Plant transposable elements: where genetics meets genomics

Feschotte, Cédric; Jiang, Ning; Wessler, Susan R.

doi:10.1038/nrg793

Cited by 863 publications

(822 citation statements)

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“…Transposable elements (TEs) have multiple roles in driving genome evolution in eukaryotes 18 . In total, we identified 2.34 and 2.35 Gb (76.4 and 79.6%, respectively) of sequence in the assembled CM334 and C. chinense genomes as TEs ( Table 1 and Supplementary Table 20).…”

Section: Sequencing Assembly and Genetic Variationmentioning

confidence: 99%

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Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

et al. 2014

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Section: Sequencing Assembly and Genetic Variationmentioning

confidence: 99%

“…17). The most common repeats in the hot pepper genome were LTR retrotransposons, as in many other plant genomes 18,[21][22][23] . However, the composition of LTR retrotransposons in the hot pepper genome was distinct from that for other plants.…”

Section: Genome Expansionmentioning

confidence: 99%

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

et al. 2014

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“…(66) Although most of them are quiescent in their respective genomes, they can be activated in response to certain stresses (67) and ''genomic shock''. (54) The combination of evolutionarily divergent genomes in allopolyploids resembles ''genomic shock'', leading to the activation of quiescent transposons in the allopolyploids (Fig.…”

Section: Activation Of Transposons and Changes In Dna Methylation In mentioning

confidence: 99%

Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

2006

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SummaryPolyploidy is produced by multiplication of a single genome (autopolyploid) or combination of two or more divergent genomes (allopolyploid). The available data obtained from the study of synthetic (newly created or human-made) plant allopolyploids have documented dynamic and stochastic changes in genomic organization and gene expression, including sequence elimination, inter-chromosomal exchanges, cytosine methylation, gene repression, novel activation, genetic dominance, subfunctionalization and transposon activation. The underlying mechanisms for these alterations are poorly understood. To promote a better understanding of genomic and gene expression changes in polyploidy, we briefly review origins and forms of polyploidy and summarize what has been learned from genome-wide gene expression analyses in newly synthesized autoand allopolyploids. We show transcriptome divergence between the progenitors and in the newly formed allopolyploids. We propose models for transcriptional regulation, chromatin modification and RNA-mediated pathways in establishing locus-specific expression of orthologous and homoeologous genes during allopolyploid formation and evolution. Polyploidy and its formsPolyploidy occurs throughout the evolutionary history of all eukaryotes, (1,2) predominately in flowering plants (3,4) including many important agricultural crops. (5) Compared to plants, polyploidy occurs rarely in animals, but clearly exists in some invertebrates (e.g. insects) and vertebrates (e.g. fish, amphibians and reptiles). (4,6) The relative paucity of polyploidy in animals is attributed to the delicate schemes of sex determination and animal development, which are disrupted by polyploidization. (7,8) Therefore, polyploid animals rarely exist. (9) Moreover, aneuploid and polyploid cells in animals and human are often associated with malignant cell proliferation or carcinogenesis. (10) However, endopolyploidy (somatic polyploid cells within a diploid individual) appears to be a physiological response to developmental changes in plants and some animals, (11,12) indicating plasticity of plant and animal genomes. In the post-sequencing era, polyploidy is proving to be a fascinating and challenging field of plant biology, stimulating many research advances and insightful reviews. (2,13 -24) Here we attempt to update the views using genomic-scale results and provide new mechanistic insights.Historically, Winkler (1916) introduced the term polyploidy, (25) and Winge (1917) called attention to the general importance of polyploidy in the evolution of angiosperms. (26) At that time, research in polyploidy was somewhat limited by the plant and animal materials that were available in nature. In 1937, Blakeslee and Avery induced polyploidy in plants using colchicine, a chemical inhibitor of mitotic cell divisions. (27) The technique has been successfully used to induce chromosome doubling in meristemic cells of diploids and interspecific hybrids. Doubling a single 'diploid' genome results in an autotetraploid, while doubling c...

