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Transposable elements

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Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture

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This pipeline annotated approximately 60% of the genome as transposable elements or repeats. Over half of the annotated repetitive el- ements belong to the Gypsy superfamily of Long Ter- minal Repeat (LTR) retrotransposons, with unclassified LTRs and the Mutator superfamily of Terminal Inverted Repeat (TIR) DNA transposons making up the next two most numerous classes of re- petitive elements.

Genome-wide characterization of LTR retrotransposons in the non-model deepsea annelid Lamellibrachia luymesi

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The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Sequence analysis of transposable elements in the sea squirt, Ciona intestinalis. Molecular structure of a novel gypsy-Ty3-like retrotransposon (Kabuki) and nested retrotransposable elements on the W chromosome of the silkworm Bombyx mori. Boudicca, a retrovirus-like long terminal repeat retrotransposon from the genome of the human blood fluke Schistosoma mansoni.

Whole genome analysis of the koa wilt pathogen (Fusarium oxysporum f. sp. koae) and the development of molecular tools for early detection and monitoring

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In contrast, the transposable el- ements and repeats comprised 19 and 20% of LSX for Fo koae 44 and Fo 170, respectively (Fig. This localization of transposable elements provides evidence that differences within the LSX are likely attributable to one or more conditionally dispensable chromosome(s) in both Fo koae 44 and Fo 170..

Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response

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However, LTR/Copia elements contributed TE-lncRNAs at a lower proportion than their proportion length among annotated TEs (22% vs.. Particularly notable is the fact that class II DNA elements produced TE-lncRNAs in our dataset at ~ 2- fold higher rate (12% vs.

Sự chuyển vị Sự chuyển vị (Transposition

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Phạm Thành Hổ Sự chuyển vị (Transposition) Các phần tử chuyển vị (transposable elements) hay phần tử di động (mobile elements) là những trình tự ADN có khả năng di chuyển từ vị trí này đến vị trí khác (mục tiêu) của bộ gen (cùng bộ gen hay khác). Sự di chuyển ADN này được gọi là transposition (sự chuyển vị). Tái tổ hợp (Recombination) trong chuyển vị (transposition) là sự kết nối (junction) giữa các đầu mút của phần tử chuyển vị với các đầu mút bị cắt hở của ADN mục tiêu (target site).

Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides

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The proportion of the whole genome made up of transposable elements also varies among species. 8.5% of the genomes in so-called Large RIP Affected Regions (LRARs, (Fig. xylarioides, with over 87% of genes supporting monophyly of the clade (Fig.

Integrative expression network analysis of microRNA and gene isoforms in sacred lotus

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TamiR1123 originated from a family of miniature inverted-repeat transposable elements (MITE) including one inserted in the Vrn-A1a promoter in wheat. A general framework for weighted gene co-expression network analysis

Comparative genomics of Alternaria species provides insights into the pathogenic lifestyle of Alternaria brassicae – a pathogen of the Brassicaceae family

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The analysis involved comparison of the overlap of each the above gene sets with transposable elements and repeat- rich regions with a random set of genes selected from the genome. List of Dothideomycetes used in the orthology analysis.. Comparison of the CAZyme profiles of the 30 Dothideomycetes including 16 Alternaria species..

DNA methylation and its effects on gene expression during primary to secondary growth in poplar stems

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Within the 2 kb down- stream regions, there were significant differences in CG methylation levels between PS and SS, in CHG between. 5 DNA methylation patterns in different genic regions. a Methylation levels in different types of transposable elements (TEs), including long terminal repeats (LTR), long interspersed nuclear elements (LINE), short interspersed nuclear elements (SINE), and DNA transposons (DNA) in primary stems (PS), transitional stems (TS), and secondary stems (SS). b Methylation levels

Identification of high-copy number long terminal repeat retrotransposons and their expansion in Phalaenopsis orchids

