Toward a Physical Map of Drosophila buzzatii: Use of Randomly Amplified Polymorphic DNA Polymorphisms and Sequence-Tagged Site Landmarks

Corresponding author: Mauro Santos, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Facultat de Ciències, Edifici Cn, 08193 Bellaterra (Barcelona), Spain., m.santos{at}cc.uab.es (E-mail)

Communicating editor: L. PARTRIDGE

	ABSTRACT

TOP ABSTRACT MATERIALS AND METHODS RESULTS AND DISCUSSION LITERATURE CITED

We present a physical map based on RAPD polymorphic fragments and sequence-tagged sites (STSs) for the repleta group species Drosophila buzzatii. One hundred forty-four RAPD markers have been used as probes for in situ hybridization to the polytene chromosomes, and positive results allowing the precise localization of 108 RAPDs were obtained. Of these, 73 behave as effectively unique markers for physical map construction, and in 9 additional cases the probes gave two hybridization signals, each on a different chromosome. Most markers (68%) are located on chromosomes 2 and 4, which partially agree with previous estimates on the distribution of genetic variation over chromosomes. One RAPD maps close to the proximal breakpoint of inversion 2z³ but is not included within the inverted fragment. However, it was possible to conclude from this RAPD that the distal breakpoint of 2z³ had previously been wrongly assigned. A total of 39 cytologically mapped RAPDs were converted to STSs and yielded an aggregate sequence of 28,431 bp. Thirty-six RAPDs (25%) did not produce any detectable hybridization signal, and we obtained the DNA sequence from three of them. Further prospects toward obtaining a more developed genetic map than the one currently available for D. buzzatii are discussed.

A common tenet in evolutionary biology is that an ultimate understanding of evolution by natural selection requires an integrated approach from genetics and ecology. Unfortunately, there seems to be an increasing gap between our current knowledge from very well-studied genomes and the ecological scenarios where these genomes have evolved. As a noteworthy example, compare the massive amount of information in recent releases of the FlyBase (FLYBASE CONSORTIUM 1999 )—the comprehensive database for the fruitfly—with the number of entries for Drosophila in ENDLER's (1986, pp. 129–153) broad review of direct demonstrations of selection on naturally occurring genetic variation: just one for Drosophila buzzatii and two for D. melanogaster! Because of this empirical restriction, we need a reasonable model where both approaches to understanding evolution can be successfully combined.

Perhaps the best-characterized ecology of any Drosophila group is for the repleta group species, and we agree with POWELL 1997 (p. 149) in that "anyone looking for a system to connect ecology with genetics would do well to consider the repleta group." Particularly, D. buzzatii provides a valuable model system for studies in natural populations and evolutionary genetics. Thus, this species is restricted to the cactus niche, feeding and breeding in rotting tissues, but has a worldwide distribution (CARSON and WASSERMAN 1965 ; BARKER 1977 ; FONTDEVILA et al. 1981 , FONTDEVILA et al. 1982 ; HAOUAS et al. 1984 ). A substantial number of articles in ecological genetics (e.g., BARKER and EAST 1980 ; BARKER 1982 ; SANTOS et al. 1989 ; THOMAS and BARKER 1990 ; QUEZADA-DIAZ et al. 1992 ; SANTOS 1994 ), life-history evolution (RUIZ et al. 1986 ; HASSON et al. 1991 ; SANTOS et al. 1992 ; BARBADILLA et al. 1994 ; BETRAN et al. 1998 ), quantitative genetics (PROUT and BARKER 1989 ; RUIZ et al. 1991 ; THOMAS and BARKER 1993 ; LEIBOWITZ et al. 1995 ; SANTOS 1996 ), thermal adaptation (KREBS and LOESCHCKE 1996 , KREBS and LOESCHCKE 1997 , KREBS and LOESCHCKE 1999 ; IMASHEVA et al. 1997 ), colonization (FONTDEVILA et al. 1981 , FONTDEVILA et al. 1982 ; HALLIBURTON and BARKER 1993 ; ROSSI et al. 1996 ), and speciation (NAVEIRA and FONTDEVILA 1986 ; NAVEIRA and FONTDEVILA 1991A , NAVEIRA and FONTDEVILA 1991B ) have focused on D. buzzatii. Conversely to D. melanogaster, this wealthy state of affairs markedly contrasts with a paucity of molecular markers in D. buzzatii, still restricted to a few allozymes (SCHAFER et al. 1993 ; BETRAN et al. 1995 ). [A molecular marker is defined here as "any genetic variant that allows scoring of conspecific individuals at the molecular level." This is a somewhat narrower definition than that provided by KING and STANSFIELD 1997 for a genetic marker, but is operationally and implicitly used in evolutionary biology (AVISE 1994 ) and quantitative genetics (LYNCH and WALSH 1998 ).]

