Evolutionarily recent insertions of mobile elements and their contribution to human genome structure

2012 ◽  
Vol 2 (5) ◽  
pp. 371-385 ◽  
Author(s):  
K. K. Baskayev ◽  
A. A. Buzdin
Keyword(s):  
Human Genome ◽  
Genome Structure ◽  
Mobile Elements

scholarly journals Mobile elements in the human genome: implications for disease

10.1186/gm311 ◽  
2012 ◽  
Vol 4 (2) ◽  
Author(s):  
Szilvia Solyom ◽  
Haig H Kazazian
Keyword(s):  
Human Genome ◽  
Mobile Elements

scholarly journals Toolbox for Mobile-Element Insertion Detection on Cancer Genomes

2015 ◽  
Vol 14s1 ◽  
pp. CIN.S24657
Author(s):  
Wan-Ping Lee ◽  
Jiantao Wu ◽  
Gabor T. Marth
Keyword(s):  
Human Genome ◽  
Mobile Element ◽  
Mobile Elements ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Next Generation Sequencing Data ◽  
Sequencing Data ◽  
Element Insertion ◽  
Human Genome Evolution ◽  
Mobile Element Insertion

Mobile elements constitute greater than 45% of the human genome as a result of repeated insertion events during human genome evolution. Although most of mobile elements are fixed within the human population, some elements (including ALU, long interspersed elements (LINE) 1 (L1), and SVA) are still actively duplicating and may result in life-threatening human diseases such as cancer, motivating the need for accurate mobile-element insertion (MEI) detection tools. We developed a software package, TANGRAM, for MEI detection in next-generation sequencing data, currently serving as the primary MEI detection tool in the 1000 Genomes Project. TANGRAM takes advantage of valuable mapping information provided by our own MOSAIK mapper, and until recently required MOSAIK mappings as its input. In this study, we report a new feature that enables TANGRAM to be used on alignments generated by any mainstream short-read mapper, making it accessible for many genomic users. To demonstrate its utility for cancer genome analysis, we have applied TANGRAM to the TCGA (The Cancer Genome Atlas) mutation calling benchmark 4 dataset. TANGRAM is fast, accurate, easy to use, and open source on https://github.com/jiantao/Tangram .

scholarly journals Complete Genome Sequence of the Anaerobic, Protein-Degrading Hyperthermophilic Crenarchaeon Desulfurococcus kamchatkensis

2008 ◽  
Vol 191 (7) ◽  
pp. 2371-2379 ◽  
Author(s):  
Nikolai V. Ravin ◽  
Andrey V. Mardanov ◽  
Alexey V. Beletsky ◽  
Ilya V. Kublanov ◽  
Tatiana V. Kolganova ◽  
...  
Keyword(s):  
Hot Spring ◽  
Genome Structure ◽  
Nucleotide Composition ◽  
Mobile Elements ◽  
Circular Chromosome ◽  
Extrachromosomal Elements ◽  
Single Region ◽  
Genes Encoding ◽  
Multiple Copies ◽  
Modified Embden Meyerhof Pathway

ABSTRACT Desulfurococcus kamchatkensis is an anaerobic organotrophic hyperthermophilic crenarchaeon isolated from a terrestrial hot spring. Its genome consists of a single circular chromosome of 1,365,223 bp with no extrachromosomal elements. A total of 1,474 protein-encoding genes were annotated, among which 205 are exclusive for D. kamchatkensis. The search for a replication origin site revealed a single region coinciding with a global extreme of the nucleotide composition disparity curve and containing a set of crenarchaeon-type origin recognition boxes. Unlike in most archaea, two genes encoding homologs of the eukaryotic initiator proteins Orc1 and Cdc6 are located distantly from this site. A number of mobile elements are present in the genome, including seven transposons representing IS607 and IS200/IS605 families and multiple copies of miniature inverted repeat transposable elements. Two large clusters of regularly interspaced repeats are present; none of the spacer sequences matches known archaeal extrachromosomal elements, except one spacer matches the sequence of a resident gene of D. kamchatkensis. Many of the predicted metabolic enzymes are associated with the fermentation of peptides and sugars, including more than 30 peptidases with diverse specificities, a number of polysaccharide degradation enzymes, and many transporters. Consistently, the genome encodes both enzymes of the modified Embden-Meyerhof pathway of glucose oxidation and a set of enzymes needed for gluconeogenesis. The genome structure and content reflect the organism's nutritionally diverse, competitive natural environment, which is periodically invaded by viruses and other mobile elements.

