PROPERTIES AND EVOLUTIONARY POTENTIAL OF NEWLY INDUCED TANDEM DUPLICATIONS IN DROSOPHILA MELANOGASTER

ABSTRACT Most of some 33 X-ray-induced duplications recovered as Suppressors of Minute loci proved to be direct tandem duplications. When heterozygous, most duplications were crossover suppressors, and duplications of short to moderate size did not reduce the fitness of their bearers. Crossover suppression by tandem duplication may be attributed to intrastrand foldbacks of the type regularly seen in somatic polytene chromosomes. As a consequence, linkage disequilibrium between duplicated elements and normal chromosomes should be more profound than has been supposed. Tandem duplications appear to be predisposed by reason of frequency of generation, crossover suppression and fitness effects to serve as the primary source of new genes.

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The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. I. Element frequencies and distribution

Genetics Research ◽

10.1017/s0016672300030792 ◽

1992 ◽

Vol 60 (2) ◽

pp. 103-114 ◽

Cited By ~ 65

Author(s):

Brian Charlesworth ◽

Angela Lapid ◽

Darlene Canada

Keyword(s):

Population Dynamics ◽

Drosophila Melanogaster ◽

Linkage Disequilibrium ◽

Transposable Elements ◽

Copy Number ◽

Polytene Chromosomes ◽

Chromosome Band ◽

High Frequencies ◽

Copy Numbers

SummaryData were collected on the distribution of nine families of transposable elements among second and third chromosomes isolated from a natural population of Drosophila melanogaster, by means of in situ hybridization of element probes to polytene chromosomes. It was found that the copy numbers per chromosome in the distal sections of the chromosome arms followed a Poisson distribution. Elements appeared to be distributed randomly along the distal sections of the chromosome arms. There was no evidence for linkage disequilibrium in the distal sections of the chromosomes, but some significant disequilibrium was detected in proximal regions. There were many significant correlations between different element families with respect to the identity of the sites that were occupied in the sample. There were also significant correlations between families with respect to sites at which elements achieved relatively high frequencies. Element frequencies per chromosome band were generally low in the distal sections, but were higher proximally. These results are discussed in the light of models of the population dynamics of transposable elements. It is concluded that they provide strong evidence for the operation of a force or forces opposing transpositional increase in copy number. The data suggest that the rate of transposition perelement per generation is of the order of 10−4, for the elements included in this study.

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Tandem duplications in Drosophila melanogaster: III. Intrachromosomal exchange of a heterozygous tandem duplication

Genetics Research ◽

10.1017/s0016672300016074 ◽

1975 ◽

Vol 26 (3) ◽

pp. 275-282

Author(s):

Wolf-Ekkehard Kalisch

Keyword(s):

Drosophila Melanogaster ◽

Homologous Chromosome ◽

Tandem Duplication ◽

Double Loop ◽

Exchange Frequency ◽

Chromosome Distribution ◽

Interchromosomal Effect ◽

Tandem Duplications ◽

Meiotic Event

SUMMARYDuring meiosis the two parts of a tandem duplication are able to pair in a double loop instead of pairing with the corresponding region of the homologous chromosome. The frequency of intrachromosomal exchange within this double loop was measured in heterozygous females of tandem duplication Dp(1; 1)Gr by the phenotypes of the exceptional F1 males. The intrachromosomal exchange frequency is increased significantly by both the ‘interchromosomal effect’ of heterozygous inversions in the autosomes and by a double inversion in the homologous X chromosome. Distribution of the exchange events depends on the pairing situation and its frequency within the double loop. The analysis of clusters of intrachromosomal recombinants observed favours the assumption that this exchange type is exclusively a meiotic event.

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TECHNIQUES FOR MANIPULATING CHROMOSOMAL REARRANGEMENTS AND THEIR APPLICATION TO DROSOPHILA MELANOGASTER. I. PERICENTRIC INVERSIONS

Genetics ◽

10.1093/genetics/99.1.75 ◽

1981 ◽

Vol 99 (1) ◽

pp. 75-97

Author(s):

Loring Craymer

Keyword(s):

Drosophila Melanogaster ◽

Tandem Duplication ◽

Chromosomal Rearrangements ◽

Pericentric Inversions ◽

Derivatives Of ◽

Tandem Duplications ◽

Dominant Lethality ◽

Inversion Loop

ABSTRACT Techniques have been developed for manipulating pericentric inversions in Drosophila that are based on the lethality of grossly aneuploid zygotes and the existence of recombinationally interconvertible genotypes for any heterozygous inversion complex: males of some of these genotypes will produce only aneuploid sperm, which can be used to rescue complementary aneuploid ova and selectively recover recombinational derivatives of inversions. Markers can be recombined into inversions through a sequence of selected single exchanges, and a novel type of duplication can be synthesized from overlapping inversions that has the characteristics of both insertional and tandem duplications; there are also applications to half-tetrad analyses.——Two cytogenetic screens are developed: (1) the dominant lethality of a large insertional-tandem duplication can be reverted by deletional events that give rise to net deficiencies or duplications, and (2) deficiencies and tandem duplications in proximal regions can be selectively recovered as the results of unequal exchanges within an inversion loop. Recombinants have been recovered between breakpoints separated by distances of as little as fifty bands, arguing against the existence of some small number of sites necessary for the initiation of recombinational pairing. In several instances, hyperploids for four to six numbered divisions were observed to be fertile in both sexes.