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“…Structurally distinct mobile elements that share some features with DNA transposons but are small and lack any coding capacity are called miniature inverted-repeat transposable elements (MITEs). First discovered in maize (Bureau and Wessler 1992), a number of MITEs distinguished by their nucleotide sequences were later identified in both monocot and dicot plants and also in animals (Feschotte et al 2002a;Feschotte et al 2002b). In contrast with other DNA transposons, MITEs occur in high copy numbers in plant genomes, reaching up to 10 4 copies per haploid genome (Bureau and Wessler 1992;Mao et al 2000;Zhang et al 2000).…”

Section: Introductionmentioning

confidence: 99%

Characterization ofStowawayMITEs in pea (Pisum sativumL.) and identification of their potential master elements

Macas¹,

Koblížková²,

Neumann³

2005

Genome

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Abstract:We have investigated miniature inverted-repeat transposable elements (MITEs) of the Stowaway family and corresponding Mariner-like master elements that could potentially facilitate their mobilization in the genome of the garden pea (Pisum sativum L.). The population of pea Stowaway MITEs consists of 10 3 -10 4 copies dispersed in the genome. Judging from a sequence analysis of 17 isolated Stowaway elements and their flanking genomic regions, the elements are relatively uniform in size and sequence and occur in the vicinity of genes as well as within repetitive sequences. Insertional polymorphism of several elements was detected among various Pisum accessions, suggesting they were still transpositionally active during diversification of these taxa. The identification of several Mariner-like elements (MLEs) harboring intact open reading frames, capable of encoding a transposase, further supports a recent mobilization of the Stowaway elements. Using transposase-coding sequences as a hybridization probe, we estimated that there are about 50 MLE sequences in the pea genome. Among the 5 elements sequenced, 3 distinct subfamilies showing mutual similarities within their transposase-coding regions, but otherwise diverged in sequence, were distinguished and designated as Psmar-1 to Psmar-3. The terminal inverted repeats (TIRs) of these MLE subfamilies differed in their homology to the TIRs of Stowaway MITEs. The homlogy ranged from 9 bp in Psmar-3 to 30 bp in Psmar-1, which corresponds to the complete Stowaway TIR sequence. Based on this feature, the Psmar-1 elements are believed to be the most likely candidates for the master elements of the Stowaway MITEs in pea.Key words: Mariner-like transposons, master elements, Stowaway MITEs, insertional polymorphism, Pisum sativum. Résumé :Les auteurs ont étudié les transposons MITE (« miniature inverted-repeat transposable elements ») de la famille Stowaway et les éléments autonomes correspondants de type Mariner, lesquels pourraient potentiellement causer la mobilité de ces éléments chez le petit pois (Pisum sativum L.). Le génome du pois compte 10 3 -10 4 copies dispersées de MITE Stowaway. L'analyse de la séquence de 17 éléments Stowaway et de l'ADN génomique qui les borde a révélé que ceux-ci sont relativement uniformes tant en matière de taille que de séquence et qu'ils sont situés à la fois à proximité de gènes et au sein de séquences répétées. Du polymorphisme insertionnel pour plusieurs éléments a été dé-tecté parmi diverses accessions de Pisum, ce qui suggère qu'ils étaient encore mobiles lors de la différenciation de ces taxons. L'identification de plusieurs éléments de type Mariner (MLE, « Mariner-like elements ») ayant des cadres de lecture ouverts intacts, capables de coder pour une transposase, vient appuyer davantage l'hypothèse d'une récente mobilité de ces éléments Stowaway. En employant la séquence codant pour la transposase comme sonde, les auteurs estiment qu'il y aurait environ 50 séquences MLE au sein du génome du pois. Parmi les 5 éléments séquenc...

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Plant transposable elements: where genetics meets genomics

Cited by 863 publications

References 107 publications

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

Characterization ofStowawayMITEs in pea (Pisum sativumL.) and identification of their potential master elements

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