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

Detecting Epigenetic Effects of Transposable Elements in Plants

Book DOI: 10.1007/978-1-62703-773-0International audienceTransposable elements (TE) represent a major fraction of eukaryotic genomes and play many roles in plant epigenetics. In this chapter, we describe the use of Sequence-Specifi c Amplifi ed Polymorphism (SSAP) as a reliable Transposon Display technique applicable for use in many plant species. We also discuss the interpretation of SSAP data and associated risks. This technique has potential to allow rapid screening of plant populations, especially in nonmodel or wild species

Three Tnt1 Subfamilies Show Different Stress-Associated Patterns of Expression in Tobacco. Consequences for Retrotransposon Control and Evolution in Plants

The genomes of most Nicotiana species contain three different subfamilies of the Tnt1 retrotransposon, which differ completely in their U3 sequence, whereas the rest of the sequence is relatively constant. The results presented here show that all three Tnt1 subfamilies are expressed in tobacco (Nicotiana tabacum) and that the U3 sequence variability correlates with differences in the pattern of expression of the Tnt1 elements. Each of the three Tnt1 subfamilies is induced by stress, but their promoters have a different response to different stress-associated signaling molecules. The Tnt1A subfamily is particularly strongly induced by elicitors and methyl jasmonate, whereas expression of the Tnt1C subfamily is more sensitive to salicylic acid and auxins. The direct relationship between U3 sequence variability and differences in the stress-associated expression of the Tnt1 elements present in a single host species gives support to our model that postulates that retrotransposons have adapted to their host genomes through the evolution of highly regulated promoters that mimic those of the stress-induced plant genes. Moreover, here we show that the analysis of the transcriptional control of a retrotransposon population such as Tnt1 provides new insights into the study of the complex and still poorly understood network of defense- and stress-induced plant signal transduction pathways

Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions

Background Initial characterization of the flax genome showed that Ty1-copia retrotransposons are abundant, with several members being recently inserted, and in close association with genes. Recent insertions indicate a potential for ongoing transpositional activity that can create genomic diversity among accessions, cultivars or varieties. The polymorphisms generated constitute a good source of molecular markers that may be associated with phenotype if the insertions alter gene activity. Flax, where accessions are bred mainly for seed nutritional properties or for fibers, constitutes a good model for studying the relationship of transpositional activity with diversification and breeding. In this study, we estimated copy number and used a type of transposon display known as Sequence-Specific Amplification Polymorphisms (SSAPs), to characterize six families of Ty1-copia elements across 14 flax accessions. Polymorphic insertion sites were sequenced to find insertions that could potentially alter gene expression, and a preliminary test was performed with selected genes bearing transposable element (TE) insertions. Results Quantification of six families of Ty1-copia elements indicated different abundances among TE families and between flax accessions, which suggested diverse transpositional histories. SSAPs showed a high level of polymorphism in most of the evaluated retrotransposon families, with a trend towards higher levels of polymorphism in low-copy number families. Ty1-copia insertion polymorphisms among cultivars allowed a general distinction between oil and fiber types, and between spring and winter types, demonstrating their utility in diversity studies. Characterization of polymorphic insertions revealed an overwhelming association with genes, with insertions disrupting exons, introns or within 1 kb of coding regions. A preliminary test on the potential transcriptional disruption by TEs of four selected genes evaluated in three different tissues, showed one case of significant impact of the insertion on gene expression. Conclusions We demonstrated that specific Ty1-copia families have been active since breeding commenced in flax. The retrotransposon-derived polymorphism can be used to separate flax types, and the close association of many insertions with genes defines a good source of potential mutations that could be associated with phenotypic changes, resulting in diversification processes.Arts and Sciences, Irving K. Barber School of (Okanagan)Non UBCBiology, Department of (Okanagan)ReviewedFacult

Elucidating the major hidden genomic components of the A, C, and AC genomes and their influence on Brassica evolution

Decoding complete genome sequences is prerequisite for comprehensive genomics studies. However, the currently available reference genome sequences of Brassica rapa (A genome), B. oleracea (C) and B. napus (AC) cover 391, 540, and 850 Mbp and represent 80.6, 85.7, and 75.2% of the estimated genome size, respectively, while remained are hidden or unassembled due to highly repetitive nature of these genome components. Here, we performed the first comprehensive genome-wide analysis using low-coverage whole-genome sequences to explore the hidden genome components based on characterization of major repeat families in the B. rapa and B. oleracea genomes. Our analysis revealed 10 major repeats (MRs) including a new family comprising about 18.8, 10.8, and 11.5% of the A, C and AC genomes, respectively. Nevertheless, these 10 MRs represented less than 0.7% of each assembled reference genome. Genomic survey and molecular cytogenetic analyses validates our insilico analysis and also pointed to diversity, differential distribution, and evolutionary dynamics in the three Brassica species. Overall, our work elucidates hidden portions of three Brassica genomes, thus providing a resource for understanding the complete genome structures. Furthermore, we observed that asymmetrical accumulation of the major repeats might be a cause of diversification between the A and C genomes