Identification and Evolution of the Silkworm Helitrons and their Contribution to Transcripts

Han, Minjin; Shen, Yihong; Xu, Mengshu; Liang, Hongyu; Zhang, Hua-Hao; Zhang, Ze

doi:10.1093/dnares/dst024

Cited by 31 publications

(60 citation statements)

References 46 publications

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“…Sequential gene captures that span speciation events were reported in the Vespertilionidae bat family (51). The sequential capture model may explain Helitrons carrying multiple gene fragments observed in other organisms (84,93,95).…”

Section: Gene Capture Occurs At Both the Dna And Rna Levelmentioning

confidence: 82%

“…Helsearch was able to successfully identify Helitrons from other plant genomes like of Arabidopsis, Medicago, rice, and sorghum, and from the animal C. elegans (81) in addition to maize (67). A similar approach was used to identify Helitrons in many genomes including those of lepidopterans and brassicas (84,85). However, this approach generates many false positives.…”

Section: Genome-wide Identification Of Candidate Helitronsmentioning

confidence: 99%

“…Examples for DNAbased and RNA-based mechanisms reveal that Helitrons capture gene fragments through multiple mechanisms. The frequency of gene captures varies between genomes (51,67,68,84,93,96) and between families. In both maize and bat the most prevalent high-copy-number families also exhibit the highest frequency of gene capture.…”

Section: Transposable Element Capturementioning

confidence: 99%

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Helitrons , the Eukaryotic Rolling-circle Transposable Elements

Thomas

Pritham

2015

Microbiol Spectr

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Helitrons, the eukaryotic rolling-circle transposable elements, are widespread but most prevalent among plant and animal genomes. Recent studies have identified three additional coding and structural variants of Helitrons called Helentrons, Proto-Helentron, and Helitron2. Helitrons and Helentrons make up a substantial fraction of many genomes where nonautonomous elements frequently outnumber the putative autonomous partner. This includes the previously ambiguously classified DINE-1-like repeats, which are highly abundant in Drosophila and many other animal genomes. The purpose of this review is to summarize what we have learned about Helitrons in the decade since their discovery. First, we describe the history of autonomous Helitrons, and their variants. Second, we explain the common coding features and difference in structure of canonical Helitrons versus the endonuclease-encoding Helentrons. Third, we review how Helitrons and Helentrons are classified and discuss why the system used for other transposable element families is not applicable. We also touch upon how genome-wide identification of candidate Helitrons is carried out and how to validate candidate Helitrons. We then shift our focus to a model of transposition and the report of an excision event. We discuss the different proposed models for the mechanism of gene capture. Finally, we will talk about where Helitrons are found, including discussions of vertical versus horizontal transfer, the propensity of Helitrons and Helentrons to capture and shuffle genes and how they impact the genome. We will end the review with a summary of open questions concerning the biology of this intriguing group of transposable elements.

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Section: Gene Capture Occurs At Both the Dna And Rna Levelmentioning

confidence: 82%

Section: Genome-wide Identification Of Candidate Helitronsmentioning

confidence: 99%

Section: Transposable Element Capturementioning

confidence: 99%

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Helitrons , the Eukaryotic Rolling-circle Transposable Elements

Thomas

Pritham

2015

Microbiol Spectr

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“…These novel eukaryotic transposons were discovered only recently from a comparative bioinformatic analysis of several plant and animal genomes (2). Helitrons have attracted widespread attention because their remarkable ability to capture gene sequences, and intergenic regions containing potential regulatory elements, makes them of considerable potential evolutionary importance (3)(4)(5)(6)(7)(8)(9)(10). Among carefully studied genomes, Helitron content has been estimated to be approximately 2% in Arabidopsis and maize (2,11,12) and 4.23% in silkworm (9).…”

