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Principles of Genome Evolution in the Drosophila Melanogaster Species Group

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Principles of Genome Evolution in the Drosophila Melanogaster Species Group PLoS BIOLOGY Principles of Genome Evolution in the Drosophila melanogaster Species Group Jose´ M. Ranz1*, Damien Maurin1¤a, Yuk S. Chan1, Marcin von Grotthuss1, LaDeana W. Hillier2, John Roote1, Michael Ashburner1, Casey M. Bergman1¤b 1 Department of Genetics, University of Cambridge, Cambridge, United Kingdom, 2 Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri, United States of America That closely related species often differ by chromosomal inversions was discovered by Sturtevant and Plunkett in 1926. Our knowledge of how these inversions originate is still very limited, although a prevailing view is that they are facilitated by ectopic recombination events between inverted repetitive sequences. The availability of genome sequences of related species now allows us to study in detail the mechanisms that generate interspecific inversions. We have analyzed the breakpoint regions of the 29 inversions that differentiate the chromosomes of Drosophila melanogaster and two closely related species, D. simulans and D. yakuba, and reconstructed the molecular events that underlie their origin. Experimental and computational analysis revealed that the breakpoint regions of 59% of the inversions (17/29) are associated with inverted duplications of genes or other nonrepetitive sequences. In only two cases do we find evidence for inverted repetitive sequences in inversion breakpoints. We propose that the presence of inverted duplications associated with inversion breakpoint regions is the result of staggered breaks, either isochromatid or chromatid, and that this, rather than ectopic exchange between inverted repetitive sequences, is the prevalent mechanism for the generation of inversions in the melanogaster species group. Outgroup analysis also revealed evidence for widespread breakpoint recycling. Lastly, we have found that expression domains in D. melanogaster may be disrupted in D. yakuba, bringing into question their potential adaptive significance. Citation: Ranz JM, Maurin D, Chan YS, von Grotthuss M, Hillier LW, et al. (2007) Principles of genome evolution in the Drosophila melanogaster species group. PLoS Biol 5(6): e152. doi:10.1371/journal.pbio.0050152 Introduction regions conserved during the process of adaptation and divergence [31,32]. ‘‘Eventually the story of the chromosomal mechanisms and The genus Drosophila has long been a model for cytogenetic its evolution will have to be entirely rewritten in molecular studies of genome evolution. Charles Metz’s pioneering terms’’ [1]. comparative studies of metaphase karyotypes in the genus Over the last century, very detailed studies have been made [33], combined with subsequent comparative genetic studies, by cytogeneticists of the intra- and interchromosomal led Muller [34] to conclude that the integrity of chromosome changes that characterize genome evolution in groups as arms is largely preserved in the genus Drosophila, despite a 2- different as mammals (e.g., [2]) and flies (e.g., [3]; see [1,4] for fold variation in haploid chromosome number (see also [35]). reviews). Chromosome rearrangements are thought to play an The maintenance of the gene content of chromosomal arms is important role in reproductive isolation between species [5– due to the paucity of inter-arm rearrangements (i.e., 7] and in the adaptation of species to their environments [8– pericentric inversions and translocations) ([36,37]; see [38] 10]. These rearrangements may affect fitness by effectively for why this is so). Sturtevant and Dobzhansky [39] first reducing recombination in heterozygotes, thereby preserving showed how chromosome inversions can be used to study the co-adapted gene complexes [11,12], or by exerting position evolutionary history of a species group, such as has been effects on loci neighboring breakpoints by modifying gene shown subsequently in the case of the endemic Hawaiian expression [13]. Only now, with the availability of ‘‘complete’’ genome sequences, can these structural changes in genomes be studied in the molecular detail, as foreseen by Michael Academic Editor: Mohamed A. F. Noor, Duke University, United States of America White [1] over 30 years ago (e.g., [14–16]). Received October 20, 2006; Accepted April 2, 2007; Published June 5, 2007 Genomic sequence data are beginning to reveal a remark- Copyright: Ó 2007 Ranz et al. This is an open-access article distributed under the able diversity of patterns of genome rearrangement in terms of the Creative Commons Attribution License, which permits unrestricted different taxa ([17–21]; reviewed in [22]). For example, we use, distribution, and reproduction in any medium, provided the original author