simple-method-for-fluorescence-dna-situ-hybridization-to-squashed

Simple Method for Fluorescence DNA <em>In Situ</em> Hybridization to Squashed Chromosomes

DNA in situ hybridization (DNA ISH) is a commonly used method for mapping sequences to specific chromosome regions. This approach is particularly ...

University of Rochester

&#x7CBE;&#x5EA6;&#x548C;&#x7075;&#x654F;&#x5EA6;&#x7684;&#x8FDB;&#x5316;&#x63A8;&#x7406;&#xFF0C;&#x6781;&#x5927;&#x5730;&#x63D0;&#x9AD8;&#x4E86;&#x7CFB;&#x7EDF;&#x53D1;&#x80B2;&#x7684;&#x6846;&#x67B6;&#x4E2D;&#x7684;&#x591A;&#x4E2A;&#x57FA;&#x56E0;&#x7EC4;&#x6BD4;&#x8F83;&#x5206;&#x6790;&#xFF0C;&#x4EA7;&#x751F;&#x66F4;&#x4E3A;&#x5F3A;&#x52B2;&#x7684;&#x4E1A;&#x7EE9;&#xFF0C;&#x6BD4;&#x5355;&#x57FA;&#x56E0;&#x7EC4;&#x5206;&#x6790;&#x53EF;&#x4EE5;&#x63D0;&#x4F9B;&#x3002;12 &#x679C;&#x8747;&#x7269;&#x79CD;&#xFF0C;&#x5176;&#x4E2D;&#x5341; (sechellia&#x3001; simulans&#x3001; &#x4E9A;&#x5E93;&#x5DF4;&#x3001; &#x83CA;&#x3001; ananassae&#x3001; &#x8910;&#x82DE;&#x3001; willistoni&#x3001; mojavensis&#x3001; virilis &#x548C; grimshawi&#xFF09; &#x7684;&#x7B2C;&#x4E00;&#x6B21;&#x5728;&#x8FD9;&#x91CC;&#x63D0;&#x51FA;&#xFF0C;&#x57FA;&#x56E0;&#x7EC4;&#x8BF4;&#x660E;&#x901F;&#x7387;&#x548C;&#x8DE8;&#x7C7B;&#x7FA4;&#x5E8F;&#x5217;&#x53D1;&#x6563;&#x578B;&#x80FD;&#x7167;&#x4EAE;&#x57FA;&#x56E0;&#x7EC4;&#x89C4;&#x6A21;&#x4E0A;&#x7684;&#x8FDB;&#x5316;&#x8FC7;&#x7A0B;&#x3002;&#x8FD9;&#x4E9B;&#x57FA;&#x56E0;&#x7EC4;&#x5E8F;&#x5217;&#x589E;&#x52A0;&#x7684;&#x4EE4;&#x4EBA;&#x751F;&#x754F;&#x7684;&#x9057;&#x4F20;&#x5DE5;&#x5177;&#x4F5C;&#x51FA;&#x4E86;&#x7684;&#x679C;&#x8747;&#x679C;&#x8747;&#x5353;&#x8D8A;&#x6A21;&#x578B;&#x52A8;&#x7269;&#x9057;&#x4F20;&#x5B66;&#x548C;&#x5C06;&#x8FDB;&#x4E00;&#x6B65;&#x4FC3;&#x8FDB;&#x673A;&#x5236;&#x7684;&#x53D1;&#x5C55;&#xFF0C;&#x57FA;&#x672C;&#x7814;&#x7A76;&#x7EC6;&#x80DE;&#x751F;&#x7269;&#x5B66;&#x3001; &#x9057;&#x4F20;&#x5B66;&#x3001; &#x75BE;&#x75C5;&#x3001; &#x795E;&#x7ECF;&#x751F;&#x7269;&#x5B66;&#x3001; &#x884C;&#x4E3A;&#x3001; &#x751F;&#x7406;&#x548C;&#x6F14;&#x53D8;&#x3002;&#x5C3D;&#x7BA1;&#x8FD9;&#x4E9B;&#x679C;&#x8747;&#x7269;&#x79CD;&#x4E4B;&#x95F4;&#x7684;&#x60CA;&#x4EBA;&#x76F8;&#x4F3C;&#x4E4B;&#x5904;&#xFF0C;&#x6211;&#x4EEC;&#x53D1;&#x73B0;&#x8BB8;&#x591A;&#x8BA4;&#x5B9A;&#x975E;&#x4E2D;&#x6027;&#x86CB;&#x767D;&#x8D28;&#x7F16;&#x7801;&#x57FA;&#x56E0;&#x548C;&#x975E;&#x7F16;&#x7801; RNA &#x57FA;&#x56E0;&#xFF0C;&#x72EC;&#x8054;&#x4F53;&#x76D1;&#x7BA1;&#x533A;&#x57DF;&#x53D8;&#x5316;&#x3002;&#x8FD9;&#x4E9B;&#x53EF;&#x80FD;&#x7684;&#x751F;&#x6001;&#x548C;&#x884C;&#x4E3A;&#x7684;&#x8FD9;&#x4E9B;&#x4E0D;&#x540C;&#x7269;&#x79CD;&#x7684;&#x5DEE;&#x5F02;&#x3002;

