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78 results for “chromosome rearrangement”
Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish
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Data from: Chromosomal rearrangements directly cause underdominant F1 pollen sterility in Mimulus lewisii-M. cardinalis hybrids
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Data from: Shared ancestral polymorphism and chromosomal rearrangements as potential drivers of local adaptation in a marine fish
<p>Gene flow has tremendous importance on local adaptation, by influencing the fate of <i>de novo</i> mutations, maintaining standing genetic variation, and driving adaptive introgression. Furthermore, structural variation as chromosomal rearrangements may facilitate adaptation despite high gene flow. However, our understanding of evolutionary mechanisms impending or favoring local adaptation in the presence of gene flow is still limited to a restricted number of study systems. In this study, we examined how demographic history, shared ancestral polymorphism, and gene flow among glacial lineages contribute to local adaptation to sea conditions in a marine fish, the capelin (<i>Mallotus villosus</i>). We first assembled a 490 Mbp draft genome of <i>M. villosus</i> to map our RAD sequence reads. Then, we used a large dataset of genome-wide single nucleotide polymorphisms (25,904 filtered SNPs) genotyped in 1,310 individuals collected from 31 spawning sites in the northwest Atlantic. We reconstructed the history of divergence among three glacial lineages and showed that they likely diverged from 3.8 to 1.8 MyA and experienced secondary contacts. Within each lineage, our analyses provided evidence for large <i>N</i><sub><i>e</i></sub> and high gene flow among spawning sites. Within the NWA lineage, we detected a polymorphic chromosomal rearrangement leading to the occurrence of three haplogroups. Genotype-environment associations revealed molecular signatures of local adaptation to environmental conditions prevailing at spawning sites. Our study also suggests that, both shared polymorphism among lineages, resulting from standing genetic variation or introgression, and chromosomal rearrangements may contribute to local adaptation in the presence of high gene flow.</p>
Data from: Putative chromosomal rearrangements are associated primarily with ecotype divergence rather than geographic separation in an intertidal, poorly-dispersing snail
<p class="western"><span><i>Littorina saxatilis</i> is becoming a model system for understanding the genomic basis of ecological speciation. The parallel formation of crab-adapted ecotypes that exhibit partial reproductive isolation from wave-adapted ecotypes has enabled genomic investigation of conspicuous shell traits. Recent genomic studies suggest that chromosomal rearrangements may enable ecotype divergence by reducing gene flow. However, the genomic architecture of traits that are divergent between ecotypes remains poorly understood. Here, we use 11,504 single nucleotide polymorphism (SNP) markers called using the recently-released <i>L. saxatilis</i> genome to genotype 462 crab ecotype, wave ecotype, and phenotypically-intermediate <i>L. saxatilis</i> individuals with scored phenotypes. We used redundancy analysis to study the genetic architecture of loci associated with shell shape, shape corrected for size, shell size, and shell ornamentation, and to compare levels of co-association among different traits. We discovered 341 SNPs associated with shell traits. Loci associated with trait divergence between ecotypes were often located inside putative chromosomal rearrangements recently characterized in Swedish <i>L. saxatilis</i>. In contrast, we found that shell shape corrected for size varied primarily by site rather than by ecotype and showed little association with these putative rearrangements. Together, these results reveal that genomic regions of elevated divergence with putative rearrangements are associated with divergence along steep environmental axes in <i>L. saxatilis</i><span> ecotypes</span>, consistent with models of adaptation with gene flow, but these regions are distinct from genomic architecture associated with site-specific variation. Our findings here further support predictions from models indicating the importance of genomic regions of reduced recombination allowing co-association of loci during ecological speciation with ongoing gene flow.</span></p>
Data from: Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes
The number of de novo genome sequence assemblies is increasing exponentially; however, relatively few contain one scaffold/contig per chromosome. Such assemblies are essential for studies of genotype-to-phenotype association, gross genomic evolution, and speciation. Inter-species differences can arise from chromosomal changes fixed during evolution, and we previously hypothesized that a higher fraction of elements under negative selection contributed to avian-specific phenotypes and avian genome organization stability. The objective of this study is to generate chromosome-level assemblies of three avian species (saker falcon, budgerigar, and ostrich) previously reported as karyotypically rearranged compared to most birds. We also test the hypothesis that the density of conserved non-coding elements is associated with the positions of evolutionary breakpoint regions.
Data from: Heterochromatin suppresses gross chromosomal rearrangements at centromeres by repressing Tfs1/TFIIS-dependent transcription
Heterochromatin that is characterized by histone H3 lysine 9 (H3K9) methylation assembles on repetitive regions including centromeres. Although centromeric heterochromatin is important for faithful segregation of chromosomes, its role in maintaining centromere integrity remains elusive. Here, we found in fission yeast that heterochromatin suppresses gross chromosomal rearrangements (GCRs) at centromeres. Mutations in Clr4/Suv39 methyltransferase increased the formation of isochromosomes whose breakpoints are present in centromere repeats. H3K9A and H3K9R mutations also increased GCRs, suggesting that Clr4 appears to suppress GCRs via H3K9 methylation. Both HP1 homologs, Swi6 and Chp2, and an RNAi component Chp1 were the chromodomain proteins that are essential for full suppression of GCRs. Remarkably, mutations in RNA polymerase II (RNAPII) or the transcription factors including Tfs1/TFIIS which facilitates restart of backtracked RNAPII specifically bypassed the requirement of Clr4 to suppress GCRs. These results demonstrate that heterochromatin suppresses GCRs by repressing Tfs1-dependent transcription of centromere repeats.
