scholarly journals The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution

Heredity ◽  
2013 ◽  
Vol 110 (2) ◽  
pp. 194-204 ◽  
Author(s):  
M C Estep ◽  
J D DeBarry ◽  
J L Bennetzen
Keyword(s):  
Ltr Retrotransposon ◽  
Grass Evolution ◽  
Panicoid Grass

scholarly journals Multiple Lineages of the Non-LTR Retrotransposon Rex1 with Varying Success in Invading Fish Genomes

2000 ◽  
Vol 17 (11) ◽  
pp. 1673-1684 ◽  
Author(s):  
Jean-Nicolas Volff ◽  
Cornelia Körting ◽  
Manfred Schartl
Keyword(s):  
Ltr Retrotransposon

scholarly journals Genome-Wide Identification and Development of LTR Retrotransposon-Based Molecular Markers for the Melilotus Genus

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 890
Author(s):  
Zifeng Ouyang ◽  
Yimeng Wang ◽  
Tiantian Ma ◽  
Gisele Kanzana ◽  
Fan Wu ◽  
...  
Keyword(s):  
Group Method ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Important Data ◽  
Breeding Programs ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Medicinal Value ◽  
Genome Wide ◽  
Melilotus Albus

Melilotus is an important genus of legumes with industrial and medicinal value, partly due to the production of coumarin. To explore the genetic diversity and population structure of Melilotus, 40 accessions were analyzed using long terminal repeat (LTR) retrotransposon-based markers. A total of 585,894,349 bp of LTR retrotransposon sequences, accounting for 55.28% of the Melilotus genome, were identified using bioinformatics tools. A total of 181,040 LTR retrotransposons were identified and classified as Gypsy, Copia, or another type. A total of 350 pairs of primers were designed for assessing polymorphisms in 15 Melilotus albus accessions. Overall, 47 polymorphic primer pairs were screened for their availability and transferability in 18 Melilotus species. All the primer pairs were transferable, and 292 alleles were detected at 47 LTR retrotransposon loci. The average polymorphism information content (PIC) value was 0.66, which indicated that these markers were highly informative. Based on unweighted pair group method with arithmetic mean (UPGMA) dendrogram cluster analysis, the 18 Melilotus species were classified into three clusters. This study provides important data for future breeding programs and for implementing genetic improvements in the Melilotus genus.

scholarly journals Unearthing LTR retrotransposon gag genes co-opted in the deep evolution of eukaryotes

2021 ◽  
Author(s):  
Jianhua Wang ◽  
Guan-Zhu Han
Keyword(s):  
Gene Expression ◽  
Selective Pressure ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Cellular Functions ◽  
The Family ◽  
Family Level ◽  
Gene Expression Analyses ◽  
Comprehensive Picture ◽  
Gypsy Retrotransposons

Abstract LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes, and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.

scholarly journals The Ty1 LTR-retrotransposon population in Saccharomyces cerevisiae genome: dynamics and sequence variations during mobility

2011 ◽  
Vol 11 (4) ◽  
pp. 334-344 ◽  
Author(s):  
Claudine Bleykasten-Grosshans ◽  
Paul P. Jung ◽  
Emilie S. Fritsch ◽  
Serge Potier ◽  
Jacky de Montigny ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Ltr Retrotransposon ◽  
Sequence Variations ◽  
Genome Dynamics

CfT-I: an LTR-retrotransposon in Cladosporium fulvum, a fungal pathogen of tomato

1992 ◽  
Vol 233 (3) ◽  
pp. 337-347 ◽  
Author(s):  
Mark T. McHale ◽  
Ian N. Roberts ◽  
Stuart M. Noble ◽  
Christine Beaumont ◽  
Michael P. Whitehead ◽  
...  
Keyword(s):  
Fungal Pathogen ◽  
Ltr Retrotransposon ◽  
Cladosporium Fulvum

scholarly journals Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jonathan Filée ◽  
Sarah Farhat ◽  
Dominique Higuet ◽  
Laure Teysset ◽  
Dominique Marie ◽  
...  
Keyword(s):  
Transposable Elements ◽  
High Throughput Sequencing ◽  
Comparative Genomic ◽  
Ltr Retrotransposon ◽  
Genomic Evolution ◽  
Genome Wide ◽  
Genomic Analyses ◽  
Different Types ◽  
Evolutionary Success ◽  
Low Coverage

Abstract Background With the expansion of high throughput sequencing, we now have access to a larger number of genome-wide studies analyzing the Transposable elements (TEs) composition in a wide variety of organisms. However, genomic analyses often remain too limited in number and diversity of species investigated to study in depth the dynamics and evolutionary success of the different types of TEs among metazoans. Therefore, we chose to investigate the use of transcriptomes to describe the diversity of TEs in phylogenetically related species by conducting the first comparative analysis of TEs in two groups of polychaetes and evaluate the diversity of TEs that might impact genomic evolution as a result of their mobility. Results We present a detailed analysis of TEs distribution in transcriptomes extracted from 15 polychaetes depending on the number of reads used during assembly, and also compare these results with additional TE scans on associated low-coverage genomes. We then characterized the clades defined by 1021 LTR-retrotransposon families identified in 26 species. Clade richness was highly dependent on the considered superfamily. Copia elements appear rare and are equally distributed in only three clades, GalEa, Hydra and CoMol. Among the eight BEL/Pao clades identified in annelids, two small clades within the Sailor lineage are new for science. We characterized 17 Gypsy clades of which only 4 are new; the C-clade largely dominates with a quarter of the families. Finally, all species also expressed for the majority two distinct transcripts encoding PIWI proteins, known to be involved in control of TEs mobilities. Conclusions This study shows that the use of transcriptomes assembled from 40 million reads was sufficient to access to the diversity and proportion of the transposable elements compared to those obtained by low coverage sequencing. Among LTR-retrotransposons Gypsy elements were unequivocally dominant but results suggest that the number of Gypsy clades, although high, may be more limited than previously thought in metazoans. For BEL/Pao elements, the organization of clades within the Sailor lineage appears more difficult to establish clearly. The Copia elements remain rare and result from the evolutionary consistent success of the same three clades.

scholarly journals Hotspots of Independent and Multiple Rounds of LTR-retrotransposon Bursts in Brassica Species

2018 ◽  
Vol 4 (4) ◽  
pp. 165-174 ◽  
Author(s):  
Xu CAI ◽  
Yinan CUI ◽  
Lei ZHANG ◽  
Jian WU ◽  
Jianli LIANG ◽  
...  
Keyword(s):  
Brassica Species ◽  
Ltr Retrotransposon

Deep Neural Network to Curate LTR Retrotransposon Libraries from Plant Genomes

2021 ◽  
pp. 85-94
Author(s):  
Simon Orozco-Arias ◽  
Mariana S. Candamil-Cortes ◽  
Paula A. Jaimes ◽  
Estiven Valencia-Castrillon ◽  
Reinel Tabares-Soto ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Neural Network ◽  
Ltr Retrotransposon ◽  
Plant Genomes
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