New Insights into Nested Long Terminal Repeat Retrotransposons in Brassica Species

Wei, Lijuan; Xiao, Meili; An, Zeshan; Ma, Bi; Mason, Annaliese S.; Qian, Wei; Li, Jiana; Fu, Donghui

doi:10.1093/mp/sss081

Cited by 25 publications

(23 citation statements)

References 77 publications

(71 reference statements)

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“…Distribution patterns are associated with their function. For example, some LTR retrotransposable elements preferentially insert within other LTR retrotransposons in centromere regions, and these elements are rapidly duplicated, inserted repeatedly, and play a role in the formation of centromeres [47]. In the present study, FISH results revealed that most of the hybridization signals are preferentially concentrated in pericentromeric and distal regions of chromosomes (Fig.…”

Section: Chromosomal Localization Of Ltr Retrotransposonssupporting

confidence: 60%

“…The distribution bias, where TEs are preferentially inserted into the heterochromatin regions, might be beneficial for the retrotransposable elements facilitating escape from negative selection that arises from insertion into genes rich regions [54,55]. Additionally, LTR retrotransposable elements found in centromeres of various plant species have also been shown to contribute to the formation and function of centromeres [47,55]. Hence, our future studies will focus on the potential roles of these elements in centromere function.…”

Section: Chromosomal Localization Of Ltr Retrotransposonsmentioning

confidence: 99%

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Reverse transcriptase sequences from mulberry LTR retrotransposons: characterization analysis

Kuang

Xin

et al. 2017

Open Life Sciences

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Copia and Gypsy play important roles in structural, functional and evolutionary dynamics of plant genomes. In this study, a total of 106 and 101, Copia and Gypsy reverse transcriptase (rt) were amplified respectively in the Morus notabilis genome using degenerate primers. All sequences exhibited high levels of heterogeneity, were rich in AT and possessed higher sequence divergence of Copia rt in comparison to Gypsy rt. Two reasons are likely to account for this phenomenon: a) these elements often experience deletions or fragmentation by illegitimate or unequal homologous recombination in the transposition process; b) strong purifying selective pressure drives the evolution of these elements through “selective silencing” with random mutation and eventual deletion from the host genome. Interestingly, mulberry rt clustered with other rt from distantly related taxa according to the phylogenetic analysis. This phenomenon did not result from horizontal transposable element transfer. Results obtained from fluorescence in situ hybridization revealed that most of the hybridization signals were preferentially concentrated in pericentromeric and distal regions of chromosomes, and these elements may play important roles in the regions in which they are found. Results of this study support the continued pursuit of further functional studies of Copia and Gypsy in the mulberry genome.

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Section: Chromosomal Localization Of Ltr Retrotransposonssupporting

confidence: 60%

Section: Chromosomal Localization Of Ltr Retrotransposonsmentioning

confidence: 99%

Reverse transcriptase sequences from mulberry LTR retrotransposons: characterization analysis

Kuang

Xin

et al. 2017

Open Life Sciences

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“…It was shown that LTR retrotransposons are more frequent in pericentromeric regions of the host genomes (for a review see Li et al 2013) and that they could play important roles in maintaining chromatin structures and centromere functions (Zhao and Ma 2013), or reshuffling the structure of the centromeric sequences (Wei et al 2013). In wheat, a Cereba-like element called centromeric retrotransposon in wheat (CRW) represents the main component of the centromeres .…”

Section: Retrotransposons Associate With Reduced Recombination Ratementioning

confidence: 99%

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

et al. 2017

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During meiosis, crossovers (COs) create new allele associations by reciprocal exchange of DNA. In bread wheat (Triticum aestivum L.), COs are mostly limited to subtelomeric regions of chromosomes, resulting in a substantial loss of breeding efficiency in the proximal regions, though these regions carry 60-70% of the genes. Identifying sequence and/or chromosome features affecting recombination occurrence is thus relevant to improve and drive recombination. Using the recent release of a reference sequence of chromosome 3B and of the draft assemblies of the 20 other wheat chromosomes, we performed fine-scale mapping of COs and revealed that 82% of COs located in the distal ends of chromosome 3B representing 19% of the chromosome length. We used 774 SNPs to genotype 180 varieties representative of the Asian and European genetic pools and a segregating population of 1270 F 6 lines. We observed a common location for ancestral COs (predicted through linkage disequilibrium) and the COs derived from the segregating population. We delineated 73 small intervals (,26 kb) on chromosome 3B that contained 252 COs. We observed a significant association of COs with genic features (73 and 54% in recombinant and nonrecombinant intervals, respectively) and with those expressed during meiosis (67% in recombinant intervals and 48% in nonrecombinant intervals). Moreover, while the recombinant intervals contained similar amounts of retrotransposons and DNA transposons (42 and 53%), nonrecombinant intervals had a higher level of retrotransposons (63%) and lower levels of DNA transposons (28%). Consistent with this, we observed a higher frequency of a DNA motif specific to the TIR-Mariner DNA transposon in recombinant intervals. KEYWORDS recombination; meiosis; bread wheat; linkage disequilibrium; transposon; hotspot; sequence motif M EIOTIC recombination is a process that allows reshuffling of diversity by the reciprocal exchange of DNA called a crossover (CO). This phenomenon is conserved in most eukaryotes (for a review see Mercier et al. 2015) and follows the formation of a double-strand break (DSB) of DNA generated by the topoisomerase SPO11 complex. However, the number of DSBs is at least 10-to 50-fold greater than the number of COs which rarely exceeds three per bivalent chromosome per meiosis (Mercier et al. 2015). This paucity of COs per meiosis with regards to the number of DSBs suggests the existence of a tight control and regulation of recombination in plants that promote DSB repair in a manner that does not lead to COs. For example, the study of the two helicases AtFANCM and RECQ4 (AtRECQ4A and AtRECQ4B) (Crismani et al. 2012;Knoll et al. 2012;Girard et al. 2014;Séguéla-Arnaud et al. 2015) revealed three-and sixfold CO frequency increases in the Atfancm single mutant and the Atrecq4a/Atrecq4b double mutant, respectively, compared to the wild type. These increases result from additional COs from the class-II pathway which suggests that FANCM and RECQ4 prevent CO formation and direct recombination intermediates towar...

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“…Such structures are known to be formed by the preferential insertion of an LTR-retrotransposon into pre-existing retrotransposons, creating large heterochromatic blocks [79,80]. Other than their potential role in centromere formation [91], and a negative influence on genome expansion [92], the cause and evolutionary significance of such structures largely remains unknown. …”

Section: Discussionmentioning

confidence: 99%

Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome

Gill

Buti

Kane

et al. 2014

Biology

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Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are “novel” to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence.

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New Insights into Nested Long Terminal Repeat Retrotransposons in Brassica Species

Cited by 25 publications

References 77 publications

Reverse transcriptase sequences from mulberry LTR retrotransposons: characterization analysis

Reverse transcriptase sequences from mulberry LTR retrotransposons: characterization analysis

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome

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