Comparative Maps of Human 19p13.3 and Mouse Chromosome 10 Allow Identification of Sequences at Evolutionary Breakpoints

Puttagunta, Radhika; Gordon, Laurie; Meyer, Gary; Kaufholdt, David; Lamerdin, Jane E.; Kantheti, Prameela; Portman, Kathleen M.; Chung, Wendy K.; Jenne, Dieter E.; Olsen, Anne S.; Burmeister, Margit

doi:10.1101/gr.145200

Cited by 34 publications

(19 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…There is evidence of at least 3170 microrearrangements (reversals) that happened within the synteny blocks (although many of them may be artifacts of incorrect assemblies). This very high estimate of the number of microrearrangements further confirms the conjecture that microrearrangements are more common than previously thought (Carver and Stubbs 1997;Puttagunta et al 2000;Thomas et al 2000;Kumar et al 2001). In fact, this number does not even include the microrearrangements within synteny blocks shorter than 1 Mb.…”

Section: Synteny Blockssupporting

confidence: 85%

Genome Rearrangements in Mammalian Evolution: Lessons From Human and Mouse Genomes

Pevzner

Tesler²

2002

Genome Res.

315

299

View full text Add to dashboard Cite

Although analysis of genome rearrangements was pioneered by Dobzhansky and Sturtevant 65 years ago, we still know very little about the rearrangement events that produced the existing varieties of genomic architectures. The genomic sequences of human and mouse provide evidence for a larger number of rearrangements than previously thought and shed some light on previously unknown features of mammalian evolution. In particular, they reveal that a large number of microrearrangements is required to explain the differences in draft human and mouse sequences. Here we describe a new algorithm for constructing synteny blocks, study arrangements of synteny blocks in human and mouse, derive a most parsimonious human-mouse rearrangement scenario, and provide evidence that intrachromosomal rearrangements are more frequent than interchromosomal rearrangements. Our analysis is based on the human-mouse breakpoint graph, which reveals related breakpoints and allows one to find a most parsimonious scenario. Because these graphs provide important insights into rearrangement scenarios, we introduce a new visualization tool that allows one to view breakpoint graphs superimposed with genomic dot-plots.[Supplemental material is available online at www.genome.org.]Analysis of genome rearrangements in molecular evolution was pioneered by Dobzhansky and Sturtevant (1938), who published a milestone paper with an evolutionary tree presenting a rearrangement scenario with 17 inversions for the species Drosophila pseudoobscura and Drosophila miranda. Every genome rearrangement study involves solving a combinatorial puzzle to find a series of genome rearrangements to transform one genome into another. Palmer and co-authors (Palmer and Herbon 1988) pioneered studies of the shortest (most parsimonious) rearrangement scenarios and applied this approach to plant mtDNA and cpDNA. Since then, the analysis of the most parsimonious scenarios has become the dominant approach in genome rearrangement studies. For unichromosomal genomes, it usually amounts to analysis of inversions (also known as reversals), which are the most common rearrangement events. The problem of finding the minimum number of reversals to transform one unichromosomal genome into another is known as the "reversal distance problem." For multichromosomal genomes, the most common rearrangements are reversals, translocations, fusions, and fissions, and the number of such rearrangements in a most parsimonious scenario is known as the "genomic distance" between multichromosomal genomes.Finding the reversal distance is a difficult combinatorial problem. In the very first computational studies of genome rearrangements, Watterson et al. (1982) and Nadeau and Taylor (1984) introduced the notion of a breakpoint (disruption of gene order) and noticed some correlations between the reversal distance and the number of breakpoints (in fact, Sturtevant and Dobzhansky [1936] implicitly discussed these correlations 65 years ago!). The shortcoming of early genome rearrangement studies is that they co...

show abstract

Section: Synteny Blockssupporting

confidence: 85%

Genome Rearrangements in Mammalian Evolution: Lessons From Human and Mouse Genomes

Pevzner

Tesler²

2002

Genome Res.

