Pack-MULE transposable elements mediate gene evolution in plants

  title={Pack-MULE transposable elements mediate gene evolution in plants},
  author={Ning Jiang and Zhirong Bao and Xiaoyu Zhang and Sean R. Eddy and Susan R. Wessler},
Mutator-like transposable elements (MULEs) are found in many eukaryotic genomes and are especially prevalent in higher plants. In maize, rice and Arabidopsis a few MULEs were shown to carry fragments of cellular genes. These chimaeric elements are called Pack-MULEs in this study. The abundance of MULEs in rice and the availability of most of the genome sequence permitted a systematic analysis of the prevalence and nature of Pack-MULEs in an entire genome. Here we report that there are over 3… 
This analysis using maize, rice, and Arabidopsis genomic sequences indicates that the acquisition of genic sequences by Pack-MULEs is not random and contributes to the increased number of genes with negative GC gradient in grasses.
The Functional Role of Pack-MULEs in Rice Inferred from Purifying Selection and Expression Profile[W]
A comprehensive analysis of expression and purifying selection on 2809 Pack-MULEs in rice (Oryza sativa), which are derived from 1501 parental genes, suggests that at least a subset of these duplicates are likely functional and have great potential in regulating gene expression as well as providing novel coding capacities.
Mutator transposon in maize and MULEs in the plant genome.
Nested Insertions and Accumulation of Indels Are Negatively Correlated with Abundance of Mutator-Like Transposable Elements in Maize and Rice
The results suggest that the amplification of retrotransposons may limit the amplified of DNA transposons but not vice versa, and more indels are detected among maize elements than rice elements whereas defects caused by point mutations are comparable between the two species.
Evolution of Mutator transposable elements across eukaryotic diversity
This study mines MULEs from online databases, combines search results with available transposase sequences retrieved from previously published studies, and performs comprehensive bioinformatic and phylogenetic analyses to address currently available MULE diversity and reconstruct evolution for the group.
The evolutionary fate of MULE-mediated duplications of host gene fragments in rice.
It is concluded that MULE-mediated host gene duplication results in the formation of pseudogenes, not novel functional protein-coding genes; however, the transcribed duplications possess characteristics consistent with a potential role in the regulation of host gene expression.
Transposon-mediated expansion and diversification of a family of ULP-like genes.
A genome-wide survey of transduplication in Mutator-like elements (MULEs) in Arabidopsis thaliana shows that the phenomenon is generally similar to rice transduPLication, with one important exception: KAONASHI (KI), suggesting that the function of KI may be selfish rather than cellular.
Plant mutator-like transposable elements (MULEs): Their evolutionary dynamics, interaction with genes, and recapitulation of transposition activity in yeast
The establishment of the MULE transposition system in yeast laid the foundation for further studying MULE biology, and revealed a critical region of the transposase, where changes of the amino acid compositions resulted in either enhanced or repressed activity.
Pack-Mutator–like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition
It is demonstrated that Pack-Mutator–like transposable elements (Pack-MULEs) that carry gene fragments specifically acquire GC-rich fragments and preferentially insert into the 5′ end of genes, thus altering the GC content in those regions.
The widespread nature of Pack-TYPE transposons reveals their importance for plant genome evolution
An automated annotation procedure is produced and used to successfully annotate and analyse more than 4000 new Pack-TYPE TEs in the rice and maize genomes and reports examples of the direct contribution of these TEs to coding genes, suggesting a generalised and extensive role of Pack- TYPETEs in plant genome evolution.


An active DNA transposon family in rice
The use of draft sequences for the two subspecies of Oryza sativa, Nipponbare and indica, provides a unique opportunity to study the dynamics of transposable elements in this important crop plant and is used in a computational approach to identify the first active DNA transposons from rice and the firstactive miniature inverted-repeat transPOSable element (MITE) from any organism.
Mutator-like elements in Arabidopsis thaliana. Structure, diversity and evolution.
Analysis of the sequence and structural diversity of Mutator-like elements (MULEs) in the genome of Arabidopsis thaliana suggests that MULEs exhibit extreme structure, sequence, and size heterogeneity, and there is evidence that Mules are capable of the acquisition of host DNA segments, which may have implications for adaptive evolution, both at the element and host levels.
Mu1-related transposable elements of maize preferentially insert into low copy number DNA.
The Mutator transposable element system of maize was originally identified through its induction of mutations at an exceptionally high frequency and at a wide variety of loci. The Mu1 subfamily of
Characterization of a highly conserved sequence related to mutator transposable elements in maize.
The results suggest that MRS-A represents a stable, functional region of the maize genome, and it is speculated that a similar sequence was encompassed by Mu termini to generate a Mu transposable element.
The generation of Mutator transposable element subfamilies in maize
Computer analyses have shown that sequence duplications are common in non-autonomous members of the Mutator, Ac/Ds, and Spm(En) systems, and suggest that many Mu element subfamilies were generated from a parental element that had termini like those of Mu5.
Survey of transposable elements from rice genomic sequences.
Members of a group of novel rice elements resembling the structurally unusual members of the Basho family in Arabidopsis suggest a wide distribution of these transposons among plants.
MuDR/Mu Transposable Elements of Maize
The MuDR/Mu two-component system is the most aggressive DNA transposon yet characterized. Even PCR strategies based on the most highly conserved sequences of the terminal inverted repeats (TIRs) may
Hop, an active Mutator-like element in the genome of the fungus Fusarium oxysporum.
The distribution of Hop elements within the Fusarium genus revealed that they are present in different species, suggesting that related elements could be present in other fungal genomes.
Transposon diversity in Arabidopsis thaliana.
This report uses sequence similarity search and analysis protocols to perform a fine-scale analysis of a large sample of the Arabidopsis thaliana genome for transposons, and provides evidence that most minedtransposons have a clear distribution preference for A + T-rich sequences and shows that structural variation for many mined transposon is partly due to interelement recombination.
The genome sequence and structure of rice chromosome 1
The essentially complete sequence of chromosome 1, the longest chromosome in the rice genome, is reported and characteristics of the chromosome structure and the biological insight gained from the sequence are summarized.