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Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

Evolution of genes and genomes on the Drosophila phylogeny.

El an&#xE1;lisis comparativo de los genomas m&#xFA;ltiples en un marco filogen&#xE9;tico mejora considerablemente la precisi&#xF3;n y la sensibilidad de la inferencia de la evoluci&#xF3;n, la producci&#xF3;n de resultados m&#xE1;s s&#xF3;lidos que los de un solo genoma an&#xE1;lisis puede proporcionar. Los genomas de 12 especies de Drosophila, diez de los cuales se presentan aqu&#xED; por primera vez (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis y grimshawi), ilustran c&#xF3;mo las tasas y patrones de divergencia en la secuencia a trav&#xE9;s de los taxones pueden iluminar los procesos evolutivos en una escala gen&#xF3;mica. Estas secuencias del genoma aumentar los formidables herramientas gen&#xE9;ticas que han hecho de Drosophila melanogaster un modelo preeminente para la gen&#xE9;tica de los animales y, adem&#xE1;s, servir&#xE1; de catalizador para la investigaci&#xF3;n fundamental sobre los mecanismos del desarrollo, biolog&#xED;a celular, gen&#xE9;tica, las enfermedades, la neurobiolog&#xED;a, el comportamiento, la fisiolog&#xED;a y la evoluci&#xF3;n. A pesar de notables similitudes entre estas especies de Drosophila, se identificaron muchos putativamente no neutrales cambios en genes que codifican prote&#xED;nas, los genes no codificantes de ARN, y regiones cis-reguladoras. Estos puede ser que la base de las diferencias en la ecolog&#xED;a y el comportamiento de estas especies diversas.

