Satellite DNA from the Y chromosome of the malaria vector Anopheles gambiae

Abstract

Satellite DNA is an enigmatic component of genomic DNA with unclear function that has been regarded as "junk." Yet, persistence of these tandem highly repetitive sequences in heterochromatic regions of most eukaryotic chromosomes attests to their importance in the genome. We explored the Anopheles gambiae genome for the presence of satellite repeats and identified 12 novel satellite DNA families. Certain families were found in close juxtaposition within the genome. Six satellites, falling into two evolutionarily linked groups, were investigated in detail. Four of them were experimentally confirmed to be linked to the Y chromosome, whereas their relatives occupy centromeric regions of either the X chromosome or the autosomes. A complex evolutionary pattern was revealed among the AgY477-like satellites, suggesting their rapid turnover in the A. gambiae complex and, potentially, recombination between sex chromosomes. The substitution pattern suggested rolling circle replication as an array expansion mechanism in the Y-linked 53-bp satellite families. Despite residing in different portions of the genome, the 53-bp satellites share the same monomer lengths, apparently maintained by molecular drive or structural constraints. Potential functional centromeric DNA structures, consisting of twofold dyad symmetries flanked by a common sequence motif, have been identified in both satellite groups.

Figure 1.—

Southern blot of genomic DNA from different geographic isolates of A. gambiae (A) and other species of the A. gambiae complex (B) probed with the AgY477 satellite monomer. GAM, A. gambiae; ARA, A. arabiensis; MEL, A. melas; MER, A. merus; QUA, A. quadriannulatus. Bands corresponding to monomers and dimers of the AgX367 and AgY477 satellite DNAs are marked with arrows and their respective sizes are given.

Figure 2.—

FISH of the AgY477 (A) and Ag53C (B) probes to A. gambiae ovarian nurse cell polytene chromosomes. The hybridization signal in B is indicated with arrows.

Figure 3.—

Alignment of AgY477 and AgX367 consensus monomer sequences. Dots, identical sites; dashes, missing sequences. Direct repeats flanking the Y-specific sequence are shaded.

Figure 4.—

Phylogenetic relationships (neighbor-joining tree) between AgY477 and AgX367 monomers isolated from species of the A. gambiae complex. Numbers represent bootstrap values. Abbreviations are given in Figure 1.

Figure 5.—

Southern blots of genomic DNA from A. gambiae resolved on a 1.5% agarose gel (A), or 0.8% agarose gel (B), and probed with the AgY53A satellite monomer. Arrows indicate bands corresponding to a monomer and selected oligomers (A) and those corresponding to the higher-order units (B); the respective fragment sizes are shown.

Figure 6.—

An alignment of the monomer consensus sequences of the 53-bp stDNAs from A. gambiae PEST strain. Identical sites are denoted by dots, and missing sequences by dashes. Arrows indicate a tandemly repeated motif in AgY53A and AgY53B.

Figure 7.—

Dyad symmetries (shaded in boldface type) identified within Ag53C and AgY477 monomers. Note identical pentanucleotide motifs (boxed) flanking both structures on the right. The GT motifs adjacent to the dyad structures are underlined.