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IN SUPPORT OF THE TELOMERE CONCEPT

Genetics ◽

10.1093/genetics/80.1.135 ◽

1975 ◽

Vol 80 (1) ◽

pp. 135-142

Author(s):

Paul A Roberts

Keyword(s):

Drosophila Melanogaster ◽

X Chromosome ◽

Mitotic Chromosome ◽

Polytene Chromosomes ◽

Metaphase Chromosomes ◽

X Chromosomes ◽

X Ray ◽

Single Exception

ABSTRACT The frequency of recovered X-ray-induced (4000R) rearrangements that, in all probability, mimic terminal deletions of the X chromosome was only one of, roughly, 105 X chromosomes screened for tip deficiencies. Although the single exception looks terminally deleted, it is probably capped by a very short or nonpolytene telomeric segment. It is apparent from these data that the probability of "healing" or stabilization of a terminally deleted X in the zygotic nucleus or developing embryo of Drosophila melanogaster is vanishingly small. The telomeric caps in two obviously interstitial deficiencies that were recovered represent, roughly, 1/500 of the length of a mitotic chromosome. These findings give some indication of the extreme difficulty of detecting short telomeric segments capping either deleted polytene chromosomes or deleted metaphase chromosomes of, for example, humans.

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Analysis of Two Cosmid Clones from Chromosome 4 of Drosophila melanogaster Reveals Two New Genes Amid an Unusual Arrangement of Repeated Sequences

Genome Research ◽

10.1101/gr.9.2.137 ◽

1999 ◽

Vol 9 (2) ◽

pp. 137-149 ◽

Cited By ~ 1

Author(s):

John Locke ◽

Lynn Podemski ◽

Ken Roy ◽

David Pilgrim ◽

Ross Hodgetts

Keyword(s):

Drosophila Melanogaster ◽

Dna Sequences ◽

Polytene Chromosomes ◽

Mobile Element ◽

The Other ◽

P Element ◽

Matrix Analysis ◽

Predicted Amino Acid Sequence ◽

Chromosome 4 ◽

New Genes

Chromosome 4 from Drosophila melanogaster has several unusual features that distinguish it from the other chromosomes. These include a diffuse appearance in salivary gland polytene chromosomes, an absence of recombination, and the variegated expression of P-element transgenes. As part of a larger project to understand these properties, we are assembling a physical map of this chromosome. Here we report the sequence of two cosmids representing ∼5% of the polytenized region. Both cosmid clones contain numerous repeated DNA sequences, as identified by cross hybridization with labeled genomic DNA, BLAST searches, and dot matrix analysis, which are positioned between and within the transcribed sequences. The repetitive sequences include three copies of the mobile element Hoppel, one copy of the mobile element HB, and 18 DINE repeats. DINE is a novel, short repeated sequence dispersed throughout both cosmid sequences. One cosmid includes the previously described cubitus interruptus(ci) gene and two new genes: that a gene with a predicted amino acid sequence similar to ribosomal protein S3a which is consistent with the Minute(4)101 locus thought to be in the region, and a novel member of the protein family that includes plexin and met–hepatocyte growth factor receptor. The other cosmid contains only the two short 5′-most exons from thezinc-finger-homolog-2 (zfh-2) gene. This is the first extensive sequence analysis of noncoding DNA from chromosome 4. The distribution of the various repeats suggests its organization is similar to the β-heterochromatic regions near the base of the major chromosome arms. Such a pattern may account for the diffuse banding of the polytene chromosome 4 and the variegation of many P-element transgenes on the chromosome.

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A novel transvection phenomenon affecting the white gene of Drosophila melanogaster.

Genetics ◽

10.1093/genetics/126.1.167 ◽

1990 ◽

Vol 126 (1) ◽

pp. 167-176

Author(s):

D Gubb ◽

M Ashburner ◽

J Roote ◽

T Davis

Keyword(s):

Drosophila Melanogaster ◽

Homologous Chromosome ◽

Tandem Duplication ◽

Gamma Ray ◽

Insertion Site ◽

Hairpin Loop ◽

Homologous Chromosomes ◽

Inverted Order ◽

In Trans ◽

In Cis

Abstract The zeste mutation of Drosophila melanogaster suppresses the expression of white genes in the eye. This suppression is normally dependent on there being two copies of w+ located close to each other in the genome--they may either be in cis (as in a tandem duplication of w+) or in trans, i.e. on homologous chromosomes. Duplicated w+ genes carried by a giant transposing element, TE146(Z), are suppressed by z whether they are in direct (tandem) or inverted order. The tandem form of the TE is very sensitive to a rearrangement on the homologous chromosome--many rearrangements with breakpoints "opposite" the TE's insertion site prevent the interaction between the white genes on a z background. These aberrations act as dominant suppressors of zeste that are specific to the tandemly duplicated form of TE146(Z). The inverted form of the TE146(Z) presumably pairs as a hairpin loop; this is more stable than the tandem form by the criterion that its zeste phenotype is unaffected by any of the aberrations. This effect of rearrangements has been used as the basis for a screen, gamma-ray induced aberrations with at least one breakpoint opposite the TE site were recovered by their suppression of the zeste phenotype.

