scholarly journals Diversity, dynamics and effects of long terminal repeat retrotransposons in the model grass Brachypodium distachyon

2019 ◽  
Vol 227 (6) ◽  
pp. 1736-1748 ◽  
Author(s):  
Christoph Stritt ◽  
Michele Wyler ◽  
Elena L. Gimmi ◽  
Martin Pippel ◽  
Anne C. Roulin
Keyword(s):  
Long Terminal Repeat ◽  
Brachypodium Distachyon ◽  
Long Terminal Repeat Retrotransposons ◽  
Terminal Repeat ◽  
Model Grass ◽  
Diversity Dynamics

Do non-long terminal repeat retrotransposons have nuclease activity?

1996 ◽  
Vol 21 (8) ◽  
pp. 283-285 ◽  
Author(s):  
F MARTIN ◽  
M OLIVARES ◽  
M LOPEZ ◽  
C ALONSO
Keyword(s):  
Long Terminal Repeat ◽  
Nuclease Activity ◽  
Long Terminal Repeat Retrotransposons ◽  
Terminal Repeat

scholarly journals Determinants of Genomic RNA Encapsidation in the Saccharomyces cerevisiae Long Terminal Repeat Retrotransposons Ty1 and Ty3

Viruses ◽  
2016 ◽  
Vol 8 (7) ◽  
pp. 193 ◽  
Author(s):  
Katarzyna Pachulska-Wieczorek ◽  
Stuart Le Grice ◽  
Katarzyna Purzycka
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Long Terminal Repeat ◽  
Long Terminal Repeat Retrotransposons ◽  
Terminal Repeat ◽  
Genomic Rna

scholarly journals LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons

Mobile DNA ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Shujun Ou ◽  
Ning Jiang
Keyword(s):  
Triticum Aestivum ◽  
Long Terminal Repeat ◽  
Bread Wheat ◽  
Repetitive Sequences ◽  
Long Terminal Repeat Retrotransposons ◽  
Rapid Identification ◽  
Terminal Repeat ◽  
Parallel Operation ◽  
Ltr Retrotransposons ◽  
Plant Genomes

AbstractAnnotation of plant genomes is still a challenging task due to the abundance of repetitive sequences, especially long terminal repeat (LTR) retrotransposons. LTR_FINDER is a widely used program for the identification of LTR retrotransposons but its application on large genomes is hindered by its single-threaded processes. Here we report an accessory program that allows parallel operation of LTR_FINDER, resulting in up to 8500X faster identification of LTR elements. It takes only 72 min to process the 14.5 Gb bread wheat (Triticum aestivum) genome in comparison to 1.16 years required by the original sequential version. LTR_FINDER_parallel is freely available at https://github.com/oushujun/LTR_FINDER_parallel.

scholarly journals Long terminal repeat retrotransposons jump between species

1999 ◽  
Vol 96 (22) ◽  
pp. 12211-12212 ◽  
Author(s):  
A. J. Flavell
Keyword(s):  
Long Terminal Repeat ◽  
Long Terminal Repeat Retrotransposons ◽  
Terminal Repeat

scholarly journals The site-specific ribosomal DNA insertion element R1Bm belongs to a class of non-long-terminal-repeat retrotransposons.

1988 ◽  
Vol 8 (1) ◽  
pp. 114-123 ◽  
Author(s):  
Y Xiong ◽  
T H Eickbush
Keyword(s):  
Amino Acids ◽  
Reverse Transcriptase ◽  
Long Terminal Repeat ◽  
Ribosomal Dna ◽  
Long Terminal Repeat Retrotransposons ◽  
Amino Acid Sequences ◽  
Terminal Repeat ◽  
Type I ◽  
Sequence Specificity ◽  
Insertion Element

Two types of insertion elements, R1 and R2 (previously called type I and type II), are known to interrupt the 28S ribosomal genes of several insect species. In the silkmoth, Bombyx mori, each element occupies approximately 10% of the estimated 240 ribosomal DNA units, while at most only a few copies are located outside the ribosomal DNA units. We present here the complete nucleotide sequence of an R1 insertion from B. mori (R1Bm). This 5.1-kilobase element contains two overlapping open reading frames (ORFs) which together occupy 88% of its length. ORF1 is 461 amino acids in length and exhibits characteristics of retroviral gag genes. ORF2 is 1,051 amino acids in length and contains homology to reverse transcriptase-like enzymes. The analysis of 3' and 5' ends of independent isolates from the ribosomal locus supports the suggestion that R1 is still functioning as a transposable element. The precise location of the element within the genome implies that its transposition must occur with remarkable insertion sequence specificity. Comparison of the deduced amino acid sequences from six retrotransposons, R1 and R2 of B. mori, I factor and F element of Drosophila melanogaster, L1 of Mus domesticus, and Ingi of Trypanosoma brucei, reveals a relatively high level of sequence homology in the reverse transcriptase region. Like R1, these elements lack long terminal repeats. We have therefore named this class of related elements the non-long-terminal-repeat (non-LTR) retrotransposons.

scholarly journals Processing and Translation Initiation of Non-long Terminal Repeat Retrotransposons by Hepatitis Delta Virus (HDV)-like Self-cleaving Ribozymes

2011 ◽  
Vol 286 (48) ◽  
pp. 41286-41295 ◽  
Author(s):  
Dana J. Ruminski ◽  
Chiu-Ho T. Webb ◽  
Nathan J. Riccitelli ◽  
Andrej Lupták
Keyword(s):  
Long Terminal Repeat ◽  
Translation Initiation ◽  
Hepatitis Delta Virus ◽  
Long Terminal Repeat Retrotransposons ◽  
Terminal Repeat ◽  
Hepatitis Delta ◽  
Delta Virus

scholarly journals Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

2009 ◽  
Vol 19 (12) ◽  
pp. 2221-2230 ◽  
Author(s):  
Z. Tian ◽  
C. Rizzon ◽  
J. Du ◽  
L. Zhu ◽  
J. L. Bennetzen ◽  
...  
Keyword(s):  
Long Terminal Repeat ◽  
Genetic Recombination ◽  
Long Terminal Repeat Retrotransposons ◽  
Gene Density ◽  
Terminal Repeat ◽  
Dna Elimination

Evolution of the large genome in Capsicum annuum occurred through accumulation of single-type long terminal repeat retrotransposons and their derivatives

2011 ◽  
Vol 69 (6) ◽  
pp. 1018-1029 ◽  
Author(s):  
Minkyu Park ◽  
Jongsun Park ◽  
Seungill Kim ◽  
Jin-Kyung Kwon ◽  
Hye Mi Park ◽  
...  
Keyword(s):  
Long Terminal Repeat ◽  
Capsicum Annuum ◽  
Long Terminal Repeat Retrotransposons ◽  
Terminal Repeat ◽  
Single Type ◽  
Large Genome

scholarly journals Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons

Mobile DNA ◽  
2010 ◽  
Vol 1 (1) ◽  
pp. 3 ◽  
Author(s):  
Weidong Bao ◽  
Vladimir V Kapitonov ◽  
Jerzy Jurka
Keyword(s):  
Long Terminal Repeat ◽  
Long Terminal Repeat Retrotransposons ◽  
Terminal Repeat ◽  
Evolutionary Relationships ◽  
Dna Transposons
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