Data from: Ancient chromosomal rearrangement associated with local adaptation of a post-glacially colonized population of Atlantic Cod in the northwest Atlantic
Intraspecific diversity is central to the management and conservation of exploited species, yet knowledge of how this diversity is distributed and maintained in the genome of many marine species is lacking. Recent advances in genomic analyses allow for genome-wide surveys of intraspecific diversity and offer new opportunities for exploring genomic patterns of divergence. Here, we analyzed genome-wide polymorphisms to measure genetic differentiation between an offshore migratory and a non-migratory population and to define conservation units of Atlantic Cod (Gadus morhua) in coastal Labrador. A total of 141 individuals, collected from offshore sites and from a coastal site within Gilbert Bay, Labrador, were genotyped using an ~11k single nucleotide polymorphism array. Analyses of population structure revealed strong genetic differentiation between migratory offshore cod and non-migratory Gilbert Bay cod. Genetic differentiation was elevated for loci within a chromosomal rearrangement found on linkage group 1 (LG1) that coincides with a previously found double inversion associated with migratory and non-migratory ecotype divergence of cod in the northeast Atlantic. This inverted region includes several genes potentially associated with adaptation to differences in salinity and temperature, as well as influencing migratory behaviour. Our work provides evidence that a chromosomal rearrangement on LG1 is associated with parallel patterns of divergence between migratory and non-migratory ecotypes on both sides of the Atlantic Ocean.
Data from: Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli
Large-scale rearrangements may be important in evolution because they can alter chromosome organization and gene expression in ways not possible through point mutations. In a long-term evolution experiment, twelve Escherichia coli populations have been propagated in a glucose-limited environment for over 25 years. We used whole-genome mapping (optical mapping) combined with genome sequencing and PCR analysis to identify the large-scale chromosomal rearrangements in clones from each population after 40,000 generations. A total of 110 rearrangement events were detected, including 82 deletions, 19 inversions, and 9 duplications, with lineages having between 5 and 20 events. In three populations, successive rearrangements impacted particular regions. In five populations, rearrangements affected over a third of the chromosome. Most rearrangements involved recombination between insertion sequence (IS) elements, illustrating their importance in mediating genome plasticity. Two lines of evidence suggest that at least some of these rearrangements conferred higher fitness. First, parallel changes were observed across the independent populations, with ~65% of the rearrangements affecting the same loci in at least two populations. For example, the ribose-utilization operon and the manB-cpsG region were deleted in 12 and 10 populations, respectively, suggesting positive selection, and this inference was previously confirmed for the former case. Second, optical maps from clones sampled over time from one population showed that most rearrangements occurred early in the experiment, when fitness was increasing most rapidly. However, some rearrangements likely occur at high frequency and may have simply hitchhiked to fixation. In any case, large-scale rearrangements clearly influenced genomic evolution in these populations.
Data from: A test of the chromosomal rearrangement model of speciation in Drosophila pseudoobscura
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Data from: Ancient chromosomal rearrangement associated with local adaptation of a post-glacially colonized population of Atlantic Cod in the northwest Atlantic
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Data from: Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli
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Data from: Chromosomal rearrangements and the genetics of reproductive barriers in Mimulus (monkeyflowers)
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Data from: Heterochromatin suppresses gross chromosomal rearrangements at centromeres by repressing Tfs1/TFIIS-dependent transcription
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Data from: Shared ancestral polymorphism and chromosomal rearrangements as potential drivers of local adaptation in a marine fish
Open the record for dataset details and reuse information.
Data from: Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes
Open the record for dataset details and reuse information.
Data from: Putative chromosomal rearrangements are associated primarily with ecotype divergence rather than geographic separation in an intertidal, poorly-dispersing snail
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PARP3 is a promoter of chromosomal rearrangements and limits G4 DNA
GEO Series GSE94588. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Whole-exome and RNA sequencing of pulmonary carcinoid reveals chromosomal rearrangements associated with recurrence (RNA)
GEO Series GSE142186. Homo sapiens. 6 samples. Type: Other.
Replication-Timing Boundaries Facilitate Cell-type and Species-specific Regulation of a Rearranged Human Chromosome in Mouse
GEO Series GSE38472. Homo sapiens; Mus musculus. 6 samples. Type: Genome variation profiling by genome tiling array.
Genomic Balancing Act: Deciphering DNA rearrangements in the Complex Chromosomal Aberration involving 5p15.2, 2q31.1 and 18q21.32
GEO Series GSE265815. Homo sapiens. 3 samples. Type: Methylation profiling by array.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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