Evoluci&#xF3;n de genes y genomas en la filogenia de la Drosophila

L&#x26;#39;analyse comparative des g&#xE9;nomes multiples dans un cadre phylog&#xE9;n&#xE9;tique am&#xE9;liore consid&#xE9;rablement la pr&#xE9;cision et la sensibilit&#xE9; de l&#x26;#39;inf&#xE9;rence de l&#x26;#39;&#xE9;volution, produisant des r&#xE9;sultats plus robustes que seul g&#xE9;nome analyses peuvent fournir. Les g&#xE9;nomes d&#x26;#39;esp&#xE8;ces de Drosophila 12, dont dix sont pr&#xE9;sent&#xE9;es ici pour la premi&#xE8;re fois (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis et grimshawi), illustrent la fa&#xE7;on dont les taux et les modes de divergence de s&#xE9;quence entre des taxons peut &#xE9;clairer les processus &#xE9;volutifs &#xE0; l&#x26;#39;&#xE9;chelle g&#xE9;nomique. Ces s&#xE9;quences g&#xE9;nomiques d&#x26;#39;augmenter les formidables outils g&#xE9;n&#xE9;tiques qui ont fait Drosophila melanogaster un mod&#xE8;le de pr&#xE9;-&#xE9;minente pour la g&#xE9;n&#xE9;tique des animaux, et catalyser davantage la recherche fondamentale sur les m&#xE9;canismes du d&#xE9;veloppement, biologie cellulaire, g&#xE9;n&#xE9;tique, la maladie, la neurobiologie, le comportement, la physiologie et de l&#x26;#39;&#xE9;volution. En d&#xE9;pit des similitudes remarquables entre ces esp&#xE8;ces Drosophila, nous avons identifi&#xE9; de nombreux putativement non-neutres changements dans les g&#xE8;nes codant pour des prot&#xE9;ines non-codantes des g&#xE8;nes d&#x26;#39;ARN, et cis-r&#xE9;gulatrices r&#xE9;gions. Ceux-ci peuvent se r&#xE9;v&#xE9;ler &#xEA;tre &#xE0; l&#x26;#39;origine des diff&#xE9;rences dans l&#x26;#39;&#xE9;cologie et le comportement de ces diverses esp&#xE8;ces.

Evolution des g&#xE8;nes et g&#xE9;nomes sur la phylog&#xE9;nie Drosophila

Vergleichende Analyse mehrerer Genome in einem phylogenetischen Rahmen dramatisch verbessert die Genauigkeit und Empfindlichkeit des evolution&auml;ren Inferenz, bieten stabilere Ergebnisse als Einzel-Genom-Analysen. Die Genome von 12 Drosophila-Arten, von die zehn hier zum ersten Mal (Sechellia, Simulans, Yakuba, Studentenblume, Ananassae, Persimilis, Willistoni, Mojavensis, Virilis und Grimshawi) vorgestellt werden, illustrieren, wie Preise und Muster der Sequenz Divergenz &uuml;ber Taxa Evolutionsprozesse auf genomischer Ebene beleuchten k&ouml;nnen. Diese Genomsequenzen erg&auml;nzen die gewaltige genetische Werkzeuge, die Drosophila Melanogaster eine herausragende Modell f&uuml;r Tiergenetik und wird weitere Grundlagenforschung auf Mechanismen der Entwicklung, katalysieren Zelle Biologie, Genetik, Krankheit, Neurobiologie, Verhalten, Physiologie und Entwicklung gemacht haben. Trotz der bemerkenswerten &Auml;hnlichkeiten zwischen dieser Drosophila-Arten haben wir viele vermeintlich nicht neutrale &Auml;nderungen im Protein-kodierenden Gene, non-coding RNA-Gene und Cis-regulatorischen Regionen identifiziert. Diese k&ouml;nnen wohl Unterschiede in der Lebensweise dieser unterschiedlichen Arten zugrunde liegen.

Entwicklung der Gene und der Genome auf die Phylogenie der Taufliege.

Analisi comparativa dei genomi multipli in un quadro filogenetico migliora notevolmente la precisione e la sensibilit&agrave; di inferenza evolutiva, producendo risultati pi&ugrave; robusti rispetto a singolo-genoma analisi pu&ograve; fornire. I genomi di 12 specie di Drosophila, dieci dei quali sono qui presentati per la prima volta (sechellia, simulans, yakuba, erecta, ananassae, persimilis, caninum, mojavensis, virilis e grimshawi), illustrano come tariffe e modelli di divergenza di sequenza tra taxa possono illuminare i processi evolutivi su scala genomica. Queste sequenze di genoma aumentano i formidabili strumenti genetici che hanno reso Drosophila melanogaster un modello preminente per la genetica degli animali e ulteriormente catalizzare fondamentali ricerche sui meccanismi di sviluppo, cellule, biologia, genetica, malattia, neurobiologia, comportamento, fisiologia ed evoluzione. Nonostante le notevoli somiglianze tra queste specie di Drosophila, abbiamo identificato molti cambiamenti fittizio non neutro in geni codificanti proteine, geni di RNA non codificanti e regioni cis-regolatori. Queste possono risultare sottendono le differenze nell&#39;ecologia e comportamento di queste specie diverse.