To overcome this deficiency, here we present the first extensive effort to map by in situ hybridization to the polytene chromosomes of D. buzzatii a large number (144) of reproducible randomly amplified polymorphic DNA (RAPD; WELSH and MCCLELLAND 1990 ; WILLIAMS et al. 1990 ) markers. RAPDs have been successfully applied to the construction of linkage maps in a variety of organisms (e.g., REITER et al. 1992 ; POSTLETHWAIT et al. 1994 ; HUNT and PAGE 1995 ; DIMOPOULOS et al. 1996 ) and are becoming a frequently used tool in population and evolutionary genetics (SMITH et al. 1994 ; DE ZANDE and BIJLSMA 1995 ; APOSTOL et al. 1996 ; ESPINASA and BOROWSKY 1998 ).

In addition to convenience for recombination mapping, RAPDs can provide sequence-tagged sites (STSs; OLSON et al. 1989 ) that serve as physical entry points to the genome. STSs can also be a rich source for detecting previously undescribed potential genes even in very well-studied genomes (LOUIS et al. 1997 ). We therefore have determined 39 STS landmarks from cloned RAPD sequences, and all sequences were checked against both nucleic acid and protein databases for potential matches. These STSs also allow us to roughly estimate the overall base composition of the D. buzzatii genome. The physical map obtained comprises a total of 73 effectively unique RAPD markers (39 of these are STSs), together with 9 RAPDs that gave two hybridization signals, each on a different chromosome. The results obtained from the combined use of different techniques allow the first comprehensive approach to the genome of D. buzzatii. We hope the information provided here will be an important tool for further development of a reasonably saturated genetic map in this species.

	MATERIALS AND METHODS

TOP ABSTRACT MATERIALS AND METHODS RESULTS AND DISCUSSION LITERATURE CITED

Fly material:
D. buzzatii flies were collected from a natural population in an abandoned Opuntia ficus-indica plantation at Carboneras on the Mediterranean coast of Spain (Almería; 37° N, 1° 9' W; see RUIZ et al. 1986 for details). Between the 10th and 12th of September 1993, 36 rotting Opuntia cladodes were collected, placed individually in transparent plastic containers on a bed of sand, closed with a fine-meshed fabric, and kept at room temperature (22–27°) in the makeshift laboratory near the field site. From the adult flies that emerged from 28 rots, a high number of isofemale strains were established by pairwise mating in vials (2 x 8 cm, with 5 ml of food) of virgin females and males. The isofemale strains were maintained at 23° by one single brother-sister mating for the first 18 generations and full-sib matings (4–8 mating pairs per vial) thereafter and passed through a minimum of 36 generations before RAPD screening. Therefore, the probability that a neutral allele was still segregating in any particular isofemale strain is practically negligible (see, e.g., GALE 1990 ). The population at Carboneras is polymorphic for the two common cosmopolitan 2st and 2j and for the two rare cosmopolitan 2jz³ and 2jq⁷, second-chromosome arrangements, as well as for the rare cosmopolitan 4st and 4s (FONTDEVILA et al. 1981 ; for a description see RUIZ et al. 1984 ).

DNA isolation:
DNA was isolated from individual males from each isofemale strain. The following protocol is a modification of that described in LATORRE et al. 1986 . Each fly was homogenized in a 1.5-ml microcentrifuge tube containing 160 µl of 10 mM Tris/60 mM NaCl/5% (wt/vol) sucrose/10 mM EDTA, pH 7.8. One hundred microliters of 1.25% SDS/300 mM Tris/5% sucrose/10 mM EDTA, pH 9, were then added. The mixture was incubated at 65° for 30 min, after which 60 µl of 5 M potassium acetate was added and the mixture was kept at -20° for 20 min. After centrifugation for 15 min in an Eppendorf centrifuge, the supernatant was added to 1 volume of 2-propanol and left standing at room temperature for 5 min, which was followed by a 10-min Eppendorf centrifugation. The pellet was washed with 70% ethanol. Residual ethanol was removed by drying the precipitate in a desiccator for 5 min, after which the DNA was resuspended in 100 µl of sterile distilled water.

