scholarly journals Successful Invasions of Short Internally Deleted Elements (SIDEs) and Its Partner CR1 in Lepidoptera Insects

2019 ◽  
Vol 11 (9) ◽  
pp. 2505-2516
Author(s):  
Ping-Lan Wang ◽  
Andrea Luchetti ◽  
Angelo Alberto Ruggieri ◽  
Xiao-Min Xiong ◽  
Min-Rui-Xuan Xu ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Inverted Repeat ◽  
Copy Number ◽  
Phylogenetic Analyses ◽  
Terminal Repeat ◽  
Dna Transposons ◽  
Chicken Repeat ◽  
Evolution Dynamics

Abstract Although DNA transposons often generated internal deleted derivatives such as miniature inverted-repeat transposable elements, short internally deleted elements (SIDEs) derived from nonlong terminal-repeat retrotransposons are rare. Here, we found a novel SIDE, named Persaeus, that originated from the chicken repeat 1 (CR1) retrotransposon Zenon and it has been found widespread in Lepidoptera insects. Our findings suggested that Persaeus and the partner Zenon have experienced a transposition burst in their host genomes and the copy number of Persaeus and Zenon in assayed genomes are significantly correlated. Accordingly, the activity though age analysis indicated that the replication wave of Persaeus coincided with that of Zenon. Phylogenetic analyses suggested that Persaeus may have evolved at least four times independently, and that it has been vertically transferred into its host genomes. Together, our results provide new insights into the evolution dynamics of SIDEs and its partner non-LTRs.

Sequence Organization and Conservation in sh2/a1-Homologous Regions of Sorghum and Rice

Genetics ◽  
1998 ◽  
Vol 148 (1) ◽  
pp. 435-443
Author(s):  
Mingsheng Chen ◽  
Phillip SanMiguel ◽  
Jeffrey L Bennetzen
Keyword(s):  
Transposable Elements ◽  
Long Terminal Repeat ◽  
Inverted Repeat ◽  
Tandem Duplication ◽  
Regulatory Gene ◽  
Terminal Repeat ◽  
Homologous Segment ◽  
Sequence Organization ◽  
Transcriptional Regulatory ◽  
Evolutionarily Conserved

Abstract Previously, we have demonstrated microcolinearity of gene composition and orientation in sh2/a1-homologous regions of the rice, sorghum, and maize genomes. However, the sh2 and a1 homologues are only about 20 kb apart in both rice and sorghum, while they are separated by about 140 kb in maize. In order to further define sequence organization and conservation in sh2/a1-homologous regions, we have completely sequenced a 42,446-bp segment of sorghum DNA. Four genes were identified: a homologue of sh2, two homologues of a1, and a putative transcriptional regulatory gene. A solo long terminal repeat of the retroelement Leviathan was detected between the two a1 homologues, and eight miniature inverted repeat transposable elements were found in this region. Comparison of the sorghum sequence with the sequence of the homologous segment from rice indicated that only the identified genes were evolutionarily conserved between these two species, which have evolved independently for over 50 million years. The introns of the a1 homologues have evolved faster than the introns of the sh2 homologue. The a1 tandem duplication appears to be an ancient event that may have preceded the ancestral divergence of maize, sorghum, and rice.

scholarly journals A genomic survey of transposable elements in the choanoflagellate Salpingoeca rosetta reveals selection on codon usage

Mobile DNA ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Jade Southworth ◽  
C. Alastair Grace ◽  
Alan O. Marron ◽  
Nazeefa Fatima ◽  
Martin Carr
Keyword(s):  
Transposable Elements ◽  
Codon Usage ◽  
Population Biology ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Translational Efficiency ◽  
Ltr Retrotransposons ◽  
Dna Transposons ◽  
Show Evidence ◽  
Salpingoeca Rosetta

Abstract Background Unicellular species make up the majority of eukaryotic diversity, however most studies on transposable elements (TEs) have centred on multicellular host species. Such studies may have therefore provided a limited picture of how transposable elements evolve across eukaryotes. The choanoflagellates, as the sister group to Metazoa, are an important study group for investigating unicellular to multicellular transitions. A previous survey of the choanoflagellate Monosiga brevicollis revealed the presence of only three families of LTR retrotransposons, all of which appeared to be active. Salpingoeca rosetta is the second choanoflagellate to have its whole genome sequenced and provides further insight into the evolution and population biology of transposable elements in the closest relative of metazoans. Results Screening the genome revealed the presence of a minimum of 20 TE families. Seven of the annotated families are DNA transposons and the remaining 13 families are LTR retrotransposons. Evidence for two putative non-LTR retrotransposons was also uncovered, but full-length sequences could not be determined. Superfamily phylogenetic trees indicate that vertical inheritance and, in the case of one family, horizontal transfer have been involved in the evolution of the choanoflagellates TEs. Phylogenetic analyses of individual families highlight recent element activity in the genome, however six families did not show evidence of current transposition. The majority of families possess young insertions and the expression levels of TE genes vary by four orders of magnitude across families. In contrast to previous studies on TEs, the families present in S. rosetta show the signature of selection on codon usage, with families favouring codons that are adapted to the host translational machinery. Selection is stronger in LTR retrotransposons than DNA transposons, with highly expressed families showing stronger codon usage bias. Mutation pressure towards guanosine and cytosine also appears to contribute to TE codon usage. Conclusions S. rosetta increases the known diversity of choanoflagellate TEs and the complement further highlights the role of horizontal gene transfer from prey species in choanoflagellate genome evolution. Unlike previously studied TEs, the S. rosetta families show evidence for selection on their codon usage, which is shown to act via translational efficiency and translational accuracy.