Evoluzione di geni e genomi su the phylogeny della drosofila.

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Phylogenetic &#xD504;&#xB808;&#xC784; &#xC6CC;&#xD06C;&#xC5D0;&#xC11C; &#xC5EC;&#xB7EC; &#xC720;&#xC804;&#xC790;&#xC758; &#xBE44;&#xAD50; &#xBD84;&#xC11D; &#xC815;&#xBC00;&#xB3C4; &#xC9C4;&#xD654; &#xC720;&#xCD94;&#xC758; &#xAC10;&#xB3C4; &#xADF9;&#xC801;&#xC73C;&#xB85C; &#xD5A5;&#xC0C1;, &#xC81C;&#xACF5;&#xD560; &#xC218; &#xC788;&#xB294; &#xB2E8;&#xC77C; &#xAC8C;&#xB188; &#xBD84;&#xC11D; &#xBCF4;&#xB2E4; &#xB354; &#xAC15;&#xB825;&#xD55C; &#xACB0;&#xACFC; &#xC0DD;&#xC0B0;. 10 &#xAC1C; (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis &#xBC0F; grimshawi) &#xCC98;&#xC74C;&#xC73C;&#xB85C; &#xC5EC;&#xAE30;&#xC5D0; &#xD45C;&#xC2DC; &#xB429;&#xB2C8;&#xB2E4;, 12 Drosophila &#xC885;&#xC758; &#xAC8C;&#xB188; &#xBE44;&#xC728;&#xACFC; taxa&#xC5D0; &#xAC78;&#xCCD0; &#xC2DC;&#xD000;&#xC2A4; &#xBC1C;&#xC0B0;&#xC758; &#xD328;&#xD134; &#xAC8C;&#xB188; &#xADDC;&#xBAA8;&#xB85C; &#xC9C4;&#xD654; &#xD504;&#xB85C;&#xC138;&#xC2A4;&#xB97C; &#xC870;&#xBA85; &#xD560; &#xC218; &#xC5B4;&#xB5BB;&#xAC8C; &#xBCF4;&#xC5EC; &#xC90D;&#xB2C8;&#xB2E4;. &#xC774;&#xB7EC;&#xD55C; &#xAC8C;&#xB188; &#xC2DC;&#xD000;&#xC2A4;&#xB97C; &#xB9CC;&#xB4E4;&#xC5C8;&#xC2B5;&#xB2C8;&#xB2E4; Drosophila melanogaster &#xC800;&#xBA85;&#xD55C; &#xBAA8;&#xB378; &#xB3D9;&#xBB3C; &#xC720;&#xC804;&#xD559; &#xB418;&#xBA70; &#xCD94;&#xAC00; catalyse &#xBA54;&#xCEE4;&#xB2C8;&#xC998; &#xAC1C;&#xBC1C;, &#xAE30;&#xCD08; &#xC5F0;&#xAD6C;&#xC5D0; &#xB300; &#xD55C; &#xC138;&#xD3EC; &#xC0DD;&#xBB3C;&#xD559;, &#xC720;&#xC804;&#xD559;, &#xC9C8;&#xBCD1;, &#xC2E0;&#xACBD; &#xC0DD;&#xBB3C;&#xD559;, &#xD589;&#xB3D9;, &#xC0DD;&#xB9AC;&#xD559;&#xACFC; &#xC9C4;&#xD654; &#xAC15;&#xB825;&#xD55C; &#xC720;&#xC804;&#xC801; &#xB3C4;&#xAD6C; &#xC99D;&#xAC00;. Drosophila &#xC885;&#xC871; &#xAC04;&#xC758; &#xB180;&#xB77C;&#xC6B4; &#xC720;&#xC0AC;&#xC131;&#xC5D0;&#xB3C4; &#xBD88;&#xAD6C; &#xD558; &#xACE0; &#xC6B0;&#xB9AC;&#xB294; &#xB2E8;&#xBC31;&#xC9C8; &#xCF54;&#xB529; &#xC720;&#xC804;&#xC790;, &#xBE44; &#xCF54;&#xB529; RNA &#xC720;&#xC804;&#xC790;&#xC640; cis &#xADDC;&#xC81C; &#xC9C0;&#xC5ED;&#xC5D0;&#xC11C; &#xB9CE;&#xC740; &#xD558;&#xAE30; &#xC911;&#xB9BD; &#xBCC0;&#xD654; &#xD655;&#xC778;. &#xC774;&#xB7EC;&#xD55C; &#xAE30;&#xCD08; &#xC0DD;&#xD0DC;&#xC640; &#xB2E4;&#xC591; &#xD55C; &#xC885;&#xC871;&#xC758; &#xD589;&#xB3D9;&#xC5D0; &#xCC28;&#xC774;&#xB97C; &#xC99D;&#xBA85;&#xD560; &#xC218; &#xC788;&#xC2B5;&#xB2C8;&#xB2E4;.

