Comparative Analysis of Satellite DNA in the Drosophila melanogaster Species Complex

Abstract

Satellite DNAs are highly repetitive sequences that account for the majority of constitutive heterochromatin in many eukaryotic genomes. It is widely recognized that sequences and locations of satellite DNAs are highly divergent even in closely related species, contributing to the hypothesis that satellite DNA differences may underlie speciation. However, due to its repetitive nature, the mapping of satellite DNAs has been mostly left out of recent genomics analyses, hampering the use of molecular genetics techniques to better understand their role in speciation and evolution. Satellite DNAs are most extensively and comprehensively mapped in Drosophila melanogaster, a species that is also an excellent model system with which to study speciation. Yet the lack of comprehensive knowledge regarding satellite DNA identity and location in its sibling species (D. simulans, D. mauritiana, and D. sechellia) has prevented the full utilization of D. melanogaster in studying speciation. To overcome this problem, we initiated the mapping of satellite DNAs on the genomes of the D. melanogaster species complex (D. melanogaster, D. simulans, D. mauritiana, and D. sechellia) using multi-color fluorescent in situ hybridization (FISH) probes. Our study confirms a striking divergence of satellite DNAs in the D. melanogaster species complex, even among the closely related species of the D. simulans clade (D. simulans, D. mauritiana, and D. sechellia), and suggests the presence of unidentified satellite sequences in these species.

Keywords: Drosophila; evolution; fluorescent in situ hybridization; heterochromatin; satellite DNA.

Figure 1

FISH on neuroblast chromosome spread from D. melanogaster, D. simulans, D. mauritiana, and D. sechellia. (A) C1 probes and (B) C2 probes. Probe sequences are indicated by the colored text. The top panels show three probes combined with DAPI, and the bottom panels show only probe hybridization signals. Bar, 2.5 µm. C, combination; DAPI, 4’,6-diamidino-2-phenylindole; FISH, fluorescent in situ hybridization.

Figure 2

FISH on neuroblast chromosome spread from D. melanogaster, D. simulans, D. mauritiana, and D. sechellia. (A) C3 probes and (B) C4 probes. Probe sequences are indicated by the colored text. The top panels show three probes combined with DAPI, and the bottom panels show only probe hybridization signals. Bar, 2.5 µm. C, combination; DAPI, 4’,6-diamidino-2-phenylindole; FISH, fluorescent in situ hybridization.

Figure 3

FISH on neuroblast chromosome spread from D. melanogaster, D. simulans, D. mauritiana, and D. sechellia. (A) C5 probes and (B) C6 probes. Probe sequences are indicated by the colored text. The top panels show three probes combined with DAPI, and the bottom panels show only probe hybridization signals. Bar, 2.5 µm. C, combination; DAPI, 4’,6-diamidino-2-phenylindole; FISH, fluorescent in situ hybridization.

Figure 4

FISH on neuroblast chromosome spread from D. melanogaster, D. simulans, D. mauritiana, and D. sechellia. (A) C7 probes and (B) C8 probes. Probe sequences are indicated by the colored text. The top panels show three probes combined with DAPI, and the bottom panels show only probe hybridization signals. Bar, 2.5 µm. C, combination; DAPI, 4’,6-diamidino-2-phenylindole; FISH, fluorescent in situ hybridization.

Figure 5

FISH on neuroblast chromosome spread from D. melanogaster, D. simulans, D. mauritiana, and D. sechellia. C11 probes were used. Probe sequences are indicated by the colored text. The top panels show three probes combined with DAPI, and the bottom panels show only probe hybridization signals. Bar, 2.5 µm. C, combination; DAPI, 4’,6-diamidino-2-phenylindole; FISH, fluorescent in situ hybridization.

Figure 6

FISH on neuroblast chromosome spread from D. simulans T(Y:2) and T(Y:3) translocation strains. C10 probes were used. Probe sequences are indicated by the colored text. The top panels show three probes combined with DAPI, the middle panels show only probe hybridization signals and the bottom panels indicate the interpretation. Bar, 2.5 µm. C, combination; DAPI, 4’,6-diamidino-2-phenylindole; FISH, fluorescent in situ hybridization.

Figure 7

FISH on neuroblast chromosome spread from D. simulans, D. mauritiana, and D. sechellia. (A) C9 probes and (B) C10 probes. Probe sequences are indicated by the colored text. The top panels show three probes combined with DAPI, and the bottom panels show only probe hybridization signals. Bar, 2.5 µm. C, combination; DAPI, 4’,6-diamidino-2-phenylindole; FISH, fluorescent in situ hybridization.