and source are credited. seeevidencefortherecurrent presence of repetitive sequences near breakpoints [23–25] and evidence for the Abbreviations: BAC, bacterial artificial chromosome; bp, base pair; kb, kilobase; Mb, megabase; Myr, million years; TE, transposable element; UCSC, the University nonrandom distribution of genome breakpoints [16,26,27]. of California, Santa Cruz Moreover, there is evidence that large-scale gene expression * To whom correspondence should be addressed. E-mail: [email protected]. domains are maintained as syntenic regions, perhaps because ac.uk of a functional co-dependency of the genes that reside in ¤a Current address: Laboratory of Enzymology at Interfaces and Physiology of these domains [20,28,29]. Comparative genomic data allow us Lipolysis, CNRS, UPR 9025, Marseille, France to reconstruct the state of ancestral genome arrangements at ¤b Current address: Faculty of Life Sciences, University of Manchester, Manchester, key phylogenetic nodes [17,30] and to identify genomic United Kingdom PLoS Biology | www.plosbiology.org1366 June 2007 | Volume 5 | Issue 6 | e152 Genome Rearrangement in Drosophila Author Summary point regions of other chromosomal rearrangements recently characterized [49,51,57]. One of the breakpoint regions The organization of genes on chromosomes changes over evolu- associated with this inversion overlaps that of another tionary time. In some organisms, such as fruit flies and mosquitoes, inversion that took place on the lineage to D. yakuba, inversions of chromosome regions are widespread. This has been suggesting that some genomic regions are repeatedly broken associated with adaptation to environmental pressures and over time. By a large-scale comparison of the molecular speciation. However, the mechanisms by which inversions are organization of the genomes of D. melanogaster and D. yakuba, generated at the molecular level are poorly understood. The we asked if the features associated with inversion prevailing view involves the interactions of sequences that are moderately repeated in the genome. Here, we use molecular and In(3R)84F1;93F6–7 reflect a recurrent pattern of genome computational methods to study 29 inversions that differentiate the rearrangement in the melanogaster species subgroup. chromosomes of three closely related fruit fly species. We find little We found that approximately 59% (17/29) of the inversions support for a causal role of repetitive sequences in the origin of fixed between D. melanogaster and D. yakuba show evidence of inversions and, instead, detect the presence of inverted duplications inverted duplication of protein-coding genes or other non- of ancestrally unique sequences (generally protein-coding genes) in repetitive sequences present at the breakpoint regions. The the breakpoint regions of many inversions. This leads us to propose prevalence of inverted duplications at inversion breakpoint an alternative model in which the generation of inversions is regions suggests a mechanism of staggered breaks, either coupled with the generation of duplications of flanking sequences. isochromatid or chromatid, as the most parsimonious Additionally, we find evidence for genomic regions that are prone to breakage, being associated with inversions generated independ- explanation for their origin. Computational analyses failed ently during the evolution of the ancestors of existing species. to find support for the generalized presence of dispersed, repetitive sequences in co-occurrent breakpoint regions, i.e., those that set the limits of a particular inversion. We conclude that the generation of chromosomal rearrange- picture-winged group [3] or in the cactophilic repleta species ments in the lineages studied is not necessarily linked to group of the Americas [40]. Drosophila is a species-rich ectopic recombination events between repetitive sequences. genus—about 1,500 species have been described [41]—and We also find evidence for the independent breakage of the has an evolutionary history of perhaps over 120 million years same genomic region in different lineages, i.e., fragile regions (Myr; Figure S1; [42]). The wealth of information on genome [16,25–27], and in one case, we are able, for the first time in rearrangement in the genus Drosophila can now be studied at Diptera, to reconstruct the reuse of a breakpoint region. the molecular level, using the genome sequences of 12 different species of Drosophila that are available (http://rana. lbl.gov/drosophila/). Hitherto, the breakpoint regions of ten Results/Discussion well-defined inversions have been characterized in Diptera: Experimental and Computational Analysis of Inversion eight in Drosophila [25,43–49], and two in Anopheles [50,51]. In(3R)84F1;93F6–7 Fixed between D. melanogaster and Here we investigate the genome-wide patterns of rearrange- Species of the simulans Clade
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