A computational genome-wide analysis of long terminal repeats retrotransposon expression in sunflower roots (Helianthus annuus L.)

Mascagni, Flavia; Vangelisti, Alberto; Usai, Gabriele; Giordani, Tommaso; Cavallini, Andrea; Natali, Lucia

doi:10.1007/s10709-020-00085-4

Cited by 13 publications

(14 citation statements)

References 66 publications

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“…The low transcript abundance of LTR-REs in plants has often been reported [51,[53][54][55][56]. In certain species, increased expression in plants exposed to biotic or abiotic stresses was reported; however, the global level of expression remained low even during stressful treatments [57][58][59][60][61][62]. Our data indicated that 21/180 sequences were barely expressed and only three sequences were transcribed at levels comparable to those of the majority of actin-and tubulin-encoding reference genes.…”

Section: Discussionsupporting

confidence: 56%

Low Long Terminal Repeat (LTR)-Retrotransposon Expression in Leaves of the Marine Phanerogam Posidonia Oceanica L.

Vangelisti

Mascagni

Usai

et al. 2020

Life

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Seagrasses as Posidonia oceanica reproduce mostly by vegetative propagation, which can reduce genetic variability within populations. Since, in clonally propagated species, insurgence of genetic variability can be determined by the activity of transposable elements, we have estimated the activity of such repeat elements by measuring their expression level in the leaves of plants from a Mediterranean site, for which Illumina complementary DNA (cDNA) sequence reads (produced from RNAs isolated by leaves of plants from deep and shallow meadows) were publicly available. Firstly, we produced a collection of retrotransposon-related sequences and then mapped Illumina cDNA reads onto these sequences. With this approach, it was evident that Posidonia retrotransposons are, in general, barely expressed; only nine elements resulted transcribed at levels comparable with those of reference genes encoding tubulins and actins. Differences in transcript abundance were observed according to the superfamily and the lineage to which the retrotransposons belonged. Only small differences were observed between retrotransposon expression levels in leaves of shallow and deep Posidonia meadow stands, whereas one TAR/Tork element resulted differentially expressed in deep plants exposed to heat. It can be concluded that, in P. oceanica, the contribution of retrotransposon activity to genetic variability is reduced, although the nine specific active elements could actually produce new structural variations.

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Section: Discussionsupporting

confidence: 56%

Low Long Terminal Repeat (LTR)-Retrotransposon Expression in Leaves of the Marine Phanerogam Posidonia Oceanica L.

Vangelisti

Mascagni

Usai

et al. 2020

Life

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Section: It Would Take 30 Years Before the Molecular Structures Of Acmentioning

confidence: 99%

“…Generally, the mobilization of a TE occurs when the organism is subject to conditions of genomic stress such as biotic or abiotic stresses, polyploidy and interspecific hybridizations typical in plants but not completely absent in animals (Bourque et al, 2018; Casacuberta & González, 2013; Dubin, Mittelsten Scheid, & Becker, 2018; Mascagni et al, 2020; Usai et al, 2020; Vangelisti, Mascagni, Giordani, et al, 2019; Vangelisti, Mascagni, Usai, et al, 2019; Vangelisti, Usai, et al, 2019, 2020; Zhao et al, 2018). Given also the irregularity in the course of evolution, with periods of rapid change alternated to long periods of stability, it is likely that in some cases the TEs have expanded within the genomes as predicted by the theory of punctuated equilibria (Eldredge & Gould, 1972).…”