&#xC720;&#xC804;&#xC790;&#xC640; &#xCD08;&#xD30C;&#xB9AC; &#xC720;&#xC804;&#xC790;&#xC5D0; &#xC720;&#xC804;&#xC790;&#xC758; &#xC9C4;&#xD654;.

To investigate the relative efficacy of both positive and purifying natural selection on the X chromosome and the autosomes in Drosophila, we compared rates and patterns of molecular evolution between these chromosome sets using the newly available alignments of orthologous genes from 12 species. Parameters that may influence the relative X versus autosomal substitution rates include the relative effective population sizes, the male and female germline mutation rates, the distribution of allelic effects on fitness, and the degree of dominance of novel mutations. Our analysis reveals that codon usage bias is consistently greater for X-linked genes, suggesting that purifying selection consistently has greater efficacy on the X chromosome than on the autosomes across the Drosophila phylogeny. However, our results are less consistent with respect to the efficacy of positive selection, with only some lineages showing a higher substitution rate on the X chromosome. This suggests that either the distribution of selective effects of mutations or other relevant parameters are sufficiently variable across species to tip the balance in different ways in individual lineages. These data suggest that rates of substitution are not solely governed by adaptive evolution. This genome-wide analysis provides a clear picture that the efficacy of selection varies intragenomically and that this effect is markedly more consistent across the phylogeny in the case of purifying selection. Our results also suggest that simple models that predict systematic differences in rates of evolution between the X and the autosomes can only be made to be compatible with these Drosophila data if the relevant population genetic parameters that drive substitution rates differ among species and chromosomal contexts.

Contrasting the efficacy of selection on the X and autosomes in Drosophila.

Several contributing factors have been implicated in evolutionary rate heterogeneity among proteins, but their evolutionary mechanisms remain poorly characterized. The recently sequenced 12 Drosophila genomes provide a unique opportunity to shed light on these unresolved issues. Here, we focus on the role of natural selection in shaping evolutionary rates. We use the Drosophila genomic data to distinguish between factors that increase the strength of purifying selection on proteins and factors that affect the amount of positive selection experienced by proteins. We confirm the importance of translational selection in shaping protein evolution in Drosophila and show that factors such as tissue bias in expression, gene essentiality, intron number, and recombination rate also contribute to evolutionary rate variation among proteins.

Evolution of protein-coding genes in Drosophila.