scholarly journals Assembly of the mariner Mos1 Synaptic Complex

2005 ◽  
Vol 25 (7) ◽  
pp. 2861-2870 ◽  
Author(s):  
Corinne Augé-Gouillou ◽  
Benjamin Brillet ◽  
Marie-Hélène Hamelin ◽  
Yves Bigot
Keyword(s):  
Transposable Elements ◽  
Binding Sites ◽  
Inverted Repeat ◽  
Terminal Repeat ◽  
Inverted Terminal Repeat ◽  
Synaptic Complex ◽  
Target Dna ◽  
Nucleoprotein Complex ◽  
Inverted Terminal Repeats ◽  
Terminal Repeats

ABSTRACT The mobility of transposable elements via a cut-and-paste mechanism depends on the elaboration of a nucleoprotein complex known as the synaptic complex. We show here that the Mos1 synaptic complex consists of the two inverted terminal repeats of the element brought together by a transposase tetramer and is designated paired-end complex 2 (PEC2). The assembly of PEC2 requires the formation of a simpler complex, containing one terminal repeat and two transposase molecules and designated single-end complex 2 (SEC2). In light of the formation of SEC2 and PEC2, we demonstrate the presence of two binding sites for the transposase within a single terminal repeat. We have found that the sequence of the Mos1 inverted terminal repeats contains overlapping palindromic and mirror motifs, which could account for the binding of two transposase molecules “side by side” on the same inverted terminal repeat. We provide data indicating that the Mos1 transposase dimer is formed within a single terminal repeat through a cooperative pathway. Finally, the concept of a tetrameric synaptic complex may simply account for the inability of a single mariner transposase molecule to interact at the same time with two kinds of DNA: the inverted repeat and the target DNA.

Miniature inverted-repeat transposable elements: discovery, distribution, and activity

Genome ◽  
2013 ◽  
Vol 56 (9) ◽  
pp. 475-486 ◽  
Author(s):  
Isam Fattash ◽  
Rebecca Rooke ◽  
Amy Wong ◽  
Caleb Hui ◽  
Tina Luu ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Inverted Repeat ◽  
Copy Number ◽  
Copy Numbers ◽  
Number Increase ◽  
Eukaryotic Organisms ◽  
Eukaryotic Genomes ◽  
Copy Number Increase

Eukaryotic organisms have dynamic genomes, with transposable elements (TEs) as a major contributing factor. Although the large autonomous TEs can significantly shape genomic structures during evolution, genomes often harbor more miniature nonautonomous TEs that can infest genomic niches where large TEs are rare. In spite of their cut-and-paste transposition mechanisms that do not inherently favor copy number increase, miniature inverted-repeat transposable elements (MITEs) are abundant in eukaryotic genomes and exist in high copy numbers. Based on the large number of MITE families revealed in previous studies, accurate annotation of MITEs, particularly in newly sequenced genomes, will identify more genomes highly rich in these elements. Novel families identified from these analyses, together with the currently known families, will further deepen our understanding of the origins, transposase sources, and dramatic amplification of these elements.

scholarly journals Three Groups of Transposable Elements with Contrasting Copy Number Dynamics and Host Responses in the Maize (Zea mays ssp. mays) Genome

PLoS Genetics ◽  
2014 ◽  
Vol 10 (4) ◽  
pp. e1004298 ◽  
Author(s):  
Concepcion M. Diez ◽  
Esteban Meca ◽  
Maud I. Tenaillon ◽  
Brandon S. Gaut
Keyword(s):  
Zea Mays ◽  
Transposable Elements ◽  
Copy Number ◽  
Host Responses ◽  
Number Dynamics

scholarly journals MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Juan Manuel Crescente ◽  
Diego Zavallo ◽  
Marcelo Helguera ◽  
Leonardo Sebastián Vanzetti
Keyword(s):  
Transposable Elements ◽  
Inverted Repeat ◽  
Large Genomes
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