Potential impact of stress activated retrotransposons on genome evolution in a marine diatom

<p>Abstract</p> <p>Background</p> <p>Transposable elements (TEs) are mobile DNA sequences present in the genomes of most organisms. They have been extensively studied in animals, fungi, and plants, and have been shown to have important functions in genome dynamics and species evolution. Recent genomic data can now enlarge the identification and study of TEs to other branches of the eukaryotic tree of life. Diatoms, which belong to the heterokont group, are unicellular eukaryotic algae responsible for around 40% of marine primary productivity. The genomes of a centric diatom, <it>Thalassiosira pseudonana</it>, and a pennate diatom, <it>Phaeodactylum tricornutum</it>, that likely diverged around 90 Mya, have recently become available.</p> <p>Results</p> <p>In the present work, we establish that LTR retrotransposons (LTR-RTs) are the most abundant TEs inhabiting these genomes, with a much higher presence in the <it>P. tricornutum </it>genome. We show that the LTR-RTs found in diatoms form two new phylogenetic lineages that appear to be diatom specific and are also found in environmental samples taken from different oceans. Comparative expression analysis in <it>P. tricornutum </it>cells cultured under 16 different conditions demonstrate high levels of transcriptional activity of LTR retrotransposons in response to nitrate limitation and upon exposure to diatom-derived reactive aldehydes, which are known to induce stress responses and cell death. Regulatory aspects of <it>P. tricornutum </it>retrotransposon transcription also include the occurrence of nitrate limitation sensitive <it>cis</it>-regulatory components within LTR elements and cytosine methylation dynamics. Differential insertion patterns in different <it>P. tricornutum </it>accessions isolated from around the world infer the role of LTR-RTs in generating intraspecific genetic variability.</p> <p>Conclusion</p> <p>Based on these findings we propose that LTR-RTs may have been important for promoting genome rearrangements in diatoms.</p

Differential Dynamics of Transposable Elements during Long-Term Diploidization of Nicotiana Section Repandae (Solanaceae) Allopolyploid Genomes

PubMed ID: 23185607This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Activation de rétrotransposons de plantes par le stress et impact sur les génomes hôtes

Les rétrotransposons sont des éléments génétiques mobiles qui s’amplifient par transcription inverse d’un intermédiaire ARN. Ils sont capables de s’insérer à différents endroits d’un génome, de s’amplifier en grand nombre de copies, et sont une source importante de diversité génétique. Le rétrotransposon de tabac Tnt1 A est activé par le stress d’origine pathogène et les séquences régulatrices impliquées dans cette activation sont similaires à celles de gènes végétaux de réponse au stress. Tnt1A appartient à une famille très ancienne présente dans de nombreuses Solanacées, et composée d’un continuum de populations d’éléments apparentés qui diffèrent dans leurs conditions d’expression. Cette expression est souvent observée en réponse au stress mais suit des modalités sensiblement différentes pour chaque population, reflètant peut-être une réponse adaptative de populations ancestrales à différents stimuli durant la radiation de la famille des Solanacées et de ses différents genres. Les facteurs microbiens stimulent très efficacement l’amplification de Tnt1A, renforçant l’hypothèse que des modifications environnementales peuvent engendrer des modifications génétiques. En outre, la transposition de Tnt1A est préférentiellement ciblée vers les régions géniques, suggèrant que l’activité des éléments transposables peut être une source naturelle de modulation des fonctions géniques et de diversité phénotypique

Diversité génétique et éléments transposables chez le tabac (Nicotiana tabacum) (impact de l'allopolyploïdie)