One of the most striking cases of sex chromosome reorganization in Drosophila occurred in the lineage ancestral to Drosophila pseudoobscura, where there was a translocation of Y-linked genes to an autosome. These genes went from being present only in males, never recombining, and having an effective population size of 0.5N to a state of autosomal linkage, where they are passed through both sexes, may recombine, and their effective population size has quadrupled. These genes appear to be functional, and they underwent a drastic reduction in intron size after the translocation. A Y-autosome translocation may pose problems in meiosis if the rDNA locus responsible for X-Y pairing had also moved to an autosome. In this study, we demonstrate that the Y-autosome translocation moved Y-linked genes onto the dot chromosome, a small, mainly heterochromatic autosome with some sex chromosome-like properties. The rDNA repeats occur exclusively on the X chromosome in D. pseudoobscura, but we found that the new Y chromosome of this species harbors four clusters bearing only the intergenic spacer region (IGS) of the rDNA repeats. This arrangement appears analogous to the situation in Drosophila simulans, where X-rDNA to Y-IGS pairing could be responsible for X-Y chromosome pairing. We postulate that the nascent D. pseudoobscura Y chromosome acquired and amplified copies of the IGS, suggesting a potential mechanism for X-Y pairing in D. pseudoobscura.

Translocation of Y-linked genes to the dot chromosome in Drosophila pseudoobscura.

Segregation Distorter (SD) is an autosomal meiotic drive gene complex found worldwide in natural populations of Drosophila melanogaster. During spermatogenesis, SD induces dysfunction of SD(+) spermatids so that SD/SD(+) males sire almost exclusively SD-bearing progeny rather than the expected 1:1 Mendelian ratio. SD is thus evolutionarily "selfish," enhancing its own transmission at the expense of its bearers. Here we review the molecular and evolutionary genetics of SD. Genetic analyses show that the SD is a multilocus gene complex involving two key loci--the driver, Segregation distorter (Sd), and the target of drive, Responder (Rsp)--and at least three upward modifiers of distortion. Molecular analyses show that Sd encodes a truncated duplication of the gene RanGAP, whereas Rsp is a large pericentromeric block of satellite DNA. The Sd-RanGAP protein is enzymatically wild type but mislocalized within cells and, for reasons that remain unclear, appears to disrupt the histone-to-protamine transition in drive-sensitive spermatids bearing many Rsp satellite repeats but not drive-insensitive spermatids bearing few or no Rsp satellite repeats. Evolutionary analyses show that the Sd-RanGAP duplication arose recently within the D. melanogaster lineage, exploiting the preexisting and considerably older Rsp satellite locus. Once established, the SD haplotype collected enhancers of distortion and suppressors of recombination. Further dissection of the molecular genetic and cellular basis of SD-mediated distortion seems likely to provide insights into several important areas currently understudied, including the genetic control of spermatogenesis, the maintenance and evolution of satellite DNAs, the possible roles of small interfering RNAs in the germline, and the molecular population genetics of the interaction of genetic linkage and natural selection.

The selfish Segregation Distorter gene complex of Drosophila melanogaster.

The nonrecombining Drosophila melanogaster Y chromosome is heterochromatic and has few genes. Despite these limitations, there remains ample opportunity for natural selection to act on the genes that are vital for male fertility and on Y factors that modulate gene expression elsewhere in the genome. Y chromosomes of many organisms have low levels of nucleotide variability, but a formal survey of D. melanogaster Y chromosome variation had yet to be performed. Here we surveyed Y-linked variation in six populations of D. melanogaster spread across the globe. We find surprisingly low levels of variability in African relative to Cosmopolitan (i.e., non-African) populations. While the low levels of Cosmopolitan Y chromosome polymorphism can be explained by the demographic histories of these populations, the staggeringly low polymorphism of African Y chromosomes cannot be explained by demographic history. An explanation that is entirely consistent with the data is that the Y chromosomes of Zimbabwe and Uganda populations have experienced recent selective sweeps. Interestingly, the Zimbabwe and Uganda Y chromosomes differ: in Zimbabwe, a European Y chromosome appears to have swept through the population.

Surprising differences in the variability of Y chromosomes in African and cosmopolitan populations of Drosophila melanogaster.

