Wheat centromeric retrotransposons: the new ones take a major role in centromeric structure

Li, Baochun; Choulet, Frédéric; Heng, Yanfang; Hao, Weiwei; Paux, Etienne; Liu, Zhao; Yue, Wei; Jin, Weiwei; Feuillet, Catherine; Zhang, Xueyong

doi:10.1111/tpj.12086

Cited by 86 publications

(119 citation statements)

References 59 publications

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“…In rice and maize, for example, all centromeres have different retrotransposon families [Nagaki et al, 2005;Bao et al, 2006]. Furthermore, retrotransposons are the main component of banana and some wheat centromeres [Čížková et al, 2013;Li et al, 2013].…”

Section: Plant Centromere and The Pericentromeric Regionmentioning

confidence: 99%

Satellite DNA in Plants: More than Just Rubbish

Garrido-Ramos

2015

Cytogenet Genome Res

150

149

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For decades, satellite DNAs have been the hidden part of genomes. Initially considered as junk DNA, there is currently an increasing appreciation of the functional significance of satellite DNA repeats and of their sequences. Satellite DNA families accumulate in the heterochromatin in different parts of the eukaryotic chromosomes, mainly in pericentromeric and subtelomeric regions, but they also span the functional centromere. Tandem repeat sequences may spread from subtelomeric to interstitial loci, leading to the formation of chromosome-specific loci or to the accumulation in equilocal sites in different chromosomes. They also appear as the main components of the heterochromatin in the sex-specific region of sex chromosomes. Satellite DNA, required for chromosome organization, also plays a role in pairing and segregation. Some satellite repeats are transcribed and can participate in the formation and maintenance of heterochromatin structure and in the modulation of gene expression. In addition to the identification of the different satellite DNA families, their characteristics and location, we are interested in determining their impact on the genomes, by identifying the mechanisms leading to their appearance and amplification as well as in understanding how they change over time, the factors affecting these changes, and the influence exerted by the evolutionary history of the organisms. On the other hand, satellite DNA sequences are rapidly evolving sequences that may cause reproductive barriers between organisms and promote speciation. The accumulation of experimental data collected in recent years and the emergence of new approaches based on next-generation sequencing and high-throughput genome analysis are opening new perspectives that are changing our understanding of satellite DNA. This review examines recent data to provide a timely update on the overall information gathered about this part of the genome, focusing on the advances in the knowledge of its origin, its evolution, and its potential functional roles.

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Section: Plant Centromere and The Pericentromeric Regionmentioning

confidence: 99%

Satellite DNA in Plants: More than Just Rubbish

Garrido-Ramos

2015

Cytogenet Genome Res

150

149

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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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“…Genome expansion is mainly mediated by the activity of class I elements, while the content of DNA transposons is much more constant [5][6][7]. Furthermore, TEs are non-randomly distributed along the genome due to insertions [8,9] and deletions [7,10] that trigger genome expansion/contraction. Hence, in rice (Oryza sativa) [11], sorghum (Sorghum bicolor) [12] and maize, long terminal repeat retrotransposons (LTR-RTs) accumulate preferentially in heterochromatin, such as centromeric regions, and are less abundant in the recombinogenic distal parts of chromosomes.…”

Section: Introductionmentioning

confidence: 99%

Organization and evolution of transposable elements along the bread wheat chromosome 3B

et al. 2014

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Background: The 17 Gb bread wheat genome has massively expanded through the proliferation of transposable elements (TEs) and two recent rounds of polyploidization. The assembly of a 774 Mb reference sequence of wheat chromosome 3B provided us with the opportunity to explore the impact of TEs on the complex wheat genome structure and evolution at a resolution and scale not reached so far. Results: We develop an automated workflow, CLARI-TE, for TE modeling in complex genomes. We delineate precisely 56,488 intact and 196,391 fragmented TEs along the 3B pseudomolecule, accounting for 85% of the sequence, and reconstruct 30,199 nested insertions. TEs have been mostly silent for the last one million years, and the 3B chromosome has been shaped by a succession of bursts that occurred between 1 to 3 million years ago. Accelerated TE elimination in the high-recombination distal regions is a driving force towards chromosome partitioning. CACTAs overrepresented in the high-recombination distal regions are significantly associated with recently duplicated genes. In addition, we identify 140 CACTA-mediated gene capture events with 17 genes potentially created by exon shuffling and show that 19 captured genes are transcribed and under selection pressure, suggesting the important role of CACTAs in the recent wheat adaptation.

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Wheat centromeric retrotransposons: the new ones take a major role in centromeric structure

Cited by 86 publications

References 59 publications

Satellite DNA in Plants: More than Just Rubbish

Satellite DNA in Plants: More than Just Rubbish

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

Organization and evolution of transposable elements along the bread wheat chromosome 3B

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