Abstract:Retroelements with long-terminal repeats (LTRs) inhabit nearly all eukaryotic genomes. During the time of their rich evolutionary history they have developed highly diverse forms, ranging from ordinary retrotransposons to complex pathogenic retroviruses such as HIV-I. Errantiviruses are a group of insect endogenous LTR elements that share structural and functional features with vertebrate endogenous retroviruses. The errantiviruses illustrate one of the evolutionary strategies of retrotransposons to become inf… Show more
“…Drosophila -associated viruses include many with positive sense RNA genomes (Dicistroviridae, Permutotetraviridae, Flaviviridae, Iflaviridae, Nodaviridae, Negeviruses, and others), negative sense RNA genomes (Rhabdoviridae; relatives of Bunyaviridae), and double-stranded RNA genomes (Birnaviridae, Totiviridae, Partitiviridae, Reoviridae), but few with DNA genomes (only the Kallithea and Drosophila innubila Nudiviruses [ 56 ] to date) and no retroviruses ( cf . “Errantivirus” endogenous retroviruses [ 100 ]; retro-elements or retrotransposons that are usually transmitted as genomic integrations). It therefore seems increasingly unlikely that the apparent wealth of RNA viruses and paucity of retroviruses and DNA viruses in Drosophila represents a sampling artefact, and this may instead reflect underlying Drosophila ecology or immune function.…”
Drosophila melanogaster is a valuable invertebrate model for viral infection and antiviral immunity, and is a focus for studies of insect-virus coevolution. Here we use a metagenomic approach to identify more than 20 previously undetected RNA viruses and a DNA virus associated with wild D. melanogaster. These viruses not only include distant relatives of known insect pathogens but also novel groups of insect-infecting viruses. By sequencing virus-derived small RNAs, we show that the viruses represent active infections of Drosophila. We find that the RNA viruses differ in the number and properties of their small RNAs, and we detect both siRNAs and a novel miRNA from the DNA virus. Analysis of small RNAs also allows us to identify putative viral sequences that lack detectable sequence similarity to known viruses. By surveying >2,000 individually collected wild adult Drosophila we show that more than 30% of D. melanogaster carry a detectable virus, and more than 6% carry multiple viruses. However, despite a high prevalence of the Wolbachia endosymbiont—which is known to be protective against virus infections in Drosophila—we were unable to detect any relationship between the presence of Wolbachia and the presence of any virus. Using publicly available RNA-seq datasets, we show that the community of viruses in Drosophila laboratories is very different from that seen in the wild, but that some of the newly discovered viruses are nevertheless widespread in laboratory lines and are ubiquitous in cell culture. By sequencing viruses from individual wild-collected flies we show that some viruses are shared between D. melanogaster and D. simulans. Our results provide an essential evolutionary and ecological context for host–virus interaction in Drosophila, and the newly reported viral sequences will help develop D. melanogaster further as a model for molecular and evolutionary virus research.
“…Drosophila -associated viruses include many with positive sense RNA genomes (Dicistroviridae, Permutotetraviridae, Flaviviridae, Iflaviridae, Nodaviridae, Negeviruses, and others), negative sense RNA genomes (Rhabdoviridae; relatives of Bunyaviridae), and double-stranded RNA genomes (Birnaviridae, Totiviridae, Partitiviridae, Reoviridae), but few with DNA genomes (only the Kallithea and Drosophila innubila Nudiviruses [ 56 ] to date) and no retroviruses ( cf . “Errantivirus” endogenous retroviruses [ 100 ]; retro-elements or retrotransposons that are usually transmitted as genomic integrations). It therefore seems increasingly unlikely that the apparent wealth of RNA viruses and paucity of retroviruses and DNA viruses in Drosophila represents a sampling artefact, and this may instead reflect underlying Drosophila ecology or immune function.…”
Drosophila melanogaster is a valuable invertebrate model for viral infection and antiviral immunity, and is a focus for studies of insect-virus coevolution. Here we use a metagenomic approach to identify more than 20 previously undetected RNA viruses and a DNA virus associated with wild D. melanogaster. These viruses not only include distant relatives of known insect pathogens but also novel groups of insect-infecting viruses. By sequencing virus-derived small RNAs, we show that the viruses represent active infections of Drosophila. We find that the RNA viruses differ in the number and properties of their small RNAs, and we detect both siRNAs and a novel miRNA from the DNA virus. Analysis of small RNAs also allows us to identify putative viral sequences that lack detectable sequence similarity to known viruses. By surveying >2,000 individually collected wild adult Drosophila we show that more than 30% of D. melanogaster carry a detectable virus, and more than 6% carry multiple viruses. However, despite a high prevalence of the Wolbachia endosymbiont—which is known to be protective against virus infections in Drosophila—we were unable to detect any relationship between the presence of Wolbachia and the presence of any virus. Using publicly available RNA-seq datasets, we show that the community of viruses in Drosophila laboratories is very different from that seen in the wild, but that some of the newly discovered viruses are nevertheless widespread in laboratory lines and are ubiquitous in cell culture. By sequencing viruses from individual wild-collected flies we show that some viruses are shared between D. melanogaster and D. simulans. Our results provide an essential evolutionary and ecological context for host–virus interaction in Drosophila, and the newly reported viral sequences will help develop D. melanogaster further as a model for molecular and evolutionary virus research.
“… 68 Many of these retrotransposons are classified as endogenous retroviruses, or errantiviruses in Drosophila and other insects, as they either arose from retroviruses that lost infectivity or LTR retrotransposons that acquired env genes from exogenous sources. 69 Figure 5. Retrotransposons and the LTR retrotransposition mechanism.…”
Transposable elements (TEs) are mobile genetic elements that can mobilize within host genomes. As TEs comprise more than 40% of the human genome and are linked to numerous diseases, understanding their mechanisms of mobilization and regulation is important. Drosophila melanogaster is an ideal model organism for the study of eukaryotic TEs as its genome contains a diverse array of active TEs. TEs universally impact host genome size via transposition and deletion events, but may also adopt unique functional roles in host organisms. There are 2 main classes of TEs: DNA transposons and retrotransposons. These classes are further divided into subgroups of TEs with unique structural and functional characteristics, demonstrating the significant variability among these elements. Despite this variability, D. melanogaster and other eukaryotic organisms utilize conserved mechanisms to regulate TEs. This review focuses on the transposition mechanisms and regulatory pathways of TEs, and their functional roles in D. melanogaster.
“…6 Ty3/gypsy families having the potential to form infectious virus-like particles (Lerat and Capy 1999; Malik et al . 2000; Stefanov et al . 2012).…”
Cultured cells are widely used in molecular biology despite poor understanding of how cell line genomes change in vitro over time. Previous work has shown that Drosophila cultured cells have a higher transposable element (TE) content than whole flies, but whether this increase in TE content resulted from an initial burst of transposition during cell line establishment or ongoing transposition in cell culture remains unclear. Here we sequence the genomes of 25 sub-lines of Drosophila S2 cells and show that TE insertions provide abundant markers for the phylogenetic reconstruction of diverse sub-lines in a model animal cell culture system. Analysis of DNA copy number evolution across S2 sub-lines revealed dramatically different patterns of genome organization that support the overall evolutionary history reconstructed using TE insertions. Analysis of TE insertion site occupancy and ancestral states support a model of ongoing transposition dominated by episodic activity of a small number of retrotransposon families. Our work demonstrates that substantial genome evolution occurs during long-term Drosophila cell culture, which may impact the reproducibility of experiments that do not control for sub-line identity.
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