An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: The Adh region

A contiguous sequence of nearly 3 Mb from the genome of Drosophila melanoga ster has been sequenced from a series of overlapping P1 and BAC clones. Thi s region covers 69 chromosome polytene bands on chromosome arm 2L, includin g the genetically well-characterized "Adh region." A computational analysis of the sequence predicts 218 protein-coding genes, 11 tRNAs, and iii trans posable element sequences. At least 38 of the protein-coding genes are arra nged in clusters of from 2 to 6 closely related genes, suggesting extensive tandem duplication. The gene density is one protein-coding gene every 13 k b; the transposable element density is one element every 171 kb. Of 73 gene s in this region identified by genetic analysis, 49 have been located on th e sequence; P-element insertions have been mapped to 43 genes. Ninety-five (44%) of the known and predicted genes match a Drosophila EST, and 144 (66% ) have clear similarities to proteins in other organisms. Genes known to ha ve mutant phenotypes are more likely to be represented in cDNA libraries, a nd far more likely to have products similar to proteins of other organisms, than are genes with no known mutant phenotype. Over 650 chromosome aberrat ion breakpoints map to this chromosome region, and their nonrandom distribu tion on the genetic map reflects variation in gene spacing on the DNA. This is the first large-scale analysis of the genome of D. melanogaster at the sequence level. In addition to the direct results obtained, this analysis h as allowed us to develop and test methods that will be needed to interpret the complete sequence of the genome of this species.