Since the pioneering studies of Thomas Hunt Morgan and coworkers at the dawn of the twentieth century, Drosophila melanogaster and its sister species have tremendously contributed to unveil the rules underlying animal genetics, development, behavior, evolution, and human disease. Recent advances in DNA sequencing technologies launched Drosophila into the post-genomic era and paved the way for unprecedented comparative genomics investigations. The complete sequencing and systematic comparison of the genomes from 12 Drosophila species represents a milestone achievement in modern biology, which allowed a plethora of different studies ranging from the annotation of known and novel genomic features to the evolution of chromosomes and, ultimately, of entire genomes. Despite the efforts of countless laboratories worldwide, the vast amount of data that were produced over the past 15 years is far from being fully explored.
In this chapter, we will review some of the bioinformatic approaches that were developed to interrogate the genomes of the 12 Drosophila species. Setting off from alignments of the entire genomic sequences, the degree of conservation can be separately evaluated for every region of the genome, providing already first hints about elements that are under purifying selection and therefore likely functional. Furthermore, the careful analysis of repeated sequences sheds light on the evolutionary dynamics of transposons, an enigmatic and fascinating class of mobile elements housed in the genomes of animals and plants. Comparative genomics also aids in the computational identification of the transcriptionally active part of the genome, first and foremost of protein-coding loci, but also of transcribed nevertheless apparently noncoding regions, which were once considered “junk” DNA. Eventually, the synergy between functional and comparative genomics also facilitates in silico and in vivo studies on cis-acting regulatory elements, like transcription factor binding sites, that due to the high degree of sequence variability usually impose increased challenges for bioinformatics approaches.
This is a preview of subscription content, log in to check access.
Springer Nature is developing a new tool to find and evaluate Protocols. Learn more
Adams MD, Celniker SE, Holt RA et al (2000) The genome sequence of Drosophila melanogaster. Science 287:2185–2195CrossRefPubMedGoogle Scholar
Misra S, Crosby MA, Mungall CJ et al (2002) Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol 3(12):research0083.1–research083.22CrossRefGoogle Scholar
Richards S, Liu Y, Bettencourt BR et al (2005) Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res 15:1–18CrossRefPubMedPubMedCentralGoogle Scholar
Bergman CM, Pfeiffer BD, Rincón-Limas DE et al (2002) Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. Genome Biol 3:RESEARCH0086CrossRefPubMedPubMedCentralGoogle Scholar
Kellis M, Patterson N, Endrizzi M et al (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241–254CrossRefPubMedGoogle Scholar
Clark AG, Eisen MB, Smith DR et al (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203–218CrossRefPubMedGoogle Scholar
Li R, Ye J, Li S et al (2005) ReAS: recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comput Biol 1:e43CrossRefPubMedPubMedCentralGoogle Scholar
Edgar RC, Myers EW (2005) PILER: identification and classification of genomic repeats. Bioinformatics 21(Suppl 1):i152–i158CrossRefPubMedGoogle Scholar