DNA amplifications:
A set of 78 random decamer oligonucleotides purchased from Genosys Biotechnologies Inc. (Cambridge, UK) and 5 from Operon Technologies Inc. (Alameda, CA) were used as single primers for the amplification of RAPD sequences. Primers are listed in Table 1 as designated by the suppliers.

The conditions reported by WILLIAMS et al. 1990 for creating RAPD markers by PCR were optimized for use with D. buzzatii template DNA. All reaction volumes were 25 µl, overlayered with 50 µl of light mineral oil (Sigma Chemical Co., St. Louis). Each reaction consisted of 1x activity buffer (GIBCO BRL, Gaithersburg, MD), 1.6 mM MgCl₂, 200 µM of each dNTP (Boehringer Mannheim, Indianapolis), 400 nM primer, template DNA (30–40 ng), and 0.8 units of Taq polymerase (GIBCO BRL). Only one primer and one genomic DNA sample were added to any single reaction. Amplification was achieved in an MJ Research Inc. (Watertown, MA) thermocycler programmed as follows: a preliminary 5-min denaturation at 94°; 45 cycles of 30 sec at 94° (denaturation), 1 min at 35° (anneal), and 1 min at 72° (extension); and a final extension at 72° for 5 min followed by storage at 4°. Electrophoresis was performed in 1.4% agarose gels (SeaKem) with Tris-HCl acetate/EDTA (TAE) buffer for 5 hr at 70 V, constant voltage. Reaction products were analyzed alongside small molecular weight marker VI (Boehringer Mannheim). Ethidium bromide-stained gels (0.5 µg/ml) were visualized on a UV transilluminator and photographed with a Polaroid camera or digitalized with a Bio-Print image management system. After testing for polymorphism and reproducibility (see below), the RAPD bands chosen as probes were gel purified, reamplified using the same decameric primer that identified the RAPD polymorphism, and labeled for in situ hybridization.

Polytene chromosome preparation and in situ hybridization:
Probes (300 ng–1 µg DNA) were labeled with digoxygenin-11-dUTP by the random primer method using the Boehringer Mannheim labeling kit, and the total yield from the labeling reaction (500 ng–2 µg) was quantified according to the instructions supplied by the manufacturer. Third instar larvae were grown at low densities at 18° in a modified version of David's killed-yeast culture medium (DAVID 1962 ). Salivary gland chromosomes suitable for in situ hybridization were prepared according to LABRADOR et al. 1990 . Prehybridization, hybridization, and detection were carried out as described by DE FRUTOS et al. 1989 . Hybridization temperature was 37°. Chromosomes were observed by phase contrast with a Zeiss Axioscope photomicroscope at x400 magnification and digitalized with a Bio-Print image management system.

Chromosome mapping:
The karyotype of most repleta species, including D. buzzatii, consists of five telocentric chromosomes (1 = X, 2, 3, 4, 5) and a dot (6) chromosome (WASSERMAN 1992 ). Hybridization signals were localized on the polytene chromosomes using the D. repleta (WHARTON 1942 ) and D. buzzatii (RUIZ et al. 1982 ; RUIZ and WASSERMAN 1993 ) cytological maps. The maps of D. buzzatii are cut-and-paste reconstructions of the D. repleta map according to the sequence of inversions proposed for their respective phylogenies. The molecular organizations of Mueller/Sturtevant/Novitski chromosomal elements D (= 4) and E (= 2) in D. repleta and D. buzzatii (see POWELL 1997 , p. 307—but note that exact correspondence of chromosomal arms in D. hydei is misplaced and readers should refer to LOUKAS and KAFATOS 1986 for exact homologies) has been compared recently by in situ hybridization (RANZ et al. 1997 ). Within the limits of potential resolution, RANZ et al. 1997 concluded that the formerly proposed cytogenetic relationships between both species seem to be consistent with the new results.

DNA sequencing:
Thirty-nine single-signal RAPD markers (see below) were converted to STSs (OLSON et al. 1989 ). Gel-purified RAPD fragments (10–100 ng) were directly cloned into pGEM-T Vector (Promega, Madison, WI). DNA mini-preparations were made from positive clones of transformed JM109 Escherichia coli cells. The DNA sequences were determined by the dideoxy method (SANGER et al. 1977 ) using an ALF sequencer (Pharmacia Biotech, Piscataway, NJ). Nucleotide sequences were determined on both DNA strands and included 80 nucleotides of the T vector flanking the cloning site.

