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A Recombinational Portrait of the Drosophila Pseudoobscura Genome

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A Recombinational Portrait of the Drosophila Pseudoobscura Genome Genet. Res., Camb. (2006), 87, pp. 23–31. f 2006 Cambridge University Press 23 doi:10.1017/S0016672306007932 Printed in the United Kingdom A recombinational portrait of the Drosophila pseudoobscura genome DANIEL ORTIZ-BARRIENTOS1,AUDREYS.CHANG1,2 1,2, AND MOHAMED A. F. NOOR * 1 Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA 2 DCMB Group/Biology Department, Box 91000, Duke University, Durham, NC 27708, USA (Received 9 September 2005 and in revised form 2 November 2005) Summary Drosophila pseudoobscura has been intensively studied by evolutionary biologists for over 70 years. The recent publication of the genome sequence not only permits studies of comparative genomics with other dipterans but also opens the door to identifying genes associated with adaptive traits or speciation or testing for the signature of natural selection across the genome. Information on regional rates of recombination, localization of inversion breakpoints distinguishing it from its sibling species D. persimilis, and known polymorphic markers may be useful in such studies. Here, we present a molecular linkage map of four of the five major chromosome arms of D. pseudoobscura. In doing so, we order and orient several sequence contig groups, localize the inversion breakpoints on chromosome 2 to intervals of 200 kilobases, and identify one error in the published sequence assembly. Our results show that regional recombination rates in D. pseudoobscura are much higher than in D. melanogaster and significantly higher even than in D. persimilis. Furthermore, we detect a non-significant positive correlation between recombination rate and published DNA sequence variation. Finally, the online Appendix presents 200 primer sequence pairs for molecular markers that can be used for mapping of quantitative trait loci, of which 125 are known to be polymorphic within or between species. 1. Introduction 1936; Tan, 1946; Orr, 1987; Noor et al., 2001a, b; Orr & Irving, 2001). The fruit fly Drosophila pseudoobscura is one of the Much of the progress in studying adaptation and most intensively studied model systems for under- speciation in D. pseudoobscura came from genetic standing adaptation and speciation. This species is mapping studies that employed either morphological perhaps best known for its rich inversion poly- mutant markers or a moderate number of micro- morphism on the third chromosome. Third chromo- satellite markers. The recent availability of the some arrangements bear striking longitudinal clines D. pseudoobscura genome sequence (Richards et al., across the species range and are associated with life- 2005) provides an opportunity for developing a higher history traits such as fecundity (e.g. Anderson et al., resolution molecular linkage map of the species. Such 1991). Cline frequencies are maintained despite a linkage map can facilitate a variety of genetic and apparently extensive gene flow among populations evolutionary efforts, including high-resolution map- (Prakash et al., 1969; Schaeffer & Miller, 1992; Noor ping of quantitative trait loci (QTL) and comparisons et al., 2000), suggesting that natural selection operates of regional recombination rate and variation. on these inversions. This species has also been studied Several recombination maps are currently available extensively with respect to the genetic basis of for D. pseudoobscura. Anderson (1993) provided an traits associated with reproductive isolation, such as early linkage map based on 63 morphological markers hybrid sterility and sexual isolation (Dobzhansky, and allozymes across the genome, Orr (1995) ident- ified linkage relationships for 23 morphological * Corresponding author. Tel: +1 (919) 6138156. Fax: +1 (919) 6138177. e-mail: [email protected] markers on the X chromosome, and Noor et al. (2000) Downloaded from https://www.cambridge.org/core. IP address: 170.106.35.234, on 27 Sep 2021 at 21:51:03, subject to the Cambridge Core terms of use, available at https://www.cambridge.org/core/terms. https://doi.org/10.1017/S0016672306007932 D. Ortiz-Barrientos et al. 24 created a molecular map using 24 microsatellite Lines of D. persimilis were established from flies markers. Although these maps have advanced our collected in Mt St Helena, California, in 1993 (line knowledge of the adaptive history of D. pseudo- MSH1993) and 1997 (line MSH3), both of which bear obscura and of speciation between D. pseudoobscura the ‘Standard’ arrangement on the third chromo- and its sister species, new genetic maps incorporating some. All lines were maintained at a constant many more molecular markers can facilitate high- temperature (20 xC) and humidity (85%) regime in resolution genome scans