scholarly journals Contrasting patterns of sequence divergence and base composition between Drosophila introns and intergenic regions

2006 ◽  
Vol 2 (4) ◽  
pp. 604-607 ◽  
Author(s):  
Lino Ometto ◽  
David De Lorenzo ◽  
Wolfgang Stephan
Keyword(s):  
Drosophila Melanogaster ◽  
Recombination Rate ◽  
Base Composition ◽  
Gc Content ◽  
Sequence Divergence ◽  
Evolutionary Patterns ◽  
Nucleotide Variability ◽  
Selective Constraints ◽  
Intergenic Regions

Two non-coding DNA classes, introns and intergenic regions, of Drosophila melanogaster exhibit contrasting evolutionary patterns. GC content is significantly higher in intergenic regions and affects their degree of nucleotide variability. Divergence is positively correlated with recombination rate in intergenic regions, but not in introns. We argue that these differences are due to different selective constraints rather than mutational or recombinational mechanisms.

Significant positive correlation between the recombination rate and GC content in the human pseudoautosomal region

Genome ◽  
2006 ◽  
Vol 49 (5) ◽  
pp. 413-419 ◽  
Author(s):  
Jin-Feng Chen ◽  
Fei Lu ◽  
Su-Shing Chen ◽  
Shi-Heng Tao
Keyword(s):  
Recombination Rate ◽  
Base Composition ◽  
Significant Positive Correlation ◽  
Gc Content ◽  
Pseudoautosomal Region ◽  
Positive Correlation ◽  
Coding Regions ◽  
Ideal System ◽  
Fixation Bias

This paper establishes that recombination drives the evolution of GC content in a significant way. Because the human P-arm pseudoautosomal region (PAR1) has been shown to have a high recombination rate, at least 20-fold more frequent than the genomic average of ~1 cM/Mb, this region provides an ideal system to study the role of recombination in the evolution of base composition. Nine non-coding regions of PAR1 are analyzed in this study. We have observed a highly significant positive correlation between the recombination rate and GC content (ρ = 0.837, p ≤ 0.005). Five regions that lie in the distal part of PAR1 are shown to be significantly higher than genomic average divergence. By comparing the intra- and inter-specific AT→GC – GC→AT ratios, we have detected no fixation bias toward GC alleles except for L254915, which has excessive AT→GC changes in the human lineage. Thus, we conclude that the high GC content of the PAR1 genes better fits the biased gene conversion (BGC) model.Key words: pseudoautosomal region, GC content, base composition, evolution, recombination.

scholarly journals Hill–Robertson interference in Drosophila melanogaster: reply to Marais, Mouchiroud and Duret

2003 ◽  
Vol 81 (2) ◽  
pp. 89-90 ◽  
Author(s):  
RICHARD M. KLIMAN ◽  
JODY HEY
Keyword(s):  
Drosophila Melanogaster ◽  
Codon Usage ◽  
Recombination Rate ◽  
Base Composition ◽  
Potential Role ◽  
Compositional Bias ◽  
Stochastic Effects ◽  
Protein Coding ◽  
Biasing Effects ◽  
Preferred Codon

The usage of preferred codons in Drosophila melanogaster is reduced in regions of lower recombination. This is consistent with population genetics theory, whereby the effectiveness of selection on multiple targets is limited by stochastic effects caused by linkage. However, because the selectively preferred codons in D. melanogaster end in C or G, it has been argued that base-composition-biasing effects of recombination can account for the observed relationship between preferred codon usage and recombination rate (Marais et al., 2003). Here, we show that the correlation between base composition (of protein-coding and intron regions) and recombination rate holds only for lower values of the latter. This is consistent with a Hill–Robertson interference model and does not support a model whereby the entire effect of recombination on codon usage can be attributed to its potential role in generating compositional bias.

scholarly journals Intramolecular heterogeneity of mitochondrial DNA of Drosophila melanogaster.

1977 ◽  
Vol 73 (2) ◽  
pp. 279-286 ◽  
Author(s):  
E S Goldring ◽  
W J Peacock
Keyword(s):  
Mitochondrial Dna ◽  
Drosophila Melanogaster ◽  
Base Composition ◽  
Gc Content ◽  
Contour Length ◽  
Regional Heterogeneity ◽  
Partial Denaturation

DNA from purified mitochondria of Drosophila melanogaster can be isolated as supercoiled molecules which when nicked have a contour length of 5.9 micron. Partial denaturation mapping shows regional heterogeneity of base composition with one early denaturing region, with a calculated GC content close to zero, extending over 20% of the genome. DNA isolated from unfertilized eggs shows nuclear and mitochondrial DNA in equal proportions; we found no evidence of other cytoplasmic species.