Nucleic acid searches were performed using the BLAST program (ALTSCHUL et al. 1997 ). BLASTN was used to search the nucleic acid database, BLASTX to search the protein database with the putative translations of the STSs in all six frames, and ORF Finder program to look for potential open reading frames (ORFs). Alignments were also obtained using the default option of the program CLUSTAL W (version 1.6) (THOMPSON et al. 1994 ).

	RESULTS AND DISCUSSION

TOP ABSTRACT MATERIALS AND METHODS RESULTS AND DISCUSSION LITERATURE CITED

RAPD products and RAPD product profiles:
Forty-four random decamer oligonucleotides (Table 1) yielded reproducible and polymorphic DNA fragments. A fragment was considered polymorphic when absent in at least 1 individual out of 14 from different (i.e., independent) isofemale strains, i.e., when the recessive (absence) allele was at an average frequency of at least 7% in the natural population (a more restrictive criterion than the standard 5 or 1% used in population genetics; see, e.g., HEDRICK 1985 ). Repeating the amplification using a set of five or more individuals that had rendered polymorphic bands tested the reproducibility of the different profiles. A particular band was considered as reproducible when the profiles from the two independent amplifications were consistent in all individuals tested.

Those 44 primers generated 547 scorable marker bands (an average of 12.4 bands per primer), of which 257 (47%) were polymorphic. RAPD reproducibility (see above) was obtained for 144 (56%) fragments, which were used as probes for in situ hybridization. RAPDs were named according to the decameric primer that identified the RAPD polymorphism, followed by a digit that increases as the relative mobility of the band increases. Fig 1 shows a typical example of RAPD products. A negative but nonsignificant correlation between the G + C content of the decameric primer (as given by the first number in the primers from Genosys Biotechnologies, Cambridge, UK) and the number of polymorphic bands scored was observed (Spearman r_S = -0.302; P = 0.055). On the other hand, there was a positive and statistically significant correlation between the G + C content of the primer and the fraction of polymorphic bands that were reproducible (r_S = 0.453; P = 0.003).

View larger version (148K): In this window In a new window Download PPT slide   Figure 1. RAPD profile for the decameric primer G-80.16. Lanes 2–15 are the PCR amplification products from individual template DNA samples coming from 14 independent isofemale strains of D. buzzatii. Lane 1 indicates the molecular weight standards, and their sizes are given on the left-hand side (in base pairs). Lane 16 is the negative control. Polymorphic and reproducible RAPD bands used as probes for in situ hybridization are indicated by arrows.

Positive hybridizations to the polytene chromosomes:
In situ hybridizations were routinely carried out using a D. buzzatii strain fixed for 2st and 4st gene arrangements. A total of 108 RAPDs produced a single or multiple signals (up to 15), and Table 2 gives the hybridization sites on the chromosomes from the salivary glands. Sixty-three RAPDs gave a single and consistently detectable hybridization signal that must correspond to the site of the polymorphic locus, and in 10 additional cases there were one or two extra secondary signals on the same or different chromosomes that were absent in some preparations. No variation in signal localization was ever detected among the several nuclei examined for a given probe. Hence, a total of 73 RAPDs with an average length of 942 bp (aggregate map length of 69 kb) were considered to behave as effectively unique and to be valuable as markers for physical map construction. Fourteen RAPDs gave two primary signals, and in nine cases these signals were located on different chromosomes, thus potentially increasing the number of useful markers for further recombinational maps. Fig 2, a–e, shows a picture of D. buzzatii polytene chromosomes indicating the cytological positions of the 73 primary-singled signal RAPDs, together with the 9 primary-doubled signal RAPDs on different chromosomes (boldface type).

