Chromosomes 21 and 22: Gene Density

AbstractIn Drosophila, as in many organisms, natural selection leads to high levels of codon bias in genes that are highly expressed. Thus codon bias is an indicator of the intensity of one kind of selection that is experienced by genes and can be used to assess the impact of other genomic factors on natural selection. Among 13,000 genes in the Drosophila genome, codon bias has a slight positive, and strongly significant, association with recombination—as expected if recombination allows natural selection to act more efficiently when multiple linked sites segregate functional variation. The same reasoning leads to the expectation that the efficiency of selection, and thus average codon bias, should decline with gene density. However, this prediction is not confirmed. Levels of codon bias and gene expression are highest for those genes in an intermediate range of gene density, a pattern that may be the result of a tradeoff between the advantages for gene expression of close gene spacing and disadvantages arising from regulatory conflicts among tightly packed genes. These factors appear to overlay the more subtle effect of linkage among selected sites that gives rise to the association between recombination rate and codon bias.

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MOLECULAR MAPPING OF A GENE CLUSTER FLANKING THE DROSOPHILA DOPA DECARBOXYLASE GENE

Genetics ◽

10.1093/genetics/106.4.679 ◽

1984 ◽

Vol 106 (4) ◽

pp. 679-694

Author(s):

Denise Gilbert ◽

Jay Hirsh ◽

T R F Wright

Keyword(s):

Gene Cluster ◽

Molecular Mapping ◽

Gene Density ◽

Dopa Decarboxylase ◽

Chromosomal Dna ◽

Potential Significance ◽

High Gene ◽

Complementation Groups ◽

High Gene Density

ABSTRACT Nine lethal complementation groups flanking the Drosophila Dopa decarboxylase (Ddc) gene, have been localized within 100 kb of cloned chromosomal DNA. Six of these complementation groups are within 23 kb of DNA, and all ten complementation groups, including Ddc, lie within 78-82 kb of DNA. The potential significance of this unusually high gene density is discussed.

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Saturation Mapping of a Gene-Rich Recombination Hot Spot Region in Wheat

Genetics ◽

10.1093/genetics/154.2.823 ◽

2000 ◽

Vol 154 (2) ◽

pp. 823-835 ◽

Cited By ~ 12

Author(s):

Justin D Faris ◽

Karri M Haen ◽

Bikram S Gill

Keyword(s):

Positional Cloning ◽

Physical Map ◽

Hot Spot ◽

Chromosome Breakage ◽

Small Chromosome ◽

Gene Density ◽

Chromosome 5B ◽

High Gene ◽

The Many ◽

Recombination Hot Spots

AbstractPhysical mapping of wheat chromosomes has revealed small chromosome segments of high gene density and frequent recombination interspersed with relatively large regions of low gene density and infrequent recombination. We constructed a detailed genetic and physical map of one highly recombinant region on the long arm of chromosome 5B. This distally located region accounts for 4% of the physical size of the long arm and at least 30% of the recombination along the entire chromosome. Multiple crossovers occurred within this region, and the degree of recombination is at least 11-fold greater than the genomic average. Characteristics of the region such as gene order and frequency of recombination appear to be conserved throughout the evolution of the Triticeae. The region is more prone to chromosome breakage by gametocidal gene action than gene-poor regions, and evidence for genomic instability was implied by loss of gene collinearity for six loci among the homeologous regions. These data suggest that a unique level of chromatin organization exists within gene-rich recombination hot spots. The many agronomically important genes in this region should be accessible by positional cloning.