to compare with the physical diurnal/nocturnal cycles of 12 h and reared on a sequence map, potentially allowing mapping of mixture of agar, dextrose and yeast. phenotype to single genes. Here, we provide a dense recombination map and information on regional rates of recombination for (ii) Recombinational maps four of five D. pseudoobscura chromosome arms. (a) Pure species linkage maps We use our linkage data to order several of the unassembled contig groups in this sequenced genome, Recombination maps were obtained by estimating and to localize some of the inversion breakpoints recombination fractions in F2 backcross populations distinguishing D. pseudoobscura and its sister species between species-specific isofemale lines. Each parental D. persimilis. We also present preliminary infor- line was tested for allelic differences in microsatellite mation on recombination rates across the second loci previously published (Noor et al., 2000) or chromosome of D. persimilis and compare them with extracted from the D. pseudoobscura genome those from D. pseudoobscura. Using this data, we test sequence (Richards et al., 2005), and scored for dif- for an association between recombination rate and ferences in amplification size of the microsatellite DNA sequence variation, and refine an earlier esti- markers. The D. pseudoobscura map was made by mate of the effective population size of D. pseudo- backcrossing F1 females of the cross between two lines obscura. Finally, we present primer sequences for 200 to the Flagstaff 1993 line (see Ortı´z-Barrientos et al., microsatellite or other size markers, of which 125 2004). The D. persimilis map was made by back- have been shown to be variable within or between crossing F1 females of the cross between two lines to D. pseudoobscura and/or D. persimilis. In conjunction the MSH1993 line. We used polytene chromosome with the genome sequence of D. pseudoobscura, our preparations of F1 progeny to confirm that these markers and map will facilitate population genomic strains also bear the same third chromosome analysis, aid in the identification of genes involved arrangement as each other. in adaptation and speciation via QTL mapping, and For each species, approximately 275 flies were ultimately help us to understand the evolutionary genotyped for such microsatellites (see online forces acting on this species and its close relatives. Appendix) and a multipoint-linkage approach, as implemented in MapMaker version 3.0 (Lander et al., 1987), was used to generate recombination maps for 2. Materials and methods the X, 2 and 4 chromosomes from D. pseudoobscura, and the second chromosome of D. persimilis.We (i) Species, lines and rearing conditions do not investigate the third chromosome despite Drosophila pseudoobscura and D. persimilis are close its complete assembly because analyses of it would relatives that hybridize in nature (Dobzhansky, 1973; be complicated by the inversion polymorphisms Powell, 1983), and some studies have suggested that within these species. Recombinational distances introgression occurs between these species primarily are reported in Kosambi centimorgans (cM), and in collinear regions of their genome (Machado et al., recombination rates in kilobases per centimorgan 2002; Machado & Hey, 2003; Hey & Nielsen, 2004). (kb/cM). These species have six chromosome arms: two on the Primer sequences for markers not used in the X chromosome (designated XL and XR), three large development of this linkage map are also presented independent autosomes (numbered 2–4), and a ‘dot’ here. Some have been used in other studies by our fifth chromosome which is not studied here. The laboratory, and the online Appendix indicates which species differ by fixed or nearly fixed inversions on are known to show intra- or interspecific variability. the XL, XR and chromosome 2 arms. The third Also, where indicated just for confirmation, some chromosome is highly polymorphic within both markers were scored on a subset of backcross progeny species, and they share one abundant arrangement rather than the full 275. (designated ‘Standard’). Lines of D. pseudoobscura were established from (b) Backcross hybrid linkage maps individuals collected at Mather, California, in 1997 and Flagstaff, Arizona, in 1993, both of which bear the Recombination maps from two interspecific back- ‘Arrowhead’ arrangement on the third chromosome. crosses between D. pseudoobscura and D. persimilis Downloaded from https://www.cambridge.org/core. IP address: 170.106.35.234, on 27 Sep 2021 at 21:51:03, subject to the Cambridge Core terms of use, available at https://www.cambridge.org/core/terms. https://doi.org/10.1017/S0016672306007932 A recombinational portrait of the D. pseudoobscura genome 25 were also analysed. These backcrosses have been Table 1. Linkage map of the Drosophila described previously (Noor et al., 2001a)
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