View larger version (146K): In this window In a new window Download PPT slide   Figure 2. Blueprints of the standard chromosome arrangements of D. buzzatii indicating the cytological localizations of the 73 RAPDs with a single primary signal, together with the 9 RAPDs that produced two primary signals, each on different chromosomes (indicated in boldface type), as inferred from the in situ hybridizations. (a) Chromosome X, (b) chromosome 2, (c) chromosome 3, (d) chromosome 4, (e) chromosome 5. The standard arrangements are cut-and-paste reconstructions of the D. repleta map (WHARTON 1942 ) according to the sequence of inversions proposed for their respective phylogenies (RUIZ and WASSERMAN 1993 ). The relative order of those markers that hybridized on the same band is not known for certain. On the basis of information in Table 4, 50.25.2sts on 4(A1g) likely marks the homologous to gene kls, and 80.12.3sts on 5(G2c) the homologous to gene shot, both in D. melanogaster. The breakpoints of the polymorphic inversions on the second (2j, 2jz3, 2jq7) and fourth (4s) chromosomes are also shown. To recover the chromosomal segments included in inversions 2z3 and 2q7, segment 2j first must be inverted. The question mark indicates that the distal breakpoint of inversion 2z3 is not the same as that for inversion 2j (see Fig 3). The positions of genes previously mapped in D. buzzatii are indicated by arrows (for Fum on chromosome X and Pgm on chromosome 4, see NAVEIRA et al. 1986 ; for Adh on chromosome 3, see LABRADOR et al. 1990 ; for the rest of the genes, see RANZ et al. 1997 , RANZ et al. 1999 ).

Two RAPDs map close to known inversion breakpoints, and they were converted to STSs for further analyses (see below). RAPD 70.18.1 maps on 2(F1d) (Fig 2B), close to the proximal breakpoint of inversion 2z³ that has been previously assigned to 2(F1c) (RUIZ et al. 1984 ). This RAPD was also used as probe for in situ hybridization on a D. buzzatii strain fixed for 2jz³ gene arrangement. Fig 3 shows the hybridization signals, and it is clear that 70.18.1 is not included within the inverted fragment. However, some discrepancies were apparent when comparing the position of the hybridization signal with the putative distal chromosome structures that should be observed. Thus, if we assume that the distal breakpoints of 2j and 2z³ were exactly the same on 2(C6c) (see RUIZ et al. 1984 ), the segment 2(E4) should lie just after (proximal distal direction) the hybridization signal and this was not the case. The most likely explanation is that the distal breakpoint of 2z³ is indeed more proximal than that for 2j, somewhere around 2(E4b-c).

View larger version (71K): In this window In a new window Download PPT slide   Figure 3. In situ hybridization of RAPD 70.18.1 (arrowheads), which maps on 2(F1d), using D. buzzatii strains fixed for (a) 2st or (b) 2jz3 gene arrangements. It is clear that this marker is not included within the inverted segment 2z3. (c) The current consensus map for 2jz3 gene arrangement of D. buzzatii; the position of the hybridization signal is marked with a thick line. As previously indicated (Fig 2B), segment 2j (from C6c to E5a; see RUIZ et al. 1984 ) must be inverted first to recover the chromosomal segment included in inversion 2z3 (from C6c to F1c). Note the position of segment E4 (indicated by arrows), which should be very close to the hybridization signal if the consensus map were correct. This is not observed in the in situ hybridization on 2jz3, and the most likely explanation is shown in d where it is assumed that the distal breakpoint of 2z3 is E4b-c.

A conspicuous feature from Fig 2, a–e, is that RAPDs are unevenly distributed among chromosomes. From the putative homologies of D. buzzatii with the Mueller/Sturtevant/Novitski chromosomal elements, and the percentage of total euchromatin assigned to each of these elements (X-A, 18%; 2-E, 22.6%; 3-B, 21.4%; 4-D, 20.3%; 5-C, 17.7%; see WASSERMAN 1982 ; SCHAFER et al. 1993 ), a higher-than-expected number of single-signal RAPDs were located on chromosomes 2 and 4 (²₍₄₎ = 22.0; P < 0.001. The conclusion does not qualitatively change after correcting for the different number of X chromosomes in males).

Twenty-one RAPDs gave more than two primary signals on the salivary gland chromosomes, and in a number of cases they were located on the centromeres (Table 2). The presence of other copies of the same gene family, pseudogenes or DNA segments sharing a sequence homology, and/or transposable elements of diverse types are probably the reason to observe multiple signals.