Les éléments transposables sont des composants majeurs des génomes et source de diversité génétique. Ils jouent un rôle important dans la variation des tailles de génomes, avec un renouvellement accru durant leur évolution. L'impact de l'allopolyploïdie, mécanisme majeur de l'évolution des génomes a été étudié chez le tabac, allotétraploïde issu du croisement entre N. sylvestris et N. tomentosiformis. La dynamique de l'évolution de populations de rétrotransposons a été analysée en évaluant leur contribution à la diversité du tabac et de ses parents, quantifiant la contribution des espèces parentales aux populations du tabac.Le génome du tabac résulte d'une restructuration majeure des séquences de rétrotransposons avec des disparitions et amplifications d'insertions. Des comportements uniques et spécifiques de chaque population de rétrotransposons ont été observés en termes de transmissibilité au génome hybride et en réponse à l'allopolyploïdie.L étude d hybrides synthétiques Th37 de génération S4 révèle des modifications importantes avec apparition et disparition de bandes SSAP tandis que l analyse d hybrides F1 ne révèle aucun changement majeur pour ces populations. L'analyse moléculaire de ces bandes a été entreprise pour deux populations, montrant que les nouvelles bandes correspondent à de nouvelles insertions d éléments actifs, tandis que les bandes disparues issues de N. tomentosiformis correspondent à des remaniements génomiques.Ces résultats montrent que l allopolyploïdie chez le tabac peut générer des restructurations génomiques importantes liées aux rétrotransposons, pouvant contribuer à générer une plasticité accrue du nouvel organisme hybride.Transposable elements are major components of genomes and an important source of genetic diversity. They play an important role in genome size variation with a turnover during their evolution. Impact of allopolyploidy, major driving force in plant evolution was studied in tobacco, an allotetraploid issued from N. sylvestris and N. tomentosiformis. Evolutionary dynamics of retrotransposon populations was characterized by estimating their contribution to the divergence of the tobacco genome and its progenitor, quantifying the contribution of progenitors species to tobacco populations.The tobacco genome results from a major turnover of retrotransposon sequences with removals concomitant to the appearance of new insertions. We have detected unique behaviours specific to each retrotransposon populations, in terms of transmission to the hybrid genome and response to allopolyploidy.The study of Th37 synthetic hybrid (S4 generation) reveals important modifications with appearance of new insertions and also removal of insertions originally from N. tomentosiformis. On the other hand, the analysis of F1 hybrids did not allow us to reveal profiles different to the parental additivity for these populations. Molecular analysis of new and disappearing bands on SSAP profiles was done for two populations and confirms that new bands detected correspond to new insertions of active elements, whereas bands which are absent when compared to N. tomentosiformis correspond to various restructurations.These results show that allopolyploidy in tobacco can generate important genomic restructurations caused by retrotransposons.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

LTR Retrotransposons as Controlling Elements of Genome Response to Stress?

absen

Specificities and Dynamics of Transposable Elements in Land Plants

Transposable elements (TEs) are important components of most plant genomes. These mobile repetitive sequences are highly diverse in terms of abundance, structure, transposition mechanisms, activity and insertion specificities across plant species. This review will survey the different mechanisms that may explain the variability of TE patterns in land plants, highlighting the tight connection between TE dynamics and host genome specificities, and their co-evolution to face and adapt to a changing environment. We present the current TE classification in land plants, and describe the different levels of genetic and epigenetic controls originating from the plant, the TE itself, or external environmental factors. Such overlapping mechanisms of TE regulation might be responsible for the high diversity and dynamics of plant TEs observed in nature.</jats:p

Specificities and Dynamics of Transposable Elements in Land Plants

Transposable elements (TEs) are important components of most plant genomes. These mobile repetitive sequences are highly diverse in terms of abundance, structure, transposition mechanisms, activity and insertion specificities across plant species. This review will survey the different mechanisms that may explain the variability of TE patterns in land plants, highlighting the tight connection between TE dynamics and host genome specificities, and their co-evolution to face and adapt to a changing environment. We present the current TE classification in land plants, and describe the different levels of genetic and epigenetic controls originating from the plant, the TE itself, or external environmental factors. Such overlapping mechanisms of TE regulation might be responsible for the high diversity and dynamics of plant TEs observed in nature

Evolutionary Implications of Genome and Karyotype Restructuring in Nicotiana tabacum L

absen