From first base: the sequence of the tip of the X chromosome of Drosophila melanogaster, a comparison of two sequencing strategies

Abstract

We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94 had been sequenced already in the course of studying the biology of their gene products, and examples of 12 different transposable elements. We show that an interval between bands 3A2 and 3C2, believed in the 1970s to show a correlation between the number of bands on the polytene chromosomes and the 20 genes identified by conventional genetics, is predicted to contain 45 genes from its DNA sequence. We have determined the insertion sites of P-elements from 111 mutant lines, about half of which are in a position likely to affect the expression of novel predicted genes, thus representing a resource for subsequent functional genomic analysis. We compare the European Drosophila Genome Project sequence with the corresponding part of the independently assembled and annotated Joint Sequence determined through "shotgun" sequencing. Discounting differences in the distribution of known transposable elements between the strains sequenced in the two projects, we detected three major sequence differences, two of which are probably explained by errors in assembly; the origin of the third major difference is unclear. In addition there are eight sequence gaps within the Joint Sequence. At least six of these eight gaps are likely to be sites of transposable elements; the other two are complex. Of the 275 genes in common to both projects, 60% are identical within 1% of their predicted amino-acid sequence and 31% show minor differences such as in choice of translation initiation or termination codons; the remaining 9% show major differences in interpretation.

Figure 1

Physical maps of the interval 1A–3C. (A) Minimal tiling pattern of clones sequenced in divisions 1A–3C. BACR clones are indicated in red; BACN and BACH clones are indicated in green; cosmid clones are indicated in blue; redundant clones sequenced are indicated in pink; a few small regions were sequenced from other clones, these are indicated in yellow. The BACR, BACN, and BACH clones are from the same strain as that sequenced by the BDGP and Celera; the cosmids are from a different strain (see Methods). Scale divisions are 10 Kb. (B) Genes, transposable elements, and P-element insertions in divisions 1A–3C. Known genes are shown in red; genes with significant protein similarities to nondrosophilid proteins are shown in blue; predicted genes with EST hits are shown in yellow; predicted genes with no EST hits are shown in green; predicted genes with protein motif matches are shown in pink. Transposable elements are shown in orange within the sequence coordinate line. The sites of P-element and EP-element insertions are indicated by gray triangles. The large square brackets from 2100 to 2480 Kb embrace the zeste-white region (Figure 2). Scale divisions are 10 Kb (bold) and 1 Kb (regular).

Figure 2

The zeste-white interval. The top is a reproduction of Figure 5 from Judd et al. (1972) showing the polytene chromosome region 3A–3C and the complementation groups discovered by mutational analysis. Below this projections are made onto the interval 2100 Kb to 2480 Kb of the EDGP sequence showing the correspondence between the genetic analysis and the genes known or predicted in this region from sequence analysis.

Figure 3

Sequence comparisons. A comparison of EDGP sequence of the tip of the X chromosome with that of the Drosophila Joint Sequence in the same region. The comparison was made using the MUMmer program (see Methods). The GenBank accession numbers corresponding to the Joint Sequence are shown on the left (AE003417–AE003425); note that this is part of a unitig (Myers et al. 2000). The blocks indicate regions of ⋝1 Kb present in one sequence but not the other. The position and length of each block of sequence ⋝1 Kb that is unique to one sequence is shown; each GenBank accession is numbered to the left of the unitig, the corresponding base position within the EDGP sequence is shown in italics to the right of the unitig. The EDGP sequence is numbered continuously. The length of each block of unique sequence is in parentheses. The nature of these sequence segments is shown in the center (note that a segment may include sequences in addition to those identified here). The segments corresponding to transposable elements are indicated in orange; those corresponding to known genes are red; a gray “neck” depicts a sequence interrupted by a large block of n's of length N (nN). The Greek superscripts (^α,^β,^γ,^ɛ,^δ) refer to the class of sequence difference (see text). Note that there are an additional nine transposable elements in the EDGP sequence that are not seen to differ in the Joint Sequence.