Clustering of RAPDs:
The extent of clustering of RAPD markers on chromosomes 2 and 4 (i.e., those with a higher number of RAPDs) was investigated by means of a goodness-of-fit test (SOKAL and ROHLF 1995 ) of the observed number of hybridization signals per chromosome section to that expected from a Poisson distribution. Chromosome 2 is divided into 38 sections (WHARTON 1942 ) of 600 kb each (assuming that D. buzzatii has 2000 bands in the polytene chromosomes as D. hydei and 50 kb per band; see LAIRD 1973 ; HARTL et al. 1994 ), and the distribution of signals (Fig 2B) was as follows: 12 sections with one signal, 4 with two, 2 with three, and 1 with six (G_{(Williams' correction)} = 9.41; P = 0.094). The previous values could overestimate the degree of clustering because RAPDs 60.03.2 and 60.03.5 [section 2(B2)], RAPDs OPA14.1 and OPA14.2 [section 2(D2)], and RAPDs 60.03.7 and 60.03.8 [section 2(E2)] might represent the same loci. Chromosome 4 is divided into 32 sections (WHARTON 1942 ), and the distribution of signals (Fig 2D) was the following: 4 sections with one signal, 5 with two, 2 with three, 1 with four, and 1 with five (G_{(Williams' correction)} = 13.18; P = 0.010). As for chromosome 2, this distribution of signals could overestimate the degree of clustering because RAPDs 70.12.3 and 70.12.4 [section 4(E4)] and RAPDs 70.01.2 and 70.01.3 [section 4(G1)] might represent the same loci.

To see whether or not that was indeed the case, we derived STSs for RAPDs 70.01.2 and 70.01.3 and compared their sequences. They could be unambiguously aligned and matched almost perfectly with a big gap from nucleotides 494 to 511 due to a higher number of GT repeats in 70.01.2sts (see Table 3 for their partial sequence information). After counting those two sets of RAPDs as a single marker, G_{(Williams' correction)} = 10.63 (P = 0.014). Therefore, RAPDs are not randomly distributed along chromosome 4, and there seems to be a higher-than-expected number of hybridization signals in the central part.

Similarly, we derived STSs for RAPDs 70.13.3 and 70.13.4 on chromosome 5(B1a) and compared their sequences. They could be unambiguously aligned but there is a big indel of 74 nucleotides and a significant number of mismatches. This suggests that they could represent two closely related loci, but for the time being we cannot discard the possibility of a length polymorphism. To summarize, it is not clear whether or not all the RAPDs that were obtained from an identical decameric primer and happen to hybridize on the same chromosome band necessarily characterize the same locus. On the other hand, dissimilar RAPDs (i.e., those obtained with different decameric primers) that map to the same location likely mark different loci (cf. 60.26.2sts and 50.30.1sts on chromosome 2 and 80.16.4sts and 80.09.5sts on chromosome 4).

Sequence analyses of RAPD markers:
A total of 39 cytologically mapped RAPD markers were gel purified, reamplified by PCR, and cloned using T vectors. The clones were subjected to partial DNA sequence analysis from both ends and thus were converted to STSs, which are valuable markers for physical map construction and can also reveal previously undescribed potential genes (LOUIS et al. 1997 ). In most cases the total base pair length of the clones was sequenced, representing an aggregate sequence of 28,431 bp (27,654 bp after excluding 70.01.3sts; see above). STS landmarks were designated by adding the suffix "sts" to the name of the original RAPD marker. Table 3 lists these STSs and presents the terminal 30 bp from each end. In all cases but three (see the slight variation in primer sequences reported as a footnote in Table 3), the decamer oligonucleotide that was used to generate the RAPD was present at each terminus as expected.

STSs allow us a rough approximation of the variation in nucleotide composition over the different chromosomes of D. buzzatii. Thus, overall G + C content is 41.18% (compared to 42.86% for D. melanogaster and 40.82% for the distant relative D. virilis; both values estimated from the buoyant densities reported in GALL et al. 1971 ), and the corresponding figures for the autosomes are the following: 36.05% for chromosome 5 (aggregate sequence of 2252 bp), 38.87% for chromosome 3 (aggregate sequence of 4809 bp), 40.54% for chromosome 4 (aggregate sequence of 9383 bp), and 43.52% for chromosome 2 (aggregate sequence of 10,219 bp). Assuming that STSs are representative of the whole genome, these figures would tentatively suggest that chromosome 2 is relatively rich in coding regions (see LI 1997 ).