The Drosophila pseudoobscura dot chromosome acquired genes from the ancestral Drosophila Y chromosome in a Y-to-dot translocation event that occurred between 12.7 and 20.8 Ma. The formerly Y-linked genes mostly retained their testis-specific expression but shrank drastically in size, mostly through intron reduction, since becoming part of the dot chromosome in this species. We investigated the impact of this translocation on the evolution of the both the Y-to-dot translocated region and the original segments of the dot chromosome in D. pseudoobscura. Our survey of polymorphism and divergence across the chromosome reveals a reduction in variation, a deletion polymorphism segregating at high frequency, and a shift in the frequency spectra, all consistent with a history of recent selective sweeps in the Y-to-dot translocated region but not on the rest of the dot chromosome. We do find evidence for recombination primarily as gene conversion on the dot chromosome; however, predicted recombination events are restricted to the part of the dot chromosome outside the translocation. It therefore appears that recombination has resulted in a degree of decoupling between the ancestral Y region and the conserved region of the dot chromosome.

Recent selection on the Y-to-dot translocation in Drosophila pseudoobscura.

BackgroundSatellite DNA can make up a substantial fraction of eukaryotic genomes and has roles in genome structure and chromosome segregation. The rapid evolution of satellite DNA can contribute to genomic instability and genetic incompatibilities between species. Despite its ubiquity and its contribution to genome evolution, we currently know little about the dynamics of satellite DNA evolution. The Responder (Rsp) satellite DNA family is found in the pericentric heterochromatin of chromosome 2 of Drosophila melanogaster. Rsp is well-known for being the target of Segregation Distorter (SD)¿ an autosomal meiotic drive system in D. melanogaster. I present an evolutionary genetic analysis of the Rsp family of repeats in D. melanogaster and its closely-related species in the melanogaster group (D. simulans, D. sechellia, D. mauritiana, D. erecta, and D. yakuba) using a combination of available BAC sequences, whole genome shotgun Sanger reads, Illumina short read deep sequencing, and fluorescence in situ hybridization.ResultsI show that Rsp repeats have euchromatic locations throughout the D. melanogaster genome, that Rsp arrays show evidence for concerted evolution, and that Rsp repeats exist outside of D. melanogaster, in the melanogaster group. The repeats in these species are considerably diverged at the sequence level compared to D. melanogaster, and have a strikingly different genomic distribution, even between closely-related sister taxa.ConclusionsThe genomic organization of the Rsp repeat in the D. melanogaster genome is complex¿it exists of large blocks of tandem repeats in the heterochromatin and small blocks of tandem repeats in the euchromatin. My discovery of heterochromatic Rsp-like sequences outside of D. melanogaster suggests that SD evolved after its target satellite and that the evolution of the Rsp satellite family is highly dynamic over a short evolutionary time scale (<240,000 years).

The organization and evolution of the Responder satellite in species of the Drosophila melanogaster group: dynamic evolution of a target of meiotic drive.

Article	Year
Evolution of genes and genomes on the Drosophila phylogeny. Nature\| PubMed ID: 17994087	2007
Contrasting the efficacy of selection on the X and autosomes in Drosophila. Molecular biology and evolution\| PubMed ID: 18083702	2008
Evolution of protein-coding genes in Drosophila. Trends in genetics : TIG\| PubMed ID: 18249460	2008
Translocation of Y-linked genes to the dot chromosome in Drosophila pseudoobscura. Molecular biology and evolution\| PubMed ID: 20147437	2010
The selfish Segregation Distorter gene complex of Drosophila melanogaster. Genetics\| PubMed ID: 22964836	2012
Surprising differences in the variability of Y chromosomes in African and cosmopolitan populations of Drosophila melanogaster. Genetics\| PubMed ID: 23086221	2013
Recent selection on the Y-to-dot translocation in Drosophila pseudoobscura. Molecular biology and evolution\| PubMed ID: 24390701	2014
The organization and evolution of the Responder satellite in species of the Drosophila melanogaster group: dynamic evolution of a target of meiotic drive. BMC evolutionary biology\| PubMed ID: 25424548	2014

Amanda M. Larracuente

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