Genomics of Ecological Adaptation in Cactophilic Drosophila

Abstract

Cactophilic Drosophila species provide a valuable model to study gene–environment interactions and ecological adaptation. Drosophila buzzatii and Drosophila mojavensis are two cactophilic species that belong to the repleta group, but have very different geographical distributions and primary host plants. To investigate the genomic basis of ecological adaptation, we sequenced the genome and developmental transcriptome of D. buzzatii and compared its gene content with that of D. mojavensis and two other noncactophilic Drosophila species in the same subgenus. The newly sequenced D. buzzatii genome (161.5 Mb) comprises 826 scaffolds (>3 kb) and contains 13,657 annotated protein-coding genes. Using RNA sequencing data of five life-stages we found expression of 15,026 genes, 80% protein-coding genes, and 20% noncoding RNA genes. In total, we detected 1,294 genes putatively under positive selection. Interestingly, among genes under positive selection in the D. mojavensis lineage, there is an excess of genes involved in metabolism of heterocyclic compounds that are abundant in Stenocereus cacti and toxic to nonresident Drosophila species. We found 117 orphan genes in the shared D. buzzatii–D. mojavensis lineage. In addition, gene duplication analysis identified lineage-specific expanded families with functional annotations associated with proteolysis, zinc ion binding, chitin binding, sensory perception, ethanol tolerance, immunity, physiology, and reproduction. In summary, we identified genetic signatures of adaptation in the shared D. buzzatii–D. mojavensis lineage, and in the two separate D. buzzatii and D. mojavensis lineages. Many of the novel lineage-specific genomic features are promising candidates for explaining the adaptation of these species to their distinct ecological niches.

Transposable Element Misregulation Is Linked to the Divergence between Parental piRNA Pathways in Drosophila Hybrids

“…All contigs were aligned to D. buzzatii genome (Guillén et al 2015) using BLAT v.35x1 (Kent 2002), with parameters –minIdentity = 80 and –maxIntron = 75000 , in order to identify chimers. Contigs that aligned partially (≤60%) on up to three genomic locations with a total alignment coverage of ≥80% were considered chimeric and split consequently.…”

Genetics on the Fly: A Primer on the Drosophila Model System

“…One goal of the modENCODE project has been to sequence the genomes of eight additional species with next-generation technology (Celniker et al 2009). Several more Drosophila species genomes are available through the efforts of individual labs (e.g., Garrigan et al 2012;Zhou and Bachtrog 2012;Nolte et al 2013;Guillen et al 2014) ( Figure 3B). The large number of sequenced Drosophila genomes provides an important resource for comparative genomics and offers a powerful approach to the discovery of functional elements in genomes and their evolution (Singh et al 2009), and ecological genomics (Markow 2015).…”

Targeted Sequencing of Venom Genes from Cone Snail Genomes Improves Understanding of Conotoxin Molecular Evolution

“…Past studies have described several genetic characteristics that seem to be associated with rapidly radiating clades or the evolution of novel phenotypes, including evidence for diversifying selection, gene gains and losses, and accelerated rates of sequence evolution (Floudas et al 2012;Brawand et al 2014;Guill en et al 2014;Cornetti et al 2015;Malmstrøm et al 2016;Pease et al 2016). Although large-scale comparative genomic studies have vastly increased our knowledge of the genetic changes associated with diversification, the link between genotype and ecologically relevant phenotypes frequently remains unclear.…”