All STS sequences were checked against both nucleic acid and protein databases for potential matches. We were particularly interested in those STSs (80.07.3sts and 70.18.1sts) derived from the two RAPDs that map near second chromosome paracentric inversion breakpoints (Fig 2B). Thus, the proximal breakpoint of inversion 2j lies between the nAcRß-96A and Pp1-96A genes, has been recently cloned and sequenced, and contains large insertions corresponding to a transposable element named Galileo (CACERES et al. 1999 ). 80.07.3sts was checked against both nucleic acid and protein databases and "hits" with an apparently unknown gene in Drosophila (see below).

As in the distant relative D. virilis (VON ALLMEN et al. 1996 ), the genes Antennapedia (Antp) and Ultrabithorax (Ubx) in D. buzzatii seem to be together because they map on the same 2(F1c-d) band (RANZ et al. 1997 ), close to the putative proximal breakpoint 2(F1c) of inversion 2z³ (RUIZ et al. 1984 ). 70.18.1sts maps on 2(F1d) (Fig 2B) and, as described above, is not included within the inversion fragment (Fig 3). No significant hits with known genes were found in BLAST searches for 70.18.1sts, and we do not know whether the relative positions of Antp-Ubx-70.18.1sts are still conserved in the 2jz³ gene arrangement.

Table 4 lists the 22 STSs that rendered significant "hits" in BLAST searches of the GenBank databases and also shows the protein alignments between conceptually translated STSs and the respective hits representing known genes. As expected, the significant hits were in most cases with protein sequences or genomic scaffolds from D. melanogaster, but in three instances (70.09.4sts, 80.07.3sts, and 70.19.1sts) the hits were with protein sequences from other taxa that have not yet been described in Drosophila. Interestingly, 70.09.4sts and 80.07.3sts show reasonably good alignments with their corresponding matches (see Table 4) and might have identified novel Drosophila putative genes.

Thirteen STSs hit with Drosophila sequences of known chromosomal location. From the alignments observed in Table 4 and the corresponding chromosomal homologies (see below), we conclude that 50.25.2sts likely marks the homologous to gene klarsicht (kls) and 80.12.3sts the homologous to gene short stop (shot); both genes were previously known and mapped in D. melanogaster (FLYBASE CONSORTIUM 1999 ). An intriguing case is the hit of 80.12.1sts with alcohol dehydrogenase (Adh) genes of D. buzzatii and the Tc1-like DNA transposable element of D. virilis. In many species of the repleta group (including D. buzzatii) the Adh region contains a pseudogene (Adh-) and two Adh functional genes (Adh-2 and Adh-1), arranged 5' to 3', that have arisen by two independent duplication events (MENOTTI-RAYMOND et al. 1991 ; YUM et al. 1991 ; SULLIVAN et al. 1994 ). Alignment of 80.12.1sts with the D. buzzatii Adh region (GenBank accession no. U65746) shows substantial matches between the intervening sequence of genes Adh-2 and Adh-1 (from nucleotides 5475 to 5580) and nucleotides 455...560 of 80.12.1sts, and alignment with Tc1-like from D. virilis (GenBank accession no. U26938) shows substantial matches for nucleotides 276...312 of 80.12.1sts with the inverted repeats of the element. Adh maps at the 3(G1a) band in D. buzzatii (LABRADOR et al. 1990 ), while RAPD 80.12.1 maps at the 3(E1f-g) band (Table 2, Fig 2C) and could reflect a transposon-mediated movement event.

An extensive reorganization within Mueller/Sturtevant/Novitski chromosome elements has occurred in Drosophila evolution, but chromosomal homologies have been generally conserved (SEGARRA and AGUADE 1992 ; KRESS 1993 ; HARTL and LOZOVSKAYA 1994 ; SEGARRA et al. 1995 , SEGARRA et al. 1996 ; RANZ et al. 1997 ; VIEIRA et al. 1997 ). This allowed us to check our hybridization signals with those reported for D. melanogaster, and in general there was a good agreement. Thus, kls maps in D. melanogaster on chromosome 3L, very close to the telomere, and this agrees quite well with the position of RAPD 50.25.2 on chromosome 4 (Table 2 and Fig 2D). shot maps on chromosome 2R and, accordingly, RAPD 80.12.3 maps on chromosome 5 in D. buzzatii (Table 2 and Fig 2E). In one case (80.16.4sts) the correspondence was with the secondary signal (chromosome 3R in D. melanogaster and chromosome 2 in D. buzzatii; Table 2 and Fig 2B), and in three additional cases (50.22.2sts, 70.03.4sts, and 80.07.2sts) there was no correspondence with the cytological location reported for the genomic scaffolds in D. melanogaster. Similarities in sequences between different proteins are likely the cause for the lack of correspondence, which is clearly suggested by the two hits of 50.22.2sts (Table 4).

