Coevolution between transposable elements and recombination

Kent, Tyler V.; Uzunović, Jasmina; Wright, Stephen I.

doi:10.1098/rstb.2016.0458

Cited by 253 publications

(300 citation statements)

References 119 publications

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“…Recombination rates vary across chromosomes in many organisms and their distribution often correlates with other genomic features. For instance, in most vascular plant species, recombination rates are significantly positively correlated with the density of genes and GC content, and negatively correlated with the abundance of repetitive elements (Paape et al , ; Glémin et al , ; Tiley and Burleigh, ; Kent et al , ). We showed that the patterns of correlation between recombination rate and genomic features mainly followed this general pattern in the M. polymorpha genome.…”

Section: Discussionmentioning

confidence: 99%

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

et al. 2019

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Summary Marchantia polymorpha has recently become a prime model for cellular, evo‐devo, synthetic biological, and evolutionary investigations. We present a pseudomolecule‐scale assembly of the M. polymorpha genome, making comparative genome structure analysis and classical genetic mapping approaches feasible. We anchored 88% of the M. polymorpha draft genome to a high‐density linkage map resulting in eight pseudomolecules. We found that the overall genome structure of M. polymorpha is in some respects different from that of the model moss Physcomitrella patens. Specifically, genome collinearity between the two bryophyte genomes and vascular plants is limited, suggesting extensive rearrangements since divergence. Furthermore, recombination rates are greatest in the middle of the chromosome arms in M. polymorpha like in most vascular plant genomes, which is in contrast with P. patens where recombination rates are evenly distributed along the chromosomes. Nevertheless, some other properties of the genome are shared with P. patens. As in P. patens, DNA methylation in M. polymorpha is spread evenly along the chromosomes, which is in stark contrast with the angiosperm model Arabidopsis thaliana, where DNA methylation is strongly enriched at the centromeres. Nevertheless, DNA methylation and recombination rate are anticorrelated in all three species. Finally, M. polymorpha and P. patens centromeres are of similar structure and marked by high abundance of retroelements unlike in vascular plants. Taken together, the highly contiguous genome assembly we present opens unexplored avenues for M. polymorpha research by linking the physical and genetic maps, making novel genomic and genetic analyses, including map‐based cloning, feasible.

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Section: Discussionmentioning

confidence: 99%

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

et al. 2019

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“…The high relatedness and spatial proximity of the four populations investigated here, considered to be predominantly selfing (Rogivue et al, ), supports the assumption that both substitution and transposition rates are negligible, arguing for drift or selection as the main drivers of observed patterns for SNPs versus TEs. However, it remains elusive to what extent polymorphic TEs modify the local recombination rate (He & Dooner, ; Kent, Uzunović, & Wright, ; Zamudio et al, ) and may thus influence the fixation of SNPs and polymorphic TEs. The unprecedented resolution of SNP and TE diversity across natural landscapes presented may serve future studies assessing the evolutionary forces driving genome‐wide variation within and among populations, at best complemented by functional studies on the fitness relevance of the genomic variation observed.…”

Section: Discussionmentioning

confidence: 99%

“…However, it remains elusive to what extent polymorphic TEs modify the local recombination rate (He & Dooner, 2009;Kent, Uzunović, & Wright, 2017;Zamudio et al, 2015) and may thus influence the fixation of SNPs and polymorphic TEs. The unprecedented resolution of SNP and TE diversity across natural landscapes presented may serve future studies assessing the evolutionary forces driving genome-wide variation within and among populations, at best complemented by functional studies on the fitness relevance of the genomic variation observed.…”

Section: Possible Adaptive Impact Of the Variantsmentioning

confidence: 99%

Genome‐wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae)