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Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Nested retrotransposons in the intergenic regions of the maize genome. A HORT1 retrotransposon insertion in the PeMYB11 promoter causes harlequin/black flowers in Phalaenopsis orchids. Identification, characterization and distribution of transposable elements in the flax (Linum usitatissimum L.) genome

Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts

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When comparing the full genome assembly of 11–12 to Al-1, large scale structural rearrangements and smaller Table 2 Transposable elements identified in Macrophomina. phaseolina genomes from an isolate recovered from strawberry that represents the strawberry genotype (11 – 12) and an isolate recovered from alfalfa (Al-1) that represents another genotype Transposable Element Category 11 – 12 Al-1.

Rapid sequence evolution driven by transposable elements at a virulence locus in a fungal wheat pathogen

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RIP) contributing to the rapid diversification of the locus.. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.. f Linkage disequilibrium r 2 heatmap of the entire region. c TE content variation of...

A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

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Prediction of paralogous genes in the Sclerotinia sclerotiorum genome and association with secondary metabolite clusters, subtelomeres and transposable elements. This file contained a subset of 21 of the 25 isolates in the whole dataset that fell into the two major S. Results from OrthoFinder showing the nodes to which orthogroups correspond along with all genes in the orthogroups.. SM: Secondary metabolite.

Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral

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Genome- wide analysis of the Association of Transposable Elements with gene regulation suggests that Alu elements have the largest overall regulatory impact. https://doi.org/10.1038/nrg3425.. https://doi.org/10.1016/S X.. Positive natural selection in the human lineage. Journal of the Royal Statistical Society. https://doi.org/10.2307/

Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum

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A survey of transposable Elements (TEs) identified a similar overall number of putative TE elements in the two assemblies (A. Despite this similarity, the overall coverage by repeats is larger in the assembly of L.. To examine genes that may underlie novel functional adaptation, we identified sequences that are unique within the predicted genes in the A.

Casparian strip membrane domain proteins in Gossypium arboreum: genome-wide identification and negative regulation of lateral root growth

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Dispersed duplicates include transposable elements that are ubiquitous in the human genome, such as mem- bers of the Alu and L1 family [47]. This suggests that dispersed dupli- cation could have contributed to the expansion of the GaCASP gene family in diploid G. We observed that in the fourth group, five CASP genes (Ga08G0113, Ga08G0114, Ga08G0116, Ga08G0117, and Ga08G0118) shared close relationships with Arabidopsis AtCASP1, which regulated the develop- ment of lateral roots.

De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linkedreads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly

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The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Assembly of the Tc1 and mariner transposition initiation complexes depends on the origins of their transposase DNA binding domains. The mitochondrial genome of the olive fly Bactrocera oleae: two haplotypes from distant geographical locations.. Embryonic development of the olive fruit fly, Bactrocera oleae Rossi (Diptera: Tephritidae), in vivo.

LncRNA: DNA triplex-forming sites are positioned at specific areas of genome organization and are predictors for Topologically Associated Domains

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Evolution of the mammalian transcription factor binding repertoire via transposable elements. LncRNA Khps1 Regulates Expression of the Proto- oncogene SPHK1 via Triplex-Mediated Changes in Chromatin Structure. PARTICLE, a triplex-forming long ncRNA, regulates locus-specific methylation in response to low-dose irradiation

MethGET: Web-based bioinformatics software for correlating genome-wide DNA methylation and gene expression

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DNA methylation at different genomic locations may have different impacts on regu- lating the expression of genes and transposable elements (TEs) [7]. Typically, DNA methylation in the promoter region may repress gene expression [8]. Dynamic changes in DNA methylation in the genome- wide profile (i.e., methylome) often affect gene expres- sion with specific functional outcomes [14].

Whole genome sequencing and comparative genomic analysis of oleaginous red yeast Sporobolomyces pararoseus NGR identifies candidate genes for biotechnological potential and ballistospores-shooting

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The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L