mentioning

confidence: 99%

HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes

Xiong

Lai

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

223

224

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Transposons make up the bulk of eukaryotic genomes, but are difficult to annotate because they evolve rapidly. Most of the unannotated portion of sequenced genomes is probably made up of various divergent transposons that have yet to be categorized. Helitrons are unusual rolling circle eukaryotic transposons that often capture gene sequences, making them of considerable evolutionary importance. Unlike other DNA transposons, Helitrons do not end in inverted repeats or create target site duplications, so they are particularly challenging to identify. Here we present HelitronScanner, a two-layered local combinational variable (LCV) tool for generalized Helitron identification that represents a major improvement over previous identification programs based on DNA sequence or structure. HelitronScanner identified 64,654 Helitrons from a wide range of plant genomes in a highly automated way. We tested HelitronScanner's predictive ability in maize, a species with highly heterogeneous Helitron elements. LCV scores for the 5′ and 3′ termini of the predicted Helitrons provide a primary confidence level and element copy number provides a secondary one. Newly identified Helitrons were validated by PCR assays or by in silico comparative analysis of insertion site polymorphism among multiple accessions. Many new Helitrons were identified in model species, such as maize, rice, and Arabidopsis, and in a variety of organisms where Helitrons had not been reported previously to our knowledge, leading to a major upward reassessment of their abundance in plant genomes. HelitronScanner promises to be a valuable tool in future comparative and evolutionary studies of this major transposon superfamily.A lthough transposable elements constitute the bulk of most sequenced eukaryotic genomes, their annotation has been hindered by their rapid evolutionary divergence. It is conceivable that a large fraction of the unannotated genome of most eukaryotes is made up of as yet unrecognized transposons. To date, elements have been assigned to a superfamily largely on the basis of terminal sequence homology to other elements that still encode vestiges of that superfamily's transposase (1). Helitrons are particularly challenging to identify because, unlike other DNA transposons, they do not end in inverted repeats or create target site duplications. These novel eukaryotic transposons were discovered only recently from a comparative bioinformatic analysis of several plant and animal genomes (2). Helitrons have attracted widespread attention because their remarkable ability to capture gene sequences, and intergenic regions containing potential regulatory elements, makes them of considerable potential evolutionary importance (3-10). Among carefully studied genomes, Helitron content has been estimated to be approximately 2% in Arabidopsis and maize (2, 11, 12) and 4.23% in silkworm (9). However, these values are most likely underestimates because Helitrons are hard to detect computationally given their lack of classical transposon structural features. As...

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“…Approximately, the helitron DNA constitutes at most 2% of the A. thaliana, the C.elegans and the maize genomes [12], [14], [18] and 4.23% of the silkworm genome [19]. These elements are mostly represented by nonautonomous elements.…”

Section: Introductionmentioning

confidence: 99%

Helitron’s Periodicities Identification in C.Elegans based on the Smoothed Spectral Analysis and the Frequency Chaos Game Signal Coding

Touati¹,

Messaoudi²,

Ouesleti³

et al. 2018

ijacsa

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Abstract-Helitrons are typical rolling circle transposons which make up the bulk of eukaryotic genomes. Unlike of other DNA transposons, these transposable elements (TEs), don't create target site duplications or end in inverted repeats, which make them particular challenge to identify and more difficult to annotate. To date, these elements are not well studied; they only attracted the interest of researchers in biology. The focus of this paper is oriented towards identifying the helitrons in C.elegans genome in the perspective of signal processing. Aiming at the helitron's identification, a novel methodology including two steps is proposed: the coding and the spectral analysis. The first step consists in converting DNA into a 1-D signal based on the statistical features of the sequence (FCGS coding). As for the second step, it aims to identify the global periodicities in helitrons using the Smoothed Fourier Transform. The resulting spectrum and spectrogram are shown to present a specific signature of each helitron's type.

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Identification and Evolution of the Silkworm Helitrons and their Contribution to Transcripts

Cited by 31 publications

References 46 publications

Helitrons , the Eukaryotic Rolling-circle Transposable Elements

Helitrons , the Eukaryotic Rolling-circle Transposable Elements

HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes

Helitron’s Periodicities Identification in C.Elegans based on the Smoothed Spectral Analysis and the Frequency Chaos Game Signal Coding

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