Mdoryco1-1 , a bidirectionally transcriptional Ty1 -copia retrotransposon from Malus × domestica

Wang, Lulu; Ya, HE; Qiu, Huarong; Guo, Jing; Han, Mengxue; Zhou, Jinjun; Sun, Qibao; Sun, Jun

doi:10.1016/j.scienta.2017.03.049

Cited by 2 publications

(3 citation statements)

References 37 publications

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“…In LTR-RTs, the response to external stresses is attributed to the LTR sequences located at both ends [88]. On the other hand, activation of TEs is not always directly produced by external stresses but by the effect of those stresses on other cellular mechanisms that allow a rapid activation of some specific families of LTR retrotransposons [34].…”

Section: Structure Diversity Dynamics and Function Of Retrotranmentioning

confidence: 99%

“…These impacts can include the imposition of intragenomic selection pressures through their effects on gene expression [76], inactivation of coding or regulatory regions of the gene [124], mutations that change the protein sequence, variation of the pattern of expression or alternative splicing [3], alteration of the expression of neighboring genes by epigenetic effects [82], or through modification of transcription factor expression [151], redirection of stress stimuli to adjacent genes [9], and the influence on the conservation, rearrangement, and deletion of gene pairs [152]. The long-term impact of such variation involves, for instance, genetic variation with important effects on species evolution [153], genomic diversification and speciation [154], and modification of the host fitness [89,108,155,156] by producing sense or antisense transcripts of the genes [88]. A known example of gene expression reprogramming is the one described by McClintock for anthocyanin pigment gene expression in maize [78] and wheat, where the activated retrotransposons Wis2-1A altered the expression of their adjacent genes [108].…”

Section: Structure Diversity Dynamics and Function Of Retrotranmentioning

confidence: 99%

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Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning

Orozco-Arias

Isaza

Guyot

2019

IJMS

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Transposable elements (TEs) are genomic units able to move within the genome of virtually all organisms. Due to their natural repetitive numbers and their high structural diversity, the identification and classification of TEs remain a challenge in sequenced genomes. Although TEs were initially regarded as “junk DNA”, it has been demonstrated that they play key roles in chromosome structures, gene expression, and regulation, as well as adaptation and evolution. A highly reliable annotation of these elements is, therefore, crucial to better understand genome functions and their evolution. To date, much bioinformatics software has been developed to address TE detection and classification processes, but many problematic aspects remain, such as the reliability, precision, and speed of the analyses. Machine learning and deep learning are algorithms that can make automatic predictions and decisions in a wide variety of scientific applications. They have been tested in bioinformatics and, more specifically for TEs, classification with encouraging results. In this review, we will discuss important aspects of TEs, such as their structure, importance in the evolution and architecture of the host, and their current classifications and nomenclatures. We will also address current methods and their limitations in identifying and classifying TEs.

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Section: Structure Diversity Dynamics and Function Of Retrotranmentioning

confidence: 99%

Section: Structure Diversity Dynamics and Function Of Retrotranmentioning

confidence: 99%

Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning

Orozco-Arias

Isaza

Guyot

2019

IJMS

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“…For example, HTLV has an antisense promoter located inside the 3 LTR (Barbeau and Mesnard, 2011). Antisense promoters have been also identified in other retrotransposons as, for example, the apple Mdoryco1-1 (Wang et al, 2017), Arabidopsis thaliana AtRE1 (Kato et al, 2005), and Drosophila hydei micropia (Lankenau et al, 1994). However, in the case of micropia, it transcribes two antisense RNAs of 1.0 and 1.6 kb with no protein coding capacity.…”

Section: Transcription Of Aorfs-3rmentioning

confidence: 99%

Additional ORFs in Plant LTR-Retrotransposons

Vicient

Casacuberta

2020

Front. Plant Sci.

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LTR-retrotransposons share a common genomic organization in which the 5 long terminal repeat (LTR) is followed by the gag and pol genes and terminates with the 3 LTR. Although GAG-POL-encoded proteins are considered sufficient to accomplish the LTR-retrotransposon transposition, a number of elements carrying additional open reading frames (aORF) have been described. In some cases, the presence of an aORF can be explained by a phenomenon similar to retrovirus gene transduction, but in these cases the aORFs are present in only one or a few copies. On the contrary, many elements contain aORFs, or derivatives, in all or most of their copies. These aORFs are more frequently located between pol and 3 LTR, and they could be in sense or antisense orientation with respect to gag-pol. Sense aORFs include those encoding for ENV-like proteins, so called because they have some structural and functional similarities with retroviral ENV proteins. Antisense aORFs between pol and 3 LTR are also relatively frequent and, for example, are present in some characterized LTR-retrotransposon families like maize Grande, rice RIRE2, or Silene Retand, although their possible roles have been not yet determined. Here, we discuss the current knowledge about these sense and antisense aORFs in plant LTR-retrotransposons, suggesting their possible origins, evolutionary relevance, and function.

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Mdoryco1-1 , a bidirectionally transcriptional Ty1 -copia retrotransposon from Malus × domestica

Cited by 2 publications

References 37 publications

Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning

Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning

Additional ORFs in Plant LTR-Retrotransposons

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