Expression of the retrotransposonsSurcoufandBlackbeardin the marine diatomPhaeodactylum tricornutumunder thermal stress

Egue, Fadoumo; Chénais, Benoı̂t; Tastard, Emmanuelle; Marchand, Justine; Hiard, Sophie; Gâteau, Hélène; Hermann, Dorothée; Morant-Manceau, Annick; Casse, Nathalie; Caruso, Aurore

doi:10.2216/15-52.1

Cited by 10 publications

(12 citation statements)

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“…TEs proved to be the most significantly enriched units of the stress response, providing the first evidence for the possible role of TEs in the temperature stress response in L. aporus, as a few others have done recently in diatoms [47,82]. All TEs were of the LTR retrotransposon superfamily, confirming the tendency of relatively high abundance of LTR retrotransposons in diatom genomes [32].…”

Section: Discussionsupporting

confidence: 61%

“…(1) their phenotypic plasticity, reflected in their physiological diversity that allows them to acclimate and face short-term environmental heterogeneity [2,3], (2) intraspecific genetic variations leading to distinct populations, each with a rather narrow physiological tolerance and response (i.e., adapted populations); numerous cases of cryptic or pseudo-cryptic diatom species have recently been uncovered [4][5][6], and even populations within species that show particular distributions as a result of adaptation to specific ecological niches [7], genetically and epigenetically-based phenotypic variation and have been associated with adaptation to the environment in numerous studies on different organisms [46,47], while two active, diatom-specific retrotransposons, namely Blackbeard and Surcouf, have been proposed to act as environmental sensors in the response to stress in the diatom Phaeodactylum tricornutum [32,47]. Thus, TEs could substantially increase genomic diversity and be a crucial element in the acclimation and even adaptation of diatoms to the ever-changing aquatic environment but when in a constant environment such as the lab, their suppression would have no effects and could hence become permanent through genetic changes, leading to the loss of the diatom adaptability.…”

Section: Introductionmentioning

confidence: 99%

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Intraspecific Diversity in the Cold Stress Response of Transposable Elements in the Diatom Leptocylindrus aporus

Pargana

Musacchia

Sanges

et al. 2019

Genes

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Transposable elements (TEs), activated as a response to unfavorable conditions, have been proposed to contribute to the generation of genetic and phenotypic diversity in diatoms. Here we explore the transcriptome of three warm water strains of the diatom Leptocylindrus aporus, and the possible involvement of TEs in their response to changing temperature conditions. At low temperature (13 • C) several stress response proteins were overexpressed, confirming low temperature to be unfavorable for L. aporus, while TE-related transcripts of the LTR retrotransposon superfamily were the most enriched transcripts. Their expression levels, as well as most of the stress-related proteins, were found to vary significantly among strains, and even within the same strains analysed at different times. The lack of overexpression after many months of culturing suggests a possible role of physiological plasticity in response to growth under controlled laboratory conditions. While further investigation on the possible central role of TEs in the diatom stress response is warranted, the strain-specific responses and possible role of in-culture evolution draw attention to the interplay between the high intraspecific variability and the physiological plasticity of diatoms, which can both contribute to the adaptation of a species to a wide range of conditions in the marine environment.Genes 2020, 11, 9 2 of 25 (3) both of the above, as plasticity can be adaptive with respect to a function and may be altered by natural selection and ultimately become or facilitate adaptation.In addition to natural environmental variability, diatoms used in experimental research are also exposed to another source of variability; they are removed from their natural environment, isolated and transferred to laboratory conditions in which evolutionary processes do not cease to occur [8]. Many cases of novel genetic variation have been shown after years of maintenance in culture collection [9][10][11]. Considering the high adaptability of diatoms, it could be hard to interpret the intra-specific algal diversity observed in related studies as the result of (a) adaptation to the natural environment from which strains were isolated or (b) evolutionary changes while being in culture.Temperature is a very significant environmental variable that affects the physiological response of diatoms and ultimately determines their phenological patterns and geographic ranges [12][13][14], as well as one of the parameters that is usually kept constant in culture conditions. An increase in temperature leads to an increase in enzyme activity in metabolic processes, including photosynthesis and respiration, so the cells are expected to grow faster. Even algae obtained from cold habitats have shown at least short-term temperature optima for photosynthesis several degrees higher than the temperature at which they were growing. Low temperatures lead to the exact opposite direction so that, in order to survive, cells respond with an increase in enzyme synthesis [15,16]. A recent study ...