Negative results:
In spite of up to three attempts, 36 RAPDs (25%) did not produce any detectable hybridization signal on the polytene chromosomes (Table 5). We have obtained the DNA sequences from a sample of three of those RAPDs (70.08.2, 70.09.7, and 70.14.5, with an aggregate sequence of 1606 bp) to further investigate whether or not they present special features to prevent in situ hybridization. The three sequences have an overall G + C content (41.10%) very similar to the STSs, and no repetitive regions were detected. No significant hits were found when these sequences were checked against both nucleic acid and protein databases. However, the sequence 70.14.05 presents an ORF of 207 amino acids (data not shown), and several additional clues to suggest that this sequence is part of a coding region (compositional differences among codon positions relatively large and similar to the functional genes in D. buzzatii; i.e., G + C highest in third position and lowest in second position).

A likely cause for the lack of hybridization signal can be an underreplication of those sequences during the formation of polytene chromosomes. This will be the case for all sequences within the -heterochromatin and some sequences within the ß-heterochromatin (GALL et al. 1971 ; GALL 1973 ; GLASER et al. 1997 ). However, no firm conclusion can be made on the available data and further work is in progress.

Conclusions and prospects:
The present results help understand the observed differences in the distribution of genetic variation over chromosomes in species of the repleta group of Drosophila (ZOUROS 1976 ). Thus, enzyme heterozygosity is highest for chromosome 2, but chromosomes 4 and 5 could not be adequately separated and were treated as a unity. The apportioning of RAPDs observed here certainly suggests that average variability levels on the autosomes of D. buzzatii are 2 4 > 3 > 5, contrary to the observed distribution of spontaneous visible markers that placed chromosome 4 as the least variable (SCHAFER et al. 1993 ).

The physical map of D. buzzatii now comprises 73 effectively unique RAPD markers (39 of these are STSs) and 53 genes whose cytological position is already known (Fig 2, a–e). On the other hand, the current genetic map is poorly developed and consists of three linkage groups (chromosomes X, 2, and 5) that include visible mutants and enzyme loci (SCHAFER et al. 1993 ). The RAPDs obtained here (along with those that gave secondary signals, those that gave hybridization signals on different chromosomes, and the 36 that did not give any signal) will be used as genetic markers to provide a link between the physical and more extensive linkage maps, also covering chromosomes 3 and 4. In addition, they will help to increase the density of markers (including microsatellites) around specific genomic regions to search for quantitative trait loci of fitness-related traits such as body size (see BETRAN et al. 1998 ). [A caveat: because the cytological maps of D. buzzatii are cut-and-paste reconstructions of the D. repleta map (see above), exact correspondence between the physical and the genetic maps for the relative positions of markers is expected, provided the proposed cytogenetic relationships between D. repleta and D. buzzatii are fully correct.]

	ACKNOWLEDGMENTS

M. Labrador and J. E. Quezada-Díaz were of great help during the initial steps of this work. We thank A. Leibowitz and J. E. Quezada-Díaz for their assistance in collecting the thousands of flies raised from Opuntia rots, L. Alarcón and F. Rodríguez-Trelles for providing information on the sequence of Xdh in D. buzzatii before publishing, M. P. García-Guerreiro for helpful advice with in situ hybridizations, F. Rodríguez-Trelles for helpful discussion and careful reading of earlier drafts, and M. Peiró for technical assistance. One of us (H.L.) is very grateful to M. R. Goldsmith for providing a stimulating intellectual environment during his stay in the Department of Zoology, University of Rhode Island. Two anonymous referees and the communicating editor provided very helpful comments on the manuscript. H.L. was supported by a FP94-00215104 fellowship from the Ministerio de Educación y Ciencia (Spain). This work was supported by grants PB93/0843 and PB96-1136 from the Dirección General de Enseñanza Superior e Investigación Científica (DGESIC, Spain) to A.F. and grant SGR98 from the Direcció General de Recerca (Generalitat de Catalunya) to the GBE.

Manuscript received December 7, 1999; Accepted for publication August 21, 2000.

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