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

Genetics ◽

10.1093/genetics/144.1.197 ◽

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.

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Identification, Expression and Evolution of Short-Chain Dehydrogenases/Reductases in Nile Tilapia (Oreochromis niloticus)

International Journal of Molecular Sciences ◽

10.3390/ijms22084201 ◽

2021 ◽

Vol 22 (8) ◽

pp. 4201

Author(s):

Shuai Zhang ◽

Lang Xie ◽

Shuqing Zheng ◽

Baoyue Lu ◽

Wenjing Tao ◽

...

Keyword(s):

Transcriptome Analysis ◽

Tandem Duplication ◽

Developmental Stages ◽

Short Chain ◽

Sexually Dimorphic ◽

Physiological Processes ◽

Genome Wide ◽

Nile Tilapia Oreochromis Niloticus ◽

Tandem Duplications

The short-chain dehydrogenases/reductases (SDR) superfamily is involved in multiple physiological processes. In this study, genome-wide identification and comprehensive analysis of SDR superfamily were carried out in 29 animal species based on the latest genome databases. Overall, the number of SDR genes in animals increased with whole genome duplication (WGD), suggesting the expansion of SDRs during evolution, especially in 3R-WGD and polyploidization of teleosts. Phylogenetic analysis indicated that vertebrates SDRs were clustered into five categories: classical, extended, undefined, atypical, and complex. Moreover, tandem duplication of hpgd-a, rdh8b and dhrs13 was observed in teleosts analyzed. Additionally, tandem duplications of dhrs11-a, dhrs7a, hsd11b1b, and cbr1-a were observed in all cichlids analyzed, and tandem duplication of rdh10-b was observed in tilapiines. Transcriptome analysis of adult fish revealed that 93 SDRs were expressed in more than one tissue and 5 in one tissue only. Transcriptome analysis of gonads from different developmental stages showed that expression of 17 SDRs were sexually dimorphic with 11 higher in ovary and 6 higher in testis. The sexually dimorphic expressions of these SDRs were confirmed by in situ hybridization (ISH) and qPCR, indicating their possible roles in steroidogenesis and gonadal differentiation. Taken together, the identification and the expression data obtained in this study contribute to a better understanding of SDR superfamily evolution and functions in teleosts.

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Identification of Chromosome Inheritance Modifiers in Drosophila melanogaster

Genetics ◽

10.1093/genetics/157.4.1623 ◽

2001 ◽

Vol 157 (4) ◽

pp. 1623-1637 ◽

Cited By ~ 7

Author(s):

Kenneth W Dobie ◽

Cameron D Kennedy ◽

Vivienne M Velasco ◽

Tory L McGrath ◽

Juliani Weko ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Biological Activity ◽

Cancer Progression ◽

Birth Defects ◽

Mitotic Chromosome ◽

P Element ◽

Inverse Pcr ◽

Gtpase Activating Protein ◽

New Genes ◽

Genomic Analyses

Abstract Faithful chromosome inheritance is a fundamental biological activity and errors contribute to birth defects and cancer progression. We have performed a P-element screen in Drosophila melanogaster with the aim of identifying novel candidate genes involved in inheritance. We used a “sensitized” minichromosome substrate (J21A) to screen ∼3,000 new P-element lines for dominant effects on chromosome inheritance and recovered 78 Sensitized chromosome inheritance modifiers (Scim). Of these, 69 decreased minichromosome inheritance while 9 increased minichromosome inheritance. Fourteen mutations are lethal or semilethal when homozygous and all exhibit dramatic mitotic defects. Inverse PCR combined with genomic analyses identified P insertions within or close to genes with previously described inheritance functions, including wings apart-like (wapl), centrosomin (cnn), and pavarotti (pav). Further, lethal insertions in replication factor complex 4 (rfc4) and GTPase-activating protein 1 (Gap1) exhibit specific mitotic chromosome defects, discovering previously unknown roles for these proteins in chromosome inheritance. The majority of the lines represent mutations in previously uncharacterized loci, many of which have human homologs, and we anticipate that this collection will provide a rich source of mutations in new genes required for chromosome inheritance in metazoans.

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Phosphoglucomutase (PGM) and Esterase-6 (EST-6) alleles in Drosophila melanogaster: An attempt to detect linkage disequilibrium

Genetica ◽

10.1007/bf00120570 ◽

1978 ◽

Vol 49 (2-3) ◽

pp. 225-227 ◽

Cited By ~ 3

Author(s):

G. Trippa ◽

G. A. Danieli ◽

R. Costa ◽

R. Scozzari

Keyword(s):

Drosophila Melanogaster ◽

Linkage Disequilibrium ◽

Esterase 6

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