The genome of the blind bee louse fly reveals deep convergences with its social host and illuminates Drosophila origins.

Social insects' nests harbor intruders known as inquilines, which are usually related to their hosts. However, distant non-social inquilines may also show convergences with their hosts, although the underlying genomic changes remain unclear. We analyzed the genome of the wingless and blind bee louse fly Braula coeca, an inquiline kleptoparasite of the western honey bee, Apis mellifera.

Evidence that hematophagous triatomine bugs may eat plants in the wild.

Blood feeding is a secondary adaptation in hematophagous bugs. Many proteins are secreted in the saliva that are devoted to coping with the host's defense and to process the blood meal. Digestive enzymes that are no longer required for a blood meal would be expected to be eventually lost.

Genome Size Variation of Chagas Disease Vectors of the Rhodniini Tribe.

The genome size of five Rhodnius species (R. milesi, R. nasutus, R.

piRNA and Transposon Dynamics in Drosophila: A Female Story.

The germlines of metazoans contain transposable elements (TEs) causing genetic instability and affecting fitness. To protect the germline from TE activity, gonads of metazoans produce TE-derived PIWI-interacting RNAs (piRNAs) that silence TE expression. In Drosophila, our understanding of piRNA biogenesis is mainly based on studies of the Drosophila melanogaster female germline.

Molecular eco-epidemiology on the sympatric Chagas disease vectors Triatoma brasiliensis and Triatoma petrocchiae: Ecotopes, genetic variation, natural infection prevalence by trypanosomatids and parasite genotyping.

Triatoma petrocchiae is the newly member of the Triatoma brasiliensis species complex. This species overlaps with T. brasiliensis in geographic and ecotypic occupation in the sylvatic habitat because both inhabit rocky outcrops in the semi-arid portion of Brazilian northeast.

Draft Genome of Busseola fusca, the Maize Stalk Borer, a Major Crop Pest in Sub-Saharan Africa.

The maize stalk borer, Busseola fusca, is an important Lepidopteran pest of cereal crops in Central, East, and Southern Africa. Crop losses due to B. fusca feeding activity vary by region, but can result in total crop loss in areas with high levels of infestation.

Mollusc genomes reveal variability in patterns of LTR-retrotransposons dynamics.

Background: The three superfamilies of Long Terminal Repeat (LTR) retrotransposons are a widespread kind of transposable element and a major factor in eukaryotic genome evolution. In metazoans, recent studies suggested that Copia LTR-retrotransposons display specific dynamic compared to the more abundant and diverse Gypsy elements. Indeed, Copia elements show a relative scarcity and the prevalence of only a few clades in specific hosts.

Giant viruses and their mobile genetic elements: the molecular symbiosis hypothesis.

Among the virus world, Giant viruses (GVs) compose one of the most successful eukaryovirus families. By contrast with other eukaryoviruses, GV genomes contain a wide array of mobile genetic elements (MGEs) that encompass diverse, mostly prokaryotic-like, transposable element families, introns, inteins, restriction-modification systems and enigmatic classes of mobile elements having little similarities with known families. Interestingly, several of these MGEs may be beneficial to the GVs, fulfilling two kinds of functions: (1) degrading host or competing virus/virophage DNA and (2) promoting viral genome integration, dissemination and excision into the host genomes.

Diversity and evolution of mariner-like elements in aphid genomes.

Background: Although transposons have been identified in almost all organisms, genome-wide information on mariner elements in Aphididae remains unknown. Genomes of Acyrthosiphon pisum, Diuraphis noxia and Myzus persicae belonging to the Macrosiphini tribe, actually available in databases, have been investigated.

Results: A total of 22 lineages were identified.

LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences.

Background: Population genomic analysis of transposable elements has greatly benefited from recent advances of sequencing technologies. However, the short size of the reads and the propensity of transposable elements to nest in highly repeated regions of genomes limits the efficiency of bioinformatic tools when Illumina or 454 technologies are used. Fortunately, long read sequencing technologies generating read length that may span the entire length of full transposons are now available.

Mariner transposons are sailing in the genome of the blood-sucking bug Rhodnius prolixus.

Background: The Triatomine bug Rhodnius prolixus is a vector of Trypanosoma cruzi, which causes the Chagas disease in Latin America. R. prolixus can also transfer transposable elements horizontally across a wide range of species.

Genomic comparison of closely related Giant Viruses supports an accordion-like model of evolution.

Genome gigantism occurs so far in Phycodnaviridae and Mimiviridae (order Megavirales). Origin and evolution of these Giant Viruses (GVs) remain open questions. Interestingly, availability of a collection of closely related GV genomes enabling genomic comparisons offer the opportunity to better understand the different evolutionary forces acting on these genomes.

Multiple occurrences of giant virus core genes acquired by eukaryotic genomes: the visible part of the iceberg?

