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 15 Present address:

Fruit Flies in Biomedical Research

“…Although studies have estimated that there are about 5000 essential genes in Drosophila (Benos et al 2001), we can only find evidence for about 2000 essential genes based on the current FlyBase information (FlyBase 2014;St Pierre et al 2014). We think this is likely not because the estimate is inaccurate as several independent estimates based on very different datasets came to similar conclusions Nusslein-Volhard et al 1984;Wieschaus et al 1984;Benos et al 2001;Ashburner et al 2005). The observation that only 2000 essential genes are annotated in FlyBase suggests that the identity and the functions of the majority of essential genes remain to be elucidated, and hence, that a large body of work remains to be done before we will have a functional annotation of most essential fly genes.…”

Analysis of Drosophila Species Genome Size and Satellite DNA Content Reveals Significant Differences Among Strains as Well as Between Species

“…For D. ananassae, previous genome size estimates (Ashburner et al 2005) are identical to ours, and our estimates do not differ with dye type, making it unlikely that this discrepancy reflects errors intrinsic to cytometric measurements of DNA content. In the case of these four species, it is possible that assembly sizes do not accurately represent euchromatic genome sizes as assembly errors have been reported for previous genome releases, including Drosophila, mouse, and human genomes (Benos et al 2001;Celniker et al 2002;Cheung et al 2003a,b).…”

The shrunken genome of Arabidopsis thaliana

“…It would also provide the potential to identify the transposons responsible for genome size changes. However, as was discovered with Drosophila, the wholegenome shotgun sequencing strategy may not be able to accurately place repetitive elements or indels, and thus it will be difficult to use the data generated to infer processes of genome size evolution (Benos et al 2001). This means that even after the completion of this project, and the effort to sequence the genome of Capsella, the role of repetitive sequences in the evolution of the A. thaliana genome may remain unclear.…”