scholarly journals Mobile elements create structural variation: Analysis of a complete human genome

2009 ◽  
Vol 19 (9) ◽  
pp. 1516-1526 ◽  
Author(s):  
J. Xing ◽  
Y. Zhang ◽  
K. Han ◽  
A. H. Salem ◽  
S. K. Sen ◽  
...  
Keyword(s):  
Human Genome ◽  
Structural Variation ◽  
Mobile Elements ◽  
Variation Analysis

scholarly journals Giant Starship elements mobilize accessory genes in fungal genomes

2021 ◽  
Author(s):  
Emile Gluck-Thaler ◽  
Timothy Ralston ◽  
Zachary Konkel ◽  
Cristhian Grabowski Ocampos ◽  
Veena Devi Ganeshan ◽  
...  
Keyword(s):  
Genome Structure ◽  
5S Rdna ◽  
Macrophomina Phaseolina ◽  
Fungal Species ◽  
Mobile Elements ◽  
Integrative And Conjugative Elements ◽  
Standing Variation ◽  
Accessory Genes ◽  
Fungal Genomes ◽  
The Impact

Accessory genes are variably present among members of a species and are a reservoir of adaptive functions. In bacteria, differences in gene distributions among individuals largely result from mobile elements that acquire and disperse accessory genes as cargo. In contrast, the impact of cargo-carrying elements on eukaryotic evolution remains largely unknown. Here, we show that variation in genome content within multiple fungal species is facilitated by Starships, a novel group of massive mobile elements that are 110 kb long on average, share conserved components, and carry diverse arrays of accessory genes. We identified hundreds of Starship-like regions across every major class of filamentous Ascomycetes, including 28 distinct Starships that range from 27-393 kb and last shared a common ancestor ca. 400 mya. Using new long-read assemblies of the plant pathogen Macrophomina phaseolina, we characterize 4 additional Starships whose past and ongoing activities contribute to standing variation in genome structure and content. One of these elements, Voyager, inserts into 5S rDNA and contains a candidate virulence factor whose increasing copy number has contrasting associations with pathogenic and saprophytic growth, suggesting Voyager activity underlies an ecological trade-off. We propose that Starships are eukaryotic analogs of bacterial integrative and conjugative elements based on parallels between their conserved components and may therefore represent the first known agents of active gene transfer in eukaryotes. Our results suggest that Starships have shaped the content and structure of fungal genomes for millions of years and reveal a new concerted route for evolution throughout an entire eukaryotic phylum.

Mobile elements and the human genome

2000 ◽  
Vol 1 (2) ◽  
pp. 134-144 ◽  
Author(s):  
Eline T. Luning Prak ◽  
Haig H. Kazazian
Keyword(s):  
Human Genome ◽  
Mobile Elements

scholarly journals Toolbox for Mobile-Element Insertion Detection on Cancer Genomes

2014 ◽  
Vol 13s4 ◽  
pp. CIN.S13979 ◽  
Author(s):  
Wan-Ping Lee ◽  
Jiantao Wu ◽  
Gabor T. Marth
Keyword(s):  
Human Genome ◽  
Mobile Element ◽  
Mobile Elements ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Next Generation Sequencing Data ◽  
Sequencing Data ◽  
Element Insertion ◽  
Human Genome Evolution ◽  
Mobile Element Insertion

Mobile elements constitute greater than 45% of the human genome as a result of repeated insertion events during human genome evolution. Although most of mobile elements are fixed within the human population, some elements (including ALU, long interspersed elements (LINE) 1 (L1), and SVA) are still actively duplicating and may result in life-threatening human diseases such as cancer, motivating the need for accurate mobile-element insertion (MEI) detection tools. We developed a software package, TANGRAM, for MEI detection in next-generation sequencing data, currently serving as the primary MEI detection tool in the 1000 Genomes Project. TANGRAM takes advantage of valuable mapping information provided by our own MOSAIK mapper, and until recently required MOSAIK mappings as its input. In this study, we report a new feature that enables TANGRAM to be used on alignments generated by any mainstream short-read mapper, making it accessible for many genomic users. To demonstrate its utility for cancer genome analysis, we have applied TANGRAM to the TCGA (The Cancer Genome Atlas) mutation calling benchmark 4 dataset. TANGRAM is fast, accurate, easy to use, and open source on https://github.com/jiantao/Tangram .

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