Section: The Discovery Of the Tesmentioning

confidence: 99%

The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations

Fambrini

Usai

Vangelisti

et al. 2020

Genesis

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Transposable elements (TEs) are DNA sequences that can change their position within genomes. TEs are present in most organisms and can be an important genomic component. Their activities are manifold: restructuring of genome size, chromosomal rearrangements, induction of gene mutations, and alteration of gene activity by insertion near or within promoters, intronic regions, or enhancer. There are several examples of mutations and other genetic variations determined by the activity of TEs, associated with the evolution of prokaryotic and eukaryotic organisms and the domestication of plants. Generally, TE mobilization occurs when the organism is subjected to stress, which can include both biotic and abiotic stresses, polyploidy conditions, and interspecific hybridizations, very common events in plants. TEs are widely distributed among organisms. TEs also play essential roles in evolution, but most of them are either dormant or inactive. This is mainly determined by epigenetic silencing mechanisms, regulatory systems, and control systems that aim to limit its proliferation. Furthermore, the host has recruited many genes originated from TEs as transcriptional regulators, especially in defense against pathogens and invasive genetic elements; this phenomenon is called molecular domestication. Therefore, TEs are responsible for horizontal gene transfer and the movement of genetic material between organisms, even phylogenetically distant, with a consequent remixing of their gene pools.

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“…Although transposon-silencing mechanisms have largely been deciphered, it is unclear how some transposons are expressed when silencing system is on. Here, we applied an integrated approach to elucidate genomic and transcriptomic features as well as the mobilome activities of expressed RTEs of sunflower, a species for which retrotransposon expression has been demonstrated [26][27][28][29][30][31]. We observed 44 expressed LTR retrotransposons in the sunflower genome and studied their genomic and transcriptomic features and transposition activity.…”

Section: Tens Of Rtes With Distinct Features Are Expressed In Plant Smentioning

confidence: 99%

“…In this study, we aimed to depict the distinct genomic and transcriptomic features and to obtain insight into the mobilome (transposition) activity of expressed RTEs. For this, we exploited sunflower (Helianthus annuus), a species with a big genome (~3 Gb), and for which RTE transcription has been shown in several previous studies [26][27][28][29][30][31]. Previous reports on RTE transcription in sunflower focused on distinct TE elements isolated from BAC clones, or those assembled by short-read clustering; they did not include genome-based characterization of expressed RTEs (exRTEs) and their transcripts.…”

Section: Introductionmentioning

confidence: 99%

Genomic and Transcriptomic Survey Provides New Insight into the Organization and Transposition Activity of Highly Expressed LTR Retrotransposons of Sunflower (Helianthus annuus L.)

Kirov

Omarov

Merkulov

et al. 2020

IJMS

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LTR retrotransposons (RTEs) play a crucial role in plant genome evolution and adaptation. Although RTEs are generally silenced in somatic plant tissues under non-stressed conditions, some expressed RTEs (exRTEs) escape genome defense mechanisms. As our understanding of exRTE organization in plants is rudimentary, we systematically surveyed the genomic and transcriptomic organization and mobilome (transposition) activity of sunflower (Helianthus annuus L.) exRTEs. We identified 44 transcribed RTEs in the sunflower genome and demonstrated their distinct genomic features: more recent insertion time, longer open reading frame (ORF) length, and smaller distance to neighboring genes. We showed that GAG-encoding ORFs are present at significantly higher frequencies in exRTEs, compared with non-expressed RTEs. Most exRTEs exhibit variation in copy number among sunflower cultivars and one exRTE Gagarin produces extrachromosomal circular DNA in seedling, demonstrating recent and ongoing transposition activity. Nanopore direct RNA sequencing of full-length RTE RNA revealed complex patterns of alternative splicing in RTE RNAs, resulting in isoforms that carry ORFs for distinct RTE proteins. Together, our study demonstrates that tens of expressed sunflower RTEs with specific genomic organization shape the hidden layer of the transcriptome, pointing to the evolution of specific strategies that circumvent existing genome defense mechanisms.

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A computational genome-wide analysis of long terminal repeats retrotransposon expression in sunflower roots (Helianthus annuus L.)

Abstract: GeneticaA computational genome-wide analysis of long terminal repeats retrotransposon expression in sunflower roots (Helianthus annuus L.

Cited by 13 publications

References 66 publications

Low Long Terminal Repeat (LTR)-Retrotransposon Expression in Leaves of the Marine Phanerogam Posidonia Oceanica L.

Low Long Terminal Repeat (LTR)-Retrotransposon Expression in Leaves of the Marine Phanerogam Posidonia Oceanica L.

The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations

Genomic and Transcriptomic Survey Provides New Insight into the Organization and Transposition Activity of Highly Expressed LTR Retrotransposons of Sunflower (Helianthus annuus L.)

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