Sequence finishing and mapping of Drosophila melanogaster heterochromatin

Abstract

Genome sequences for most metazoans and plants are incomplete because of the presence of repeated DNA in the heterochromatin. The heterochromatic regions of Drosophila melanogaster contain 20 million bases (Mb) of sequence amenable to mapping, sequence assembly, and finishing. We describe the generation of 15 Mb of finished or improved heterochromatic sequence with the use of available clone resources and assembly methods. We also constructed a bacterial artificial chromosome-based physical map that spans 13 Mb of the pericentromeric heterochromatin and a cytogenetic map that positions 11 Mb in specific chromosomal locations. We have approached a complete assembly and mapping of the nonsatellite component of Drosophila heterochromatin. The strategy we describe is also applicable to generating substantially more information about heterochromatin in other species, including humans.

Fig. 1

Comparison of WGS scaffolds to the corresponding Release 5 scaffold. WGS scaffolds (gray, same orientation; tan, opposite orientation) are diagrammed above the Release 5 scaffold (blue). Sequence gaps (thin horizontal lines) in WGS scaffolds are indicated.

Fig. 2

Sequenced regions of D. melanogaster pericentromeric heterochromatin. The heterochromatin extends proximally from the euchromatin (black) and includes sequenced and assembled regions (aqua) and unsequenced regions (gray). The actual gap sizes between sequence scaffolds are unknown and are presented with an arbitrary 0.5-Mb separation. Finished or improved scaffolds, which end in known or novel simple repeats, are shown with the terminal repeat sequence indicated. The scaffold CP000217, originally identified as part of 2RHet but subsequently mapped to 3LHet, is shown here at its updated location (see text).

Fig. 3

Integrated map of D. melanogaster pericentromeric heterochromatin. The cytogenetic reference map of the heterochromatic regions of the chromosomes with numbered divisions (h1 to h58) and centromeres (C) is shown (22). The fourth chromosome (h58 to h61) is not shown. Release 5 sequence scaffolds are indicated at their cytogenetic map locations, and Het scaffolds are labeled with their GenBank accession numbers. Scaffolds (13.9 Mb in total; see scale bar) and the heterochromatin (100 Mb in total) are represented at different scales. Sequence contigs (thick bars) and sequence gaps (thin bars) within scaffolds are shown. Some sequence gaps are too small to be represented at this scale. A clone gap in the 2Lh sequence is indicated. Joins between Release 5 scaffolds present in the BAC map assembly but not yet incorporated in the sequence assembly are shown. Cytogenetic locations are indicated by lines connecting scaffolds to cytogenetic ranges. The heterochromatin-euchromatin boundaries within the sequence of the chromosome arms, based on BAC FISH (6), are indicated by dashed magenta lines. The orientations of Het scaffolds are not necessarily known (11, 23). CP000217, originally identified as part of 2RHet but subsequently mapped to 3LHet, is shown here at its updated location; CP000206, originally identified as part of 3RHet but subsequently removed to the unlocalized scaffolds, is not shown (11).