Recurrent Deletion and Gene Presence/Absence Polymorphism: Telomere Dynamics Dominate Evolution at the Tip of 3L in<i>Drosophila melanogaster</i>and<i>D. simulans</i>

Kern, Andrew D.; Begun, David J.

doi:10.1534/genetics.107.078345

Cited by 30 publications

(29 citation statements)

References 45 publications

(31 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Significant expansions in gene families involved response to toxins, response to hydrogen peroxide, and olfactory perception were also found in an interspecific study of copy number in the genus Drosophila (Hahn et al 2007). Also notable is a common deletion that was found in the mthl-8 gene, although this may be due to recurrent mutational events (Kern and Begun 2008).…”

Section: Copy-number Variationmentioning

confidence: 81%

Genomic Variation in Natural Populations ofDrosophila melanogaster

et al. 2012

Self Cite

View full text Add to dashboard Cite

This report of independent genome sequences of two natural populations of Drosophila melanogaster (37 from North America and 6 from Africa) provides unique insight into forces shaping genomic polymorphism and divergence. Evidence of interactions between natural selection and genetic linkage is abundant not only in centromere-and telomere-proximal regions, but also throughout the euchromatic arms. Linkage disequilibrium, which decays within 1 kbp, exhibits a strong bias toward coupling of the more frequent alleles and provides a high-resolution map of recombination rate. The juxtaposition of population genetics statistics in small genomic windows with gene structures and chromatin states yields a rich, high-resolution annotation, including the following: (1) 59-and 39-UTRs are enriched for regions of reduced polymorphism relative to lineage-specific divergence; (2) exons overlap with windows of excess relative polymorphism; (3) epigenetic marks associated with active transcription initiation sites overlap with regions of reduced relative polymorphism and relatively reduced estimates of the rate of recombination; (4) the rate of adaptive nonsynonymous fixation increases with the rate of crossing over per base pair; and (5) both duplications and deletions are enriched near origins of replication and their density correlates negatively with the rate of crossing over. Available demographic models of X and autosome descent cannot account for the increased divergence on the X and loss of diversity associated with the out-of-Africa migration. Comparison of the variation among these genomes to variation among genomes from D. simulans suggests that many targets of directional selection are shared between these species. A CCESS to sequenced genomes from natural, outbreeding populations (Begun et al. 2007; Li and Durbin 2011) places our theoretical understanding of the forces that determine patterns of genomic variation within and between taxa in a new empirical light. Alignment of the predictions of classical evolutionary genetic models with richly annotated population genomic survey data is an exciting challenge. Descriptions of the patterns of variation in these first sets of population genomic data can foster efficient sieving of hypotheses and serve as a foundation for the design of subsequent studies. Here we present the description of the genomic sequence assemblies from two collections of natural populations of Drosophila melanogaster. The polymorphism, divergence, and copy-number variation revealed in these data are presented at several scales that all support the hypothesis by Maynard Smith and Haigh (1974) The study of genetic variation in natural populations of D. melanogaster has played an important role in the development of evolutionary theory, largely because of the central role of the species in the advancement of knowledge of genetic inheritance. Our fundamental understanding of the biology of D. melanogaster, as well as the advanced methods and unique resources available for its study, has fuel...

show abstract

Section: Copy-number Variationmentioning

confidence: 81%

Genomic Variation in Natural Populations ofDrosophila melanogaster

et al. 2012

Self Cite

View full text Add to dashboard Cite

show abstract

“…Subtelomeric regions have high levels of gene presence/ absence polymorphism not seen in the adjacent euchromatin. At least some of this structural polymorphism is due to terminal deletions that were subsequently healed by transposition of HeT-A, as shown by early studies of lethal giant larvae (2) near the 2L tip (38) and a recent, more extensive study of the tip of 3L (39).…”

Section: Analyses Of 5′-truncated Elements Suggestmentioning

confidence: 99%

Retrotransposons that maintain chromosome ends

Pardue

DeBaryshe

2011

Proc. Natl. Acad. Sci. U.S.A.

108

View full text Add to dashboard Cite

Reverse transcriptases have shaped genomes in many ways. A remarkable example of this shaping is found on telomeres of the genus Drosophila , where retrotransposons have a vital role in chromosome structure. Drosophila lacks telomerase; instead, three telomere-specific retrotransposons maintain chromosome ends. Repeated transpositions to chromosome ends produce long head to tail arrays of these elements. In both form and function, these arrays are analogous to the arrays of repeats added by telomerase to chromosomes in other organisms. Distantly related Drosophila exhibit this variant mechanism of telomere maintenance, which was established before the separation of extant Drosophila species. Nevertheless, the telomere-specific elements still have the hallmarks that characterize non-long terminal repeat (non-LTR) retrotransposons; they have also acquired characteristics associated with their roles at telomeres. These telomeric retrotransposons have shaped the Drosophila genome, but they have also been shaped by the genome. Here, we discuss ways in which these three telomere-specific retrotransposons have been modified for their roles in Drosophila chromosomes.