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Section: Discussionsupporting

confidence: 61%

Section: Introductionmentioning

confidence: 99%

Intraspecific Diversity in the Cold Stress Response of Transposable Elements in the Diatom Leptocylindrus aporus

Pargana

Musacchia

Sanges

et al. 2019

Genes

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“…Few studies have investigated TE activity in microalgal genomes and their role is poorly known. Regarding Class I TEs, some studies reported expression of LTR elements in dinoflagellate and diatom species under thermal stress or nitrogen limitation [ 16 , 48 – 50 ]. Concerning Class II elements, a previous study reported a case of phenotypic evolution for the microalga Chlamydomonas reinhardtii caused by the transposition of a MITE in the presence of vitamin B 12 [ 17 ].…”

Section: Discussionmentioning

confidence: 99%

“…They can also create new genes and participate in the rise of new phenotypes. The role of TEs has been widely studied in animals [ 12 ], land plants [ 13 ] and insects [ 14 , 15 ], but work on their impact on microalgal genomes is only just beginning [ 16 – 19 ]. Microalgae form a diverse polyphyletic group composed of eukaryotic, unicellular and multicellular, photosynthetic organisms [ 20 ].…”

Section: Introductionmentioning

confidence: 99%

“…Expression of two LTR/Copia families was identified under nitrate starvation or exposure to diatom-derived reactive aldehydes in the diatom species Thalassiosira pseudonana and Phaeodactylum tricornutum [ 18 ]. Moreover, expression of LTR/Copia or TIR/Mariner elements was also reported under thermal stress in P. tricornutum , Amphora acutiuscula , Amphora coffeaeformis and Symbiodinium microadriaticum [ 16 , 48 – 50 ]. Evidence of transposition events was only identified for a MITE element in a clone of Chlamydomonas reinhardtii in the presence of vitamin B 12 , resulting in a new phenotype [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

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A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea

et al. 2018

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BackgroundTransposable elements (TEs) are mobile DNA sequences known as drivers of genome evolution. Their impacts have been widely studied in animals, plants and insects, but little is known about them in microalgae. In a previous study, we compared the genetic polymorphisms between strains of the haptophyte microalga Tisochrysis lutea and suggested the involvement of active autonomous TEs in their genome evolution.ResultsTo identify potentially autonomous TEs, we designed a pipeline named PiRATE (Pipeline to Retrieve and Annotate Transposable Elements, download: 10.17882/51795), and conducted an accurate TE annotation on a new genome assembly of T. lutea. PiRATE is composed of detection, classification and annotation steps. Its detection step combines multiple, existing analysis packages representing all major approaches for TE detection and its classification step was optimized for microalgal genomes. The efficiency of the detection and classification steps was evaluated with data on the model species Arabidopsis thaliana. PiRATE detected 81% of the TE families of A. thaliana and correctly classified 75% of them. We applied PiRATE to T. lutea genomic data and established that its genome contains 15.89% Class I and 4.95% Class II TEs. In these, 3.79 and 17.05% correspond to potentially autonomous and non-autonomous TEs, respectively. Annotation data was combined with transcriptomic and proteomic data to identify potentially active autonomous TEs. We identified 17 expressed TE families and, among these, a TIR/Mariner and a TIR/hAT family were able to synthesize their transposase. Both these TE families were among the three highest expressed genes in a previous transcriptomic study and are composed of highly similar copies throughout the genome of T. lutea. This sum of evidence reveals that both these TE families could be capable of transposing or triggering the transposition of potential related MITE elements.ConclusionThis manuscript provides an example of a de novo transposable element annotation of a non-model organism characterized by a fragmented genome assembly and belonging to a poorly studied phylum at genomic level. Integration of multi-omics data enabled the discovery of potential mobile TEs and opens the way for new discoveries on the role of these repeated elements in genomic evolution of microalgae.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4763-1) contains supplementary material, which is available to authorized users.

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Transcriptomic and physiological responses of a model diatom (Phaeodactylum tricornutum) to heat shock and heat selection

Hong

Huang

et al. 2023

Ecological Indicators

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Expression of the retrotransposonsSurcoufandBlackbeardin the marine diatomPhaeodactylum tricornutumunder thermal stress

Cited by 10 publications

References 70 publications

Intraspecific Diversity in the Cold Stress Response of Transposable Elements in the Diatom Leptocylindrus aporus

Intraspecific Diversity in the Cold Stress Response of Transposable Elements in the Diatom Leptocylindrus aporus

A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea

Transcriptomic and physiological responses of a model diatom (Phaeodactylum tricornutum) to heat shock and heat selection

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