Genome Plasticity in Evolution

2007 ◽  
pp. 153-165 ◽  
Author(s):  
Mariano Rocchi ◽  
Nicoletta Archidiacono
Keyword(s):  
Genome Plasticity

scholarly journals panRGP: a pangenome-based method to predict genomic islands and explore their diversity

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i651-i658 ◽  
Author(s):  
Adelme Bazin ◽  
Guillaume Gautreau ◽  
Claudine Médigue ◽  
David Vallenet ◽  
Alexandra Calteau
Keyword(s):  
Escherichia Coli ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Species Level ◽  
Genomic Islands ◽  
Genome Plasticity ◽  
Reference Dataset ◽  
Prokaryotic Genomes ◽  
Ideal Approach ◽  
Genomic Regions

Abstract Motivation Horizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions of genome plasticity (RGPs) are clusters of genes located in highly variable genomic regions. Most of them arise from HGT and correspond to genomic islands (GIs). The study of those regions at the species level has become increasingly difficult with the data deluge of genomes. To date, no methods are available to identify GIs using hundreds of genomes to explore their diversity. Results We present here the panRGP method that predicts RGPs using pangenome graphs made of all available genomes for a given species. It allows the study of thousands of genomes in order to access the diversity of RGPs and to predict spots of insertions. It gave the best predictions when benchmarked along other GI detection tools against a reference dataset. In addition, we illustrated its use on metagenome assembled genomes by redefining the borders of the leuX tRNA hotspot, a well-studied spot of insertion in Escherichia coli. panRPG is a scalable and reliable tool to predict GIs and spots making it an ideal approach for large comparative studies. Availability and implementation The methods presented in the current work are available through the following software: https://github.com/labgem/PPanGGOLiN. Detailed results and scripts to compute the benchmark metrics are available at https://github.com/axbazin/panrgp_supdata.

scholarly journals A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Shan-Shan Zhou ◽  
Xue-Mei Yan ◽  
Kai-Fu Zhang ◽  
Hui Liu ◽  
Jie Xu ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Age Determination ◽  
Genome Plasticity ◽  
Ltr Retrotransposons ◽  
Functional Variation ◽  
Plant Genomes ◽  
Sequencing Technologies ◽  
Plant Groups ◽  
Functional Implications ◽  
Classification Information

AbstractLTR retrotransposons (LTR-RTs) are ubiquitous and represent the dominant repeat element in plant genomes, playing important roles in functional variation, genome plasticity and evolution. With the advent of new sequencing technologies, a growing number of whole-genome sequences have been made publicly available, making it possible to carry out systematic analyses of LTR-RTs. However, a comprehensive and unified annotation of LTR-RTs in plant groups is still lacking. Here, we constructed a plant intact LTR-RTs dataset, which is designed to classify and annotate intact LTR-RTs with a standardized procedure. The dataset currently comprises a total of 2,593,685 intact LTR-RTs from genomes of 300 plant species representing 93 families of 46 orders. The dataset is accompanied by sequence, diverse structural and functional annotation, age determination and classification information associated with the LTR-RTs. This dataset will contribute valuable resources for investigating the evolutionary dynamics and functional implications of LTR-RTs in plant genomes.

scholarly journals Ca. Endozoicomonas cretensis: A Novel Fish Pathogen Characterized by Genome Plasticity

2018 ◽  
Vol 10 (6) ◽  
pp. 1363-1374 ◽  
Author(s):  
Weihong Qi ◽  
Maria Chiara Cascarano ◽  
Ralph Schlapbach ◽  
Pantelis Katharios ◽  
Lloyd Vaughan ◽  
...  
Keyword(s):  
Genome Plasticity ◽  
Fish Pathogen

PacBio SMRT assembly of a complex multi-replicon genome reveals chlorocatechol degradative operon in a region of genome plasticity

Gene ◽  
2016 ◽  
Vol 586 (2) ◽  
pp. 239-247 ◽  
Author(s):  
N. Ricker ◽  
S.Y. Shen ◽  
J. Goordial ◽  
S. Jin ◽  
R.R. Fulthorpe
Keyword(s):  
Genome Plasticity

scholarly journals A novel site of insertion of IS6110 in the moaB3 gene of a clinical isolate of Mycobacterium tuberculosis

2011 ◽  
Vol 2 (1) ◽  
pp. 7
Author(s):  
Suma Sarojini ◽  
GK Madhavilatha ◽  
Smitha Soman ◽  
R Ajay Kumar ◽  
Sathish Mundayoor
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Clinical Isolate ◽  
Biosynthetic Pathway ◽  
Mobile Genetic Element ◽  
Point Mutations ◽  
Tuberculosis H37rv ◽  
Genomic Variation ◽  
Clinical Isolates ◽  
Pcr Analysis ◽  
Genome Plasticity

In Mycobacterium tuberculosis, genomic variation is generated mainly by insertions and deletions rather than by point mutations. RvD5 is one such deletion in M. tuberculosis H37Rv. Previous studies from our laboratory have shown the presence of moaA3 gene in the RvD5 region in a large number of clinical isolates, that is absent in M. tuberculosis H37Rv and H37Ra. The present study was aimed at investigating the RvD5 locus of the clinical isolates by a detailed PCR analysis. Here we report a new point of insertion of the mobile genetic element, IS6110 in the genome of one clinical isolate of M. tuberculosis. The insertion has disrupted the moaB3 gene, one of the ORFs in the RvD5 region, which is involved in the molybdopterin biosynthetic pathway. This insertion of IS6110 in the moaB3 of the clinical isolate is different when compared to the insertion in the moaB3 gene of M. tuberculosis H37Rv where 4kb RvD5 region has been lost by homologous recombination and only a truncated form of the gene is present. This finding is of relevance since IS6110 is a major element determining the genome plasticity of M. tuberculosis and its numerical and positional polymorphism has always been of special interest.

FamilyFlexiviridae: A Case Study in Virion and Genome Plasticity

2007 ◽  
Vol 45 (1) ◽  
pp. 73-100 ◽  
Author(s):  
Giovanni P. Martelli ◽  
Michael J. Adams ◽  
Jan F. Kreuze ◽  
Valerian V. Dolja
Keyword(s):  
Genome Plasticity

scholarly journals Gene Amplification and the Extrachromosomal Circular DNA

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1533
Author(s):  
Noriaki Shimizu
Keyword(s):  
Gene Amplification ◽  
Malignant Tumors ◽  
Human Cancer ◽  
Replication Initiation ◽  
Matrix Attachment Region ◽  
Genome Plasticity ◽  
Sequence Element ◽  
Circular Dna ◽  
Attachment Region ◽  
Human Malignant Tumors

Oncogene amplification is closely linked to the pathogenesis of a broad spectrum of human malignant tumors. The amplified genes localize either to the extrachromosomal circular DNA, which has been referred to as cytogenetically visible double minutes (DMs), or submicroscopic episome, or to the chromosomal homogeneously staining region (HSR). The extrachromosomal circle from a chromosome arm can initiate gene amplification, resulting in the formation of DMs or HSR, if it had a sequence element required for replication initiation (the replication initiation region/matrix attachment region; the IR/MAR), under a genetic background that permits gene amplification. In this article, the nature, intracellular behavior, generation, and contribution to cancer genome plasticity of such extrachromosomal circles are summarized and discussed by reviewing recent articles on these topics. Such studies are critical in the understanding and treating human cancer, and also for the production of recombinant proteins such as biopharmaceuticals by increasing the recombinant genes in the cells.

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