315

299

View full text Add to dashboard Cite

show abstract

“…Multiple evolutionary breakpoints between the human and mouse genomes have been examined at the sequence level (Lund et al 2000;Dehal et al 2001;Puttagunta et al 2000). In many cases, these breakpoint sequences were found to be enriched for simple-sequence repeats and L1 repetitive elements or associated with clustered gene families, gene family expansions, and more limited gene duplications.…”

Section: Discussionmentioning

confidence: 99%

Pericentromeric Duplications in the Laboratory Mouse

et al. 2002

View full text Add to dashboard Cite

Duplications have long been postulated to be an important mechanism by which genomes evolve. Interspecies genomic comparisons are one method by which the origin and molecular mechanism of duplications can be inferred. By comparative mapping in human, mouse, and rat, we previously found evidence for a recent chromosome-fission event that occurred in the mouse lineage. Cytogenetic mapping revealed that the genomic segments flanking the fission site appeared to be duplicated, with copies residing near the centromere of multiple mouse chromosomes. Here we report the mapping and sequencing of the regions of mouse chromosomes 5 and 6 involved in this chromosome-fission event as well as the results of comparative sequence analysis with the orthologous human and rat genomic regions. Our data indicate that the duplications associated with mouse chromosomes 5 and 6 are recent and that the resulting duplicated segments share significant sequence similarity with a series of regions near the centromeres of the mouse chromosomes previously identified by cytogenetic mapping. We also identified pericentromeric duplicated segments shared between mouse chromosomes 5 and 1. Finally, novel mouse satellite sequences as well as putative chimeric transcripts were found to be associated with the duplicated segments. Together, these findings demonstrate that pericentromeric duplications are not restricted to primates and may be a common mechanism for genome evolution in mammals.

show abstract

“…Studies by Puttagunta et al (2000) and Pletcher et al (2000) on evolutionary breakpoints in mouse chromosome 10 showed an association with a region of very high (60%-70%) repeated sequence content and Dehal et al (2001) found a concentration of LINEs and LTR elements at evolutionary breakpoints. Consideration of the gross distribution of repeated elements, including simple repeats, and base composition in segment 5 (the breakpoint region) as a whole compared with the rest of the Del36H sequence, showed no apparent associations.…”

Section: Sites Of Evolutionary Rearrangementmentioning

confidence: 95%

“…The accumulating information on genome sequences from a number of species raises many questions about genome evolution. Important among these are the relative roles of whole-genome, segmental, and individual gene duplication, and the mechanisms underlying these processes (Lynch and Conery 2000; Dehal et al 2001;Eichler and Sankoff 2003;Friedman and Hughes 2004); the usefulness of inter-genome comparisons for identifying selectively conserved regions in genomes, including not only genes, but regulatory regions and functional RNA genes (Mallon et al 2000;Dehal et al 2001;Dermitzakis et al 2002;Kondrashov and Shabalina 2002;Margulies et al 2003;Frazer et al 2004); the roles of repeated (transposable element-like) and repetitive (satellites, microsatellites, and minisatellites) sequences in genome evolution (Toth et al 2000;Hancock 2002;Babcock et al 2003;Alba and Guigo 2004;Han et al 2004;Kazazian Jr. 2004); and the characteristics of sites of evolutionary chromosome breakpoints (Puttagunta et al 2000;Dehal et al 2001;Pevzner and Tesler 2003).…”

mentioning

confidence: 99%

Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse

Mallon¹,

Wilming²,

Weekes³

et al. 2004

Genome Res.

View full text Add to dashboard Cite

Del(13)Svea36H (Del36H) is a deletion of ∼20% of mouse chromosome 13 showing conserved synteny with human chromosome 6p22.1-6p22.3/6p25. The human region is lost in some deletion syndromes and is the site of several disease loci. Heterozygous Del36H mice show numerous phenotypes and may model aspects of human genetic disease. We describe 12.7 Mb of finished, annotated sequence from Del36H. Del36H has a higher gene density than the draft mouse genome, reflecting high local densities of three gene families (vomeronasal receptors, serpins, and prolactins) which are greatly expanded relative to human. Transposable elements are concentrated near these gene families. We therefore suggest that their neighborhoods are gene factories, regions of frequent recombination in which gene duplication is more frequent. The gene families show different proportions of pseudogenes, likely reflecting different strengths of purifying selection and/or gene conversion. They are also associated with relatively low simple sequence concentrations, which vary across the region with a periodicity of ∼5 Mb. Del36H contains numerous evolutionarily conserved regions (ECRs). Many lie in noncoding regions, are detectable in species as distant as Ciona intestinalis, and therefore are candidate regulatory sequences. This analysis will facilitate functional genomic analysis of Del36H and provides insights into mouse genome evolution.

show abstract

Comparative Maps of Human 19p13.3 and Mouse Chromosome 10 Allow Identification of Sequences at Evolutionary Breakpoints

Cited by 34 publications

References 48 publications

Genome Rearrangements in Mammalian Evolution: Lessons From Human and Mouse Genomes

Genome Rearrangements in Mammalian Evolution: Lessons From Human and Mouse Genomes

Pericentromeric Duplications in the Laboratory Mouse

Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse

Contact Info

Product

Resources

About