Rogivue

Choudhury

Zoller

et al. 2019

Molecular Ecology Resources

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Advances in high‐throughput sequencing have promoted the collection of reference genomes and genome‐wide diversity. However, the assessment of genomic variation among populations has hitherto mainly been surveyed through single‐nucleotide polymorphisms (SNPs) and largely ignored the often major fraction of genomes represented by transposable elements (TEs). Despite accumulating evidence supporting the evolutionary significance of TEs, comprehensive surveys remain scarce. Here, we sequenced the full genomes of 304 individuals of Arabis alpina sampled from four nearby natural populations to genotype SNPs as well as polymorphic long terminal repeat retrotransposons (polymorphic TEs; i.e., presence/absence of TE insertions at specific loci). We identified 291,396 SNPs and 20,548 polymorphic TEs, comparing their contributions to genomic diversity and divergence across populations. Few SNPs were shared among populations and overall showed high population‐specific variation, whereas most polymorphic TEs segregated among populations. The genomic context of these two classes of variants further highlighted candidate adaptive loci having a putative impact on functional genes. In particular, 4.96% of the SNPs were identified as nonsynonymous or affecting start/stop codons. In contrast, 43% of the polymorphic TEs were present next to Arabis genes enriched in functional categories related to the regulation of reproduction and responses to biotic as well as abiotic stresses. This unprecedented data set, mapping variation gained from SNPs and complementary polymorphic TEs within and among populations, will serve as a rich resource for addressing microevolutionary processes shaping genome variation.

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“…The relationship between gene density, TE density, and recombination rate has been a long-453 standing discussion (reviewed in Kent et al 2017). It is difficult to parse out these relationships 454 because there are many factors influencing distribution of TEs, genes, and crossovers.…”

Section: Recombination and Genomic Features 452mentioning

confidence: 99%

“…It has been suggested that active silencing of TEs could lead to the silencing or suppression of 464 recombination around those regions (Kent, Uzunović, and Wright 2017). Therefore, it is difficult 465 to determine whether or how TE density and gene density affect recombination rates.…”

Section: Recombination and Genomic Features 452mentioning

confidence: 99%

Centromere-proximal meiotic crossovers inDrosophila melanogasterare suppressed by both highly-repetitive heterochromatin and the centromere effect

Hartmann

Umbanhowar

Sekelsky

2019

Preprint

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Hartmann et al. Centromere effect in Drosophila 1 1 Centromere-proximal meiotic crossovers in Drosophila melanogaster are 2 suppressed by both highly-repetitive heterochromatin 3 and the centromere effect 4 5 23 Hartmann et al. Centromere effect in Drosophila 2 Abstract 24Crossovers are essential in meiosis of most organisms to ensure the proper segregation of 25 chromosomes. The lack or improper placement of crossovers can result in nondisjunction and 26 aneuploidy in progeny. Crossovers near the centromere can cause nondisjunction; centromere-27 proximal crossovers are suppressed by what is termed the centromere effect, but the mechanism is 28 unknown. Here, we investigate contributions to centromere-proximal crossover suppression in 29 Drosophila melanogaster. We mapped a large number of centromere-proximal crossovers and find 30 that crossovers are essentially absent from the highly-repetitive (HR)-heterochromatin 31 surrounding the centromere but occur at a low frequency within the less-repetitive 32 (LR)-heterochromatic region and adjacent euchromatin. Previous research suggested that flies that 33 lack the Bloom syndrome helicase (Blm) lose meiotic of crossover patterning, including the 34 centromere effect. Mapping of centromere-proximal crossovers in Blm mutants reveals that the 35 suppression within the HR-heterochromatin is intact, but the centromere effect is lost. We conclude 36 that centromere-proximal crossovers are suppressed by two separable mechanisms: the HR-37 heterochromatin effect, which completely suppresses crossovers in the HR-heterochromatin, and 38 the centromere effect, which suppresses crossovers with a dissipating effect with distance from the 39 centromere. 40 41

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Coevolution between transposable elements and recombination

Cited by 253 publications

References 119 publications

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

Genome‐wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae)

Centromere-proximal meiotic crossovers inDrosophila melanogasterare suppressed by both highly-repetitive heterochromatin and the centromere effect

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