show abstract

“…High levels of subtelomere polymorphism are found in many organisms, including vertebrates (Wilkie et al 1991;Bassham et al 1998;Baird et al 2000;Mefford et al 2001), insects (Biessmann et al 1998;Anderson et al 2008;Kern and Begun 2008), plants (Yang et al 2005), and fungi (Naumov et al 1995Naumova et al 1996;Cuomo et al 2007;Kasuga et al 2009). Indeed, genome-wide analyses of polymorphism often point to the subtelomere regions as being the most variable parts of the genome (Kellis et al 2003;Winzeler et al 2003;Cuomo et al 2007;Kasuga et al 2009), suggesting that they are "hotbeds" for the rapid evolution of genes and gene families (Mefford et al 2001;Fan et al 2008;Kern and Begun 2008).…”

mentioning

confidence: 99%

Telomere-Targeted Retrotransposons in the Rice Blast Fungus Magnaporthe oryzae: Agents of Telomere Instability

Starnes¹,

Thornbury

Новикова

et al. 2012

Genetics

View full text Add to dashboard Cite

The fungus Magnaporthe oryzae is a serious pathogen of rice and other grasses. Telomeric restriction fragments in Magnaporthe isolates that infect perennial ryegrass (prg) are hotspots for genomic rearrangement and undergo frequent, spontaneous alterations during fungal culture. The telomeres of rice-infecting isolates are very stable by comparison. Sequencing of chromosome ends from a number of prg-infecting isolates revealed two related non-LTR retrotransposons (M. oryzae Telomeric Retrotransposons or MoTeRs) inserted in the telomere repeats. This contrasts with rice pathogen telomeres that are uninterrupted by other sequences. Genetic evidence indicates that the MoTeR elements are responsible for the observed instability. MoTeRs represent a new family of telomere-targeted transposons whose members are found exclusively in fungi.T ELOMERES are the sequences that form the ends of linear chromosomes and are essential for maintaining the integrity of terminal DNA. In most organisms, the telomeres are composed of tandem arrays of short sequence motifs that are added on to the 39 ends of chromosomes by telomerase-a specialized reverse transcriptase (Greider and Blackburn 1989;Yu et al. 1990). This prevents the loss of DNA that would normally occur as a result of conservative DNA replication. The telomeres are bound by numerous proteins that shelter the terminal sequences from degradation (Garvik et al. 1995;Vodenicharov and Wellinger 2006) and illegitimate recombination (Dubois et al. 2002). Certain Diptera lack telomerase and, instead, their chromosome termini are maintained by different types of repeats (Saiga and Edstrom 1985;Biessmann et al. 1998;. The most striking example is in Drosophila whose telomeres are composed of arrays of non-LTR retrotransposons George et al. 2006), which are capable of transposing to free DNA ends (Traverse and Pardue 1988;Biessmann et al. 1990). The extension of chromosome ends through the addition of transposon sequences not only solves the end-replication problem but also serves to establish a nucleoprotein complex that is essential for protecting the chromosome ends and maintaining telomere homoeostasis (Fanti et al. 1998;Perrini et al. 2004).In many organisms, the telomeres are attached to a specific sequence that is duplicated (although often not perfectly) at many, and sometimes all, chromosome ends. Such sequences, which usually are TG-rich and often contain short tandem repeats, define a distinct distal subtelomere domain (Pryde et al. 1997). In addition to possessing distally located subtelomere domains, several organisms have proximal domains that contain genes and gene families that are also variously dispersed among different chromosome ends (Pryde et al. 1997). High levels of subtelomere polymorphism are found in many organisms, including vertebrates (Wilkie et al. 1991;Bassham et al. 1998;Baird et al. 2000;Mefford et al. 2001), insects (Biessmann et al. 1998Anderson et al. 2008;Kern and Begun 2008), plants (Yang et al. 2005), and fungi (Naumov et al. 1995Na...

show abstract

Recurrent Deletion and Gene Presence/Absence Polymorphism: Telomere Dynamics Dominate Evolution at the Tip of 3L inDrosophila melanogasterandD. simulans

Cited by 30 publications

References 45 publications

Genomic Variation in Natural Populations ofDrosophila melanogaster

Genomic Variation in Natural Populations ofDrosophila melanogaster

Retrotransposons that maintain chromosome ends

Telomere-Targeted Retrotransposons in the Rice Blast Fungus Magnaporthe oryzae: Agents of Telomere Instability

Contact Info

Product

Resources

About