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Abstract Background Arthropoda, the most numerous and diverse metazoan phylum, has species in many habitats where they encounter various microorganisms and, as a result, mechanisms for pathogen recognition and elimination have evolved. The Toll pathway, involved in the innate immune system, was first described as part of the developmental pathway for dorsal-ventral differentiation in Drosophila. Its later discovery in vertebrates suggested that this system was extremely conserved. However, there is variation in presence/absence, copy number and sequence divergence in various genes along the pathway. As most studies have only focused on Diptera, for a comprehensive and accurate homology-based approach it is important to understand gene function in a number of different species and, in a group as diverse as insects, the use of species belonging to different taxonomic groups is essential. Results We evaluated the diversity of Toll pathway gene families in 39 Arthropod genomes, encompassing 13 different Insect Orders. Through computational methods, we shed some light into the evolution and functional annotation of protein families involved in the Toll pathway innate immune response. Our data indicates that: 1) intracellular proteins of the Toll pathway show mostly species-specific expansions; 2) the different Toll subfamilies seem to have distinct evolutionary backgrounds; 3) patterns of gene expansion observed in the Toll phylogenetic tree indicate that homology based methods of functional inference might not be accurate for some subfamilies; 4) Spatzle subfamilies are highly divergent and also pose a problem for homology based inference; 5) Spatzle subfamilies should not be analyzed together in the same phylogenetic framework; 6) network analyses seem to be a good first step in inferring functional groups in these cases. We specifically show that understanding Drosophila’s Toll functions might not indicate the same function in other species. Conclusions Our results show the importance of using species representing the different orders to better understand insect gene content, origin and evolution. More specifically, in intracellular Toll pathway gene families the presence of orthologues has important implications for homology based functional inference. Also, the different evolutionary backgrounds of Toll gene subfamilies should be taken into consideration when functional studies are performed, especially for TOLL9, TOLL, TOLL2_7, and the new TOLL10 clade. The presence of Diptera specific clades or the ones lacking Diptera species show the importance of overcoming the Diptera bias when performing functional characterization of Toll pathways.

Abstract Background The genetic diversity of Neotropical fish fauna is underrepresented in public databases. This distortion is evident for the order Siluriformes, in which the suborders Siluroidei and Loricarioidei share equivalent proportion of species, although far less is known about the genetics of the latter clade, endemic to the Neotropical Region. Recently, this information gap was evident in a study about the structural diversity of fish mitochondrial genomes, and hampered a precise chronological resolution of Siluriformes. It has also prevented molecular ecology investigations about these catfishes, their interactions with the environment, responses to anthropogenic changes and potential uses. Results Using high-throughput sequencing, we provide the nearly complete mitochondrial genomes for 26 Loricariidae and one Callichthyidae species. Structural features were highly conserved. A notable exception was identified in the monophyletic clade comprising species of the Hemiancistrus, Hypostomini and Peckoltia-clades, a ~60 nucleotide-long deletion encompassing the seven nucleotides at the 3′ end of the Conserved Sequence Block (CSB) D of the control region. The expression of mitochondrial genes followed the usual punctuation pattern. Heteroplasmic sites were identified in most species. The retrieved phylogeny strongly corroborates the currently accepted tree, although bringing to debate the relationship between Schizolecis guntheri and Pareiorhaphis garbei, and highlighting the low genetic variability within the Peckoltia-clade, an eco-morphologically diverse and taxonomically problematic group. Conclusions Herein we have launched the use of high-throughput mitochondrial genomics in the studies of the Loricarioidei species. The new genomic resources reduce the information gap on the molecular diversity of Neotropical fish fauna, impacting the capacity to investigate a variety of aspects of the molecular ecology and evolution of these fishes. Additionally, the species showing the partial CSB-D are candidate models to study the replication and transcription of vertebrate mitochondrial genome.

Abstract Background NADPH oxidases (NOX) are ROS producing enzymes that perform essential roles in cell physiology, including cell signaling and antimicrobial defense. This gene family is present in most eukaryotes, suggesting a common ancestor. To date, only a limited number of phylogenetic studies of metazoan NOXes have been performed, with few arthropod genes. In arthropods, only NOX5 and DUOX genes have been found and a gene called NOXm was found in mosquitoes but its origin and function has not been examined. In this study, we analyzed the evolution of this gene family in arthropods. A thorough search of genomes and transcriptomes was performed enabling us to browse most branches of arthropod phylogeny. Results We have found that the subfamilies NOX5 and DUOX are present in all arthropod groups. We also show that a NOX gene, closely related to NOX4 and previously found only in mosquitoes (NOXm), can also be found in other taxonomic groups, leading us to rename it as NOX4-art. Although the accessory protein p22-phox, essential for NOX1-4 activation, was not found in any of the arthropods studied, NOX4-art of Aedes aegypti encodes an active protein that produces H2O2. Although NOX4-art has been lost in a number of arthropod lineages, it has all the domains and many signature residues and motifs necessary for ROS production and, when silenced, H2O2 production is considerably diminished in A. aegypti cells. Conclusions Combining all bioinformatic analyses and laboratory work we have reached interesting conclusions regarding arthropod NOX gene family evolution. NOX5 and DUOX are present in all arthropod lineages but it seems that a NOX2-like gene was lost in the ancestral lineage leading to Ecdysozoa. The NOX4-art gene originated from a NOX4-like ancestor and is functional. Although no p22-phox was observed in arthropods, there was no evidence of neo-functionalization and this gene probably produces H2O2 as in other metazoan NOX4 genes. Although functional and present in the genomes of many species, NOX4-art was lost in a number of arthropod lineages.