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Comparative Genomics in Drosophila

  • Martin Oti
  • Attilio Pane
  • Michael SammethEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1704)

Abstract

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.

Key words

Comparative genomics Drosophila 12 genomes project Multiple genome alignment Evolutionary conservation Homology-based prediction of protein-coding genes Noncoding RNAs miRNAs Transcription factor binding sites 

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Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  1. 1.Institute of Biophysics Carlos Chagas Filho (IBCCF)Federal University of Rio de Janeiro (UFRJ)Rio de JaneiroBrazil
  2. 2.Institute of Biomedical Sciences (ICB)Federal University of Rio de Janeiro (UFRJ)Rio de JaneiroBrazil

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