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Mapping barley Ds insertions using wheat deletion lines reveals high insertion frequencies in gene-rich regions with high to moderate recombination rates

Genome ◽

10.1139/g09-029 ◽

2009 ◽

Vol 52 (6) ◽

pp. 566-575 ◽

Cited By ~ 4

Author(s):

Harpinder S. Randhawa ◽

Jaswinder Singh ◽

Peggy G. Lemaux ◽

Kulvinder S. Gill

Keyword(s):

Gene Cloning ◽

Single Copy ◽

Gene Density ◽

Targeted Mutagenesis ◽

Recombination Rates ◽

Transposition Frequency ◽

Deletion Lines ◽

Gene Distribution ◽

Flanking Sequences ◽

Large Genomes

Gene distribution is highly uneven in the large genomes of barley and wheat; however, location, order, and gene density of gene-containing regions are very similar between the two genomes. Flanking sequences from 35 unique, single-copy, barley Ds insertion events were physically mapped using wheat nullisomic-tetrasomic, ditelosomic, and deletion lines. Of the 35 sequences, 23 (66%) detected 34 loci mapping on all 7 homoeologous wheat groups. Seven sequences were not mapped owing to lack of polymorphism and the remaining 5 (14%) were barley-specific. All 34 loci physically mapped to the previously identified gene-rich regions (GRRs) of wheat, making the contained genes candidates for targeted mutagenesis by remobilization. Transpositions occurred preferentially into GRRs with higher recombination rates. The GRRs containing 17 of the 23 Ds insertions accounted for 60%–89% of the respective arm’s recombination. The remaining 6 (17%) insertions mapped to GRRs with <15% of the arm’s recombination. Overall, kb/cM estimates for the Ds-containing GRRs were twofold higher than those for regions without insertions. These results suggest that all genes may be targeted by transposon-based gene cloning, although the transposition frequency for genes present in recombination-poor regions is significantly less than that present in highly recombinogenic regions.

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

Genetics ◽

10.1093/genetics/159.2.581 ◽

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.

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Interspecies conservation of gene order and intron-exon structure in a genomic locus of high gene density and complexity in Plasmodium

Nucleic Acids Research ◽

10.1093/nar/29.10.2059 ◽

2001 ◽

Vol 29 (10) ◽

pp. 2059-2068 ◽

Cited By ~ 20

Author(s):

L. H. M. van Lin

Keyword(s):

Gene Order ◽

Gene Density ◽

Genomic Locus ◽

High Gene ◽

Exon Structure ◽

High Gene Density

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UV-A breakage sensitivity of human chromosomes as measured by COMET-FISH depends on gene density and not on the chromosome size

Journal of Photochemistry and Photobiology B Biology ◽

10.1016/s1011-1344(00)00052-x ◽

2000 ◽

Vol 56 (2-3) ◽

pp. 109-117 ◽

Cited By ~ 37

Author(s):

Alexander Rapp ◽

Claudia Bock ◽

Heike Dittmar ◽

Karl-Otto Greulich

Keyword(s):

Gene Density ◽

Chromosome Size ◽

Human Chromosomes

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Different chromosomal distribution patterns of radiation-induced interchange breakpoints in barley: First post-treatment mitosis versus viable offspring

Genome ◽

10.1139/g00-104 ◽

2001 ◽

Vol 44 (1) ◽

pp. 128-132 ◽

Cited By ~ 10

Author(s):

G Künzel ◽

K I Gecheff ◽

I Schubert

Keyword(s):

Distribution Patterns ◽

Gene Density ◽

Post Treatment ◽

Recombination Rates ◽

Chromosomal Distribution ◽

Chromosome Breaks ◽

Translocation Breakpoints ◽

High Gene ◽

Radiation Induced ◽

High Gene Density

Translocation breakpoints (TBs) induced by ionizing radiation are nonrandomly distributed along barley chromosomes. When first post-treatment mitoses were evaluated, centromeres and the heterochromatin-containing proximal segments tended to be more than randomly involved, and terminal segments to be less than randomly involved in translocations. Contrary to this, small chromosomal regions in median and distal arm positions, characterized by high recombination rates and high gene density, were identified as preferred sites for the origination of viable translocations, probably due to deviations in chromatin organization. Apparently, the position of a TB has an influence on the rate of viability versus elimination of the carrier cells. Surprisingly, TBs within centromeres and heterochromatin-containing segments seem to be more harmful for survival than those induced in gene-rich regions.Key words: Hordeum vulgare, radiation-induced chromosome breaks, translocation lines, breakpoint distribution.

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