discovered a novel homing endonuclease F-CphI encoded by ORF177 of cyanophage S-PM2. F-CphI does not resemble any characterized homing endonucleases. Instead, the C-terminus of F-CphI aligns well with the N-terminal catalytic domain of a Holliday junction DNA resolvase, phage T4 endonuclease VII (Endo VII)...
2018: Mobile DNA
https://read.qxmd.com/read/30079119/srnapipe-a-galaxy-based-pipeline-for-bioinformatic-in-depth-exploration-of-small-rnaseq-data
#20
Romain Pogorelcnik, Chantal Vaury, Pierre Pouchin, Silke Jensen, Emilie Brasset
Background: The field of small RNA is one of the most investigated research areas since they were shown to regulate transposable elements and gene expression and play essential roles in fundamental biological processes. Small RNA deep sequencing (sRNA-seq) is now routinely used for large-scale analyses of small RNA. Such high-throughput sequencing typically produces several millions reads. Results: Here we present a computational pipeline (sRNAPipe: small RNA pipeline) based on the Galaxy framework that takes as input a fastq file of small RNA-seq reads and performs successive steps of mapping to categories of genomic sequences: transposable elements, gene transcripts, microRNAs, small nuclear RNAs, ribosomal RNAs and transfer RNAs...
2018: Mobile DNA
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