Snake Recombination Landscapes Are Concentrated in Functional Regions despite PRDM9

2020 ◽  
Vol 37 (5) ◽  
pp. 1272-1294 ◽  
Author(s):  
Drew R Schield ◽  
Giulia I M Pasquesi ◽  
Blair W Perry ◽  
Richard H Adams ◽  
Zachary L Nikolakis ◽  
...  
Keyword(s):  
Recombination Rate ◽  
Gc Content ◽  
Substantial Variation ◽  
Recombination Rates ◽  
Recombination Hotspots ◽  
Functional Regions ◽  
Intergenic Regions ◽  
Positive Correlations ◽  
Adaptive Role

Abstract Meiotic recombination in vertebrates is concentrated in hotspots throughout the genome. The location and stability of hotspots have been linked to the presence or absence of PRDM9, leading to two primary models for hotspot evolution derived from mammals and birds. Species with PRDM9-directed recombination have rapid turnover of hotspots concentrated in intergenic regions (i.e., mammals), whereas hotspots in species lacking PRDM9 are concentrated in functional regions and have greater stability over time (i.e., birds). Snakes possess PRDM9, yet virtually nothing is known about snake recombination. Here, we examine the recombination landscape and test hypotheses about the roles of PRDM9 in rattlesnakes. We find substantial variation in recombination rate within and among snake chromosomes, and positive correlations between recombination rate and gene density, GC content, and genetic diversity. Like mammals, snakes appear to have a functional and active PRDM9, but rather than being directed away from genes, snake hotspots are concentrated in promoters and functional regions—a pattern previously associated only with species that lack a functional PRDM9. Snakes therefore provide a unique example of recombination landscapes in which PRDM9 is functional, yet recombination hotspots are associated with functional genic regions—a combination of features that defy existing paradigms for recombination landscapes in vertebrates. Our findings also provide evidence that high recombination rates are a shared feature of vertebrate microchromosomes. Our results challenge previous assumptions about the adaptive role of PRDM9 and highlight the diversity of recombination landscape features among vertebrate lineages.

scholarly journals Selective Constraints on Intron Evolution in Drosophila

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 1843-1851 ◽  
Author(s):  
John Parsch
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Selection ◽  
Common Ancestor ◽  
Length Distribution ◽  
Short Length ◽  
Intron Length ◽  
Intron Evolution ◽  
Intron Size ◽  
Duplicated Genes ◽  
Selective Constraints

AbstractIntron sizes show an asymmetrical distribution in a number of organisms, with a large number of “short” introns clustered around a minimal intron length and a much broader distribution of longer introns. In Drosophila melanogaster, the short intron class is centered around 61 bp. The narrow length distribution suggests that natural selection may play a role in maintaining intron size. A comparison of 15 orthologous introns among species of the D. melanogaster subgroup indicates that, in general, short introns are not under greater DNA sequence or length constraints than long introns. There is a bias toward deletions in all introns (deletion/insertion ratio is 1.66), and the vast majority of indels are of short length (<10 bp). Indels occurring on the internal branches of the phylogenetic tree are significantly longer than those occurring on the terminal branches. These results are consistent with a compensatory model of intron length evolution in which slightly deleterious short deletions are frequently fixed within species by genetic drift, and relatively rare larger insertions that restore intron length are fixed by positive selection. A comparison of paralogous introns shared among duplicated genes suggests that length constraints differ between introns within the same gene. The janusA, janusB, and ocnus genes share two short introns derived from a common ancestor. The first of these introns shows significantly fewer indels than the second intron, although the two introns show a comparable number of substitutions. This indicates that intron-specific selective constraints have been maintained following gene duplication, which preceded the divergence of the D. melanogaster species subgroup.

scholarly journals Chromosomal Distribution of Transposable Elements in Drosophila melanogaster Test of the Ectopic Recombination Model for Maintenance of Insertion Site Number