Giant Viruses are a widespread group of viruses, characterized by huge genomes composed of a small subset of ancestral, vertically inherited core genes along with a large body of highly variable genes. In this study, I report the acquisition of 23 core ancestral Giant Virus genes by diverse eukaryotic species including various protists, a moss and a cnidarian. The viral genes are inserted in large scaffolds or chromosomes with intron-rich, eukaryotic-like genomic contexts, refuting the possibility of DNA contaminations.

Improving prokaryotic transposable elements identification using a combination of de novo and profile HMM methods.

Background: Insertion Sequences (ISs) and their non-autonomous derivatives (MITEs) are important components of prokaryotic genomes inducing duplication, deletion, rearrangement or lateral gene transfers. Although ISs and MITEs are relatively simple and basic genetic elements, their detection remains a difficult task due to their remarkable sequence diversity. With the advent of high-throughput genome and metagenome sequencing technologies, the development of fast, reliable and sensitive methods of ISs and MITEs detection become an important challenge.

Route of NCLDV evolution: the genomic accordion.

Nucleo cytoplasmic large DNA virus (NCLDV) superfamily forms a diverse group of viruses that infects a wide range of eukaryotic hosts (e.g. vertebrates, insects, protests, etc.

Evolution of the Australian lungfish (Neoceratodus forsteri) genome: a major role for CR1 and L2 LINE elements.

Haploid genomes greater than 25,000 Mb are rare, within the animals only the lungfish and some of the salamanders and crustaceans are known to have genomes this large. There is very little data on the structure of genomes this size. It is known, however, that for animal genomes up to 3,000 Mb, there is in general a good correlation between genome size and the percent of the genome composed of repetitive sequence and that this repetitive component is highly dynamic.

The struggle for life of the genome's selfish architects.

Unlabelled: Transposable elements (TEs) were first discovered more than 50 years ago, but were totally ignored for a long time. Over the last few decades they have gradually attracted increasing interest from research scientists. Initially they were viewed as totally marginal and anecdotic, but TEs have been revealed as potentially harmful parasitic entities, ubiquitous in genomes, and finally as unavoidable actors in the diversity, structure, and evolution of the genome.

Gene exchange and the origin of giant viruses.

Giant viruses or nucleocytoplasmic large DNA viruses (NCLDVs) infect a wide range of eukaryotic hosts (including, algae, amoebae and metazoans) and show a very large range in genome size (between 100 kb and 1.2 Mb). Here we review some recent results concerning the extensive lateral gene transfer which appears to have occurred during NCLDV evolution.

Automatic classification within families of transposable elements: application to the mariner Family.

The higher levels of the classification of transposable elements (TEs) from Classes to Superfamilies or Families, is regularly updated, but the lower levels (below the Family) have received little investigation. In particular, this applies to the Families that include a large number of copies. In this article we propose an automatic classification of DNA sequences.

Lateral gene transfer, lineage-specific gene expansion and the evolution of Nucleo Cytoplasmic Large DNA viruses.

Nucleo Cytoplasmic Large DNA viruses (NCLDVs) are a diverse group that infects a wide range of eukaryotic hosts (for example, vertebrates, insects, protists,...

Phylogenetic evidence for extensive lateral acquisition of cellular genes by Nucleocytoplasmic large DNA viruses.

Background: Nucleo-Cytoplasmic Large DNA viruses (NCLDV), a diverse group that infects a wide range of eukaryotic hosts, exhibit a large heterogeneity in genome size (between 100 kb and 1.2 Mb) but have been suggested to form a monophyletic group on the basis of a small subset of approximately 30 conserved genes. NCLDV were proposed to have evolved by simplification from cellular organism although some of the giant NCLDV have clearly grown by gene accretion from a bacterial origin.

Convergent mechanisms of genome evolution of large and giant DNA viruses.

We have taken advantage of the availability of the genome sequences of a collection of large and giant viruses infecting bacteria (T4 family) and eukaryotes (NCLDV group) to assess some of the evolutionary forces which might have shaped their genomes. Despite having apparently different ancestors, these two groups of viruses are affected by convergent evolutionary forces. Both types of virus probably originated from a simple and ancient viral ancestor with a small subset of 30-35 genes encoding replication and structural proteins.

I am what I eat and I eat what I am: acquisition of bacterial genes by giant viruses.

Giant viruses are nucleocytoplasmic large DNA viruses (NCLDVs) that infect algae (phycodnaviruses) and amoebae (Mimivirus). We report an unexpected abundance in these giant viruses of islands of bacterial-type genes, including apparently intact prokaryotic mobile genetic elements, and hypothesize that NCLDV genomes undergo successive accretions of bacterial genes. The viruses could acquire bacterial genes within their bacteria-feeding eukaryotic hosts, and we suggest that such acquisition is driven by the intimate coupling of recombination and replication in NCLDVs.