scholarly journals Massive Intron Gain in the Most Intron-Rich Eukaryotes is Driven by Introner-Like Transposable Elements of Unprecedented Diversity and Flexibility

2020 ◽  
Author(s):  
Scott William Roy ◽  
Landen Gozashti ◽  
Bradley A. Bowser ◽  
Brooke N. Weinstein ◽  
Graham E. Larue
Keyword(s):  
Transposable Elements ◽  
Intron Gain

scholarly journals What Can Domesticated Genes Tell Us about the Intron Gain in Mammals?

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Dušan Kordiš ◽  
Janez Kokošar
Keyword(s):  
Transposable Elements ◽  
De Novo ◽  
Single Copy ◽  
Intron Gain ◽  
Current Understanding ◽  
Dna Transposons ◽  
Coding Regions ◽  
Positional Bias ◽  
Ideal System

Domesticated genes, originating from retroelements or from DNA-transposons, constitute an ideal system for testing the hypothesis on the absence of intron gain in mammals. Since single-copy domesticated genes originated from the intronless multicopy transposable elements, the ancestral intron state for domesticated genes is zero. A phylogenomic approach has been used to analyse all domesticated genes in mammals and chordates that originated from the coding parts of transposable elements. A significant amount of intron gain was found only in domesticated genes of placental mammals, where more than 70 cases were identified. De novo gained introns show clear positional bias, since they are distributed mainly in 5′ UTR and coding regions, while 3′ UTR introns are very rare. In the coding regions of some domesticated genes up to 8 de novo gained introns have been found. Surprisingly, the majority of intron gains have occurred in the ancestor of placental mammals. Domesticated genes could constitute an excellent system on which to analyse the mechanisms of intron gain. This paper summarizes the current understanding of intron gain in mammals.

scholarly journals Massive intron gain in the most intron-rich eukaryotes is driven by introner-like transposable elements of unprecedented diversity and flexibility

2020 ◽  
Author(s):  
Scott William Roy ◽  
Landen Gozashti ◽  
Bradley A. Bowser ◽  
Brooke N. Weinstein ◽  
Graham E. Larue
Keyword(s):  
Transposable Elements ◽  
Insertion Site ◽  
Intron Loss ◽  
Intron Gain ◽  
Nuclear Genes ◽  
Spliceosomal Intron ◽  
Intron Evolution ◽  
Evolutionary Mechanisms ◽  
Spliceosomal Introns ◽  
History Of

SummarySpliceosomal introns, which interrupt nuclear genes and are removed from RNA transcripts by machinery termed spliceosomes, are ubiquitous features of eukaryotic nuclear genes [1]. Patterns of spliceosomal intron evolution are complex, with some lineages exhibiting virtually no intron creation while others experience thousands of intron gains [2–5]. One possibility is that this punctate phylogenetic distribution is explained by intron creation by Introner-Like Elements (ILEs), transposable elements capable of creating introns, with only those lineages harboring ILEs undergoing massive intron gain [6–10]. However, ILEs have been reported in only four lineages. Here we study intron evolution in dinoflagellates. The remarkable fragmentation of nuclear genes by spliceosomal introns reaches its apex in dinoflagellates, which have some twenty introns per gene [11,12]. Despite this, almost nothing is known about the molecular and evolutionary mechanisms governing dinoflagellate intron evolution. We reconstructed intron evolution in five dinoflagellate genomes, revealing a dynamic history of intron loss and gain. ILEs are found in 4/5 studied species. In one species, Polarella glacialis, we find an unprecedented diversity of ILEs, with ILE insertion leading to creation of some 12,253 introns, and with 15 separate families of ILEs accounting for at least 100 introns each. These ILE families range in mobilization mechanism, mechanism of intron creation, and flexibility of mechanism of intron creation. Comparison within and between ILE families provides evidence that biases in so-called intron phase, the distribution of introns relative to codon periodicity, are driven by ILE insertion site requirements [9,13,14]. Finally, we find evidence for multiple additional transformations of the spliceosomal system in dinoflagellates, including widespread loss of ancestral introns, and alterations in required, tolerated and favored splice motifs. These results reveal unappreciated intron creating elements diversity and spliceosomal evolutionary capacity, and suggest complex evolutionary dependencies shaping genome structures.

Survey of transposable elements from rice genomic sequences

2001 ◽  
Vol 25 (2) ◽  
pp. 169-179 ◽  
Author(s):  
Kime Turcotte ◽  
Sujatha Srinivasan ◽  
Thomas Bureau
Keyword(s):  
Transposable Elements ◽  
Genomic Sequences

The utility of transposable elements as tools for the isolation of plant genes

1990 ◽  
Vol 79 (1) ◽  
pp. 105-115 ◽  
Author(s):  
Joel M. Chandlee
Keyword(s):  
Transposable Elements ◽  
Plant Genes
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