Genetics ◽  
1996 ◽  
Vol 144 (1) ◽  
pp. 197-204
Author(s):  
Christine Hoogland ◽  
Christian Biémont
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Dna Content ◽  
Recombination Rate ◽  
Alternative Hypothesis ◽  
Insertion Site ◽  
Polytene Chromosomes ◽  
Negative Relationship ◽  
Site Occupancy ◽  
Site Number

Abstract Data of insertion site localization and site occupancy frequency of P, hobo, I, copia, mdg1, mdg3, 412, 297, and roo transposable elements (TEs) on the polytene chromosomes of Drosophila melanogaster were extracted from the literature. We show that TE insertion site number per chromosomal division was significantly correlated with the amount of DNA. The insertion site number weighted by DNA content was not correlated with recombination rate for all TEs except hobo, for which a positive correlation was detected. No global tendency emerged in the relationship between TE site occupancy frequency, weighted by DNA content, and recombination rate; a strong negative correlation was, however, found for the 3L arm. A possible dominant deleterious effect of chromosomal rearrangements due to recombination between TE insertions is thus not the main factor explaining the dynamics of TEs, since this hypothesis implies a negative relationship between recombination rate and both TE insertion site number and site occupancy frequency. The alternative hypothesis of selection against deleterious effects of insertional mutations is discussed.

scholarly journals Patterns of DNA Variability at X-Linked Loci in Mus domesticus

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1303-1316
Author(s):  
Michael W Nachman
Keyword(s):  
Drosophila Melanogaster ◽  
X Chromosome ◽  
House Mouse ◽  
Recombination Rate ◽  
Nucleotide Diversity ◽  
Mus Domesticus ◽  
Substantial Variation ◽  
Intraspecific Polymorphism ◽  
Recombination Rates ◽  
Interspecific Divergence

Introns of four X-linked genes (Hprt, Plp, Glra2, and Amg) were sequenced to provide an estimate of nucleotide diversity at nuclear genes within the house mouse and to test the neutral prediction that the ratio of intraspecific polymorphism to interspecific divergence is the same for different loci. Hprt and Plp lie in a region of the X chromosome that experiences relatively low recombination rates, while Glra2 and Amg lie near the telomere of the X chromosome, a region that experiences higher recombination rates. A total of 6022 bases were sequenced in each of 10 Mus domesticus and one M. caroli. Average nucleotide diversity (π) for introns within M. domesticus was quite low (π = 0.078%). However, there was substantial variation in the level of heterozygosity among loci. The two telomeric loci, Glra2 and Amg, had higher ratios of polymorphism to divergence than the two loci experiencing lower recombination rates. These results are consistent with the hypothesis that heterozygosity is reduced in regions with lower rates of recombination, although sampling of additional genes is needed to establish whether there is a general correlation between heterozygosity and recombination rate as in Drosophila melanogaster.

scholarly journals Consequences of Recombination Rate Variation on Quantitative Trait Locus Mapping Studies: Simulations Based on the Drosophila melanogaster Genome

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 581-588
Author(s):  
Mohamed A F Noor ◽  
Aimee L Cunningham ◽  
John C Larkin
Keyword(s):  
Quantitative Trait Locus ◽  
Drosophila Melanogaster ◽  
Qtl Mapping ◽  
Quantitative Trait ◽  
Recombination Rate ◽  
Genome Project ◽  
Gene Density ◽  
Rate Variation ◽  
Trait Locus ◽  
Recombination Rate Variation

Abstract We examine the effect of variation in gene density per centimorgan on quantitative trait locus (QTL) mapping studies using data from the Drosophila melanogaster genome project and documented regional rates of recombination. There is tremendous variation in gene density per centimorgan across this genome, and we observe that this variation can cause systematic biases in QTL mapping studies. Specifically, in our simulated mapping experiments of 50 equal-effect QTL distributed randomly across the physical genome, very strong QTL are consistently detected near the centromeres of the two major autosomes, and few or no QTL are often detected on the X chromosome. This pattern persisted with varying heritability, marker density, QTL effect sizes, and transgressive segregation. Our results are consistent with empirical data collected from QTL mapping studies of this species and its close relatives, and they explain the “small X-effect” that has been documented in genetic studies of sexual isolation in the D. melanogaster group. Because of the biases resulting from recombination rate variation, results of QTL mapping studies should be taken as hypotheses to be tested by additional genetic methods, particularly in species for which detailed genetic and physical genome maps are not available.

Sign in / Sign up

Export Citation Format

Share Document