Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution.

BACKGROUND: Gene duplication events play an important role in the evolution and adaptation of organisms. Duplicated genes can arise through different mechanisms, including whole-genome duplications (WGDs). Recently, WGD was suggested to be an important driver of evolution, also in hexapod animals. RESULTS: Here, we analyzed 20 high-quality hexapod genomes using whole-paranome distributions of estimated synonymous distances (KS), patterns of within-genome co-linearity, and phylogenomic gene tree-species tree reconciliation methods. We observe an abundance of gene duplicates in the majority of these hexapod genomes, yet we find little evidence for WGD. The majority of gene duplicates seem to have originated through small-scale gene duplication processes. We did detect segmental duplications in six genomes, but these lacked the within-genome co-linearity signature typically associated with WGD, and the age of these duplications did not coincide with particular peaks in KS distributions. Furthermore, statistical gene tree-species tree reconciliation failed to support all but one of the previously hypothesized WGDs. CONCLUSIONS: Our analyses therefore provide very limited evidence for WGD having played a significant role in the evolution of hexapods and suggest that alternative mechanisms drive gene duplication events in this group of animals. For instance, we propose that, along with small-scale gene duplication events, episodes of increased transposable element activity could have been an important source for gene duplicates in hexapods.

Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida.

BACKGROUND: Folsomia candida is a model in soil biology, belonging to the family of Isotomidae, subclass Collembola. It reproduces parthenogenetically in the presence of Wolbachia, and exhibits remarkable physiological adaptations to stress. To better understand these features and adaptations to life in the soil, we studied its genome in the context of its parthenogenetic lifestyle. RESULTS: We applied Pacific Bioscience sequencing and assembly to generate a reference genome for F. candida of 221.7 Mbp, comprising only 162 scaffolds. The complete genome of its endosymbiont Wolbachia, was also assembled and turned out to be the largest strain identified so far. Substantial gene family expansions and lineage-specific gene clusters were linked to stress response. A large number of genes (809) were acquired by horizontal gene transfer. A substantial fraction of these genes are involved in lignocellulose degradation. Also, the presence of genes involved in antibiotic biosynthesis was confirmed. Intra-genomic rearrangements of collinear gene clusters were observed, of which 11 were organized as palindromes. The Hox gene cluster of F. candida showed major rearrangements compared to arthropod consensus cluster, resulting in a disorganized cluster. CONCLUSIONS: The expansion of stress response gene families suggests that stress defense was important to facilitate colonization of soils. The large number of HGT genes related to lignocellulose degradation could be beneficial to unlock carbohydrate sources in soil, especially those contained in decaying plant and fungal organic matter. Intra- as well as inter-scaffold duplications of gene clusters may be a consequence of its parthenogenetic lifestyle. This high quality genome will be instrumental for evolutionary biologists investigating deep phylogenetic lineages among arthropods and will provide the basis for a more mechanistic understanding in soil ecology and ecotoxicology.

Pesticide stress on plants negatively affects parasitoid fitness through a bypass of their phytophage hosts.

Pesticides taken up by plants from the soil or interstitial (pore) water can cascade to higher trophic levels, which are expected to be more affected due to cumulative bottom-up effects. Knowledge about the impact of indirect exposure to pesticides on non-target terrestrial trophic chains, however, is still lacking. Therefore, we examined the direct and indirect effects of three concentrations of the herbicide 2,6-dichlorobenzonitrile (DCBN) and an insecticide with a similar molecular structure (1,4-dichlorobenzene, DCB) on the fitness traits of a tritrophic system: the wheat plant Triticum aestivum, the aphid Sitobion avenae and its specialist parasitoid Aphidius rhopalosiphi. To mimic exposure via interstitial water the toxicants were added to the growth medium of the plant. Passive dosing between the medium and a silicon layer was used to achieve constant exposure of the poorly soluble pesticides. Wheat plants exposed to both pesticides grew smaller and had reduced biomasses. Negative effects on the reproductive rate, biomass and the number of aphids were only observable at the highest concentration of DCBN. Overall parasitism rate decreased when exposed to both pesticides and parasitoid attack rates decreased at lower concentrations of DCBN and at the highest DCB concentration. The parasitoid sex ratio was extremely male-biased in the presence of DCBN. Our results demonstrate that pesticides can alter the performance of higher trophic levels by sublethal effects, through a bypass of the second trophic level. In addition, the novel test system used was suitable for detecting such carryover effects on non-target organisms.

Transmission of Brucella canis in a canine kennel following introduction of an infected dog.

Brucella canis is a zoonotic pathogen and the main causative agent of canine brucellosis. In the Netherlands, B. canis had previously only been detected in individual cases of imported dogs. However, an outbreak of B. canis occurred for the first time in a cohort of autochthonous dogs in a breeding kennel in 2019. The outbreak began with a positive serological test result of an imported intact male dog showing clinical symptoms of brucellosis. Consequently, urine and blood samples were collected and tested positive for B. canis by culture, matrix-assisted laser desorption/ionization - time of flight mass spectrometry (MALDI-TOF MS) and whole-genome-sequencing (WGS). Screening of the contact dogs in the kennel where the index case was kept, revealed that antibodies against B. canis could be detected in 23 out of 69 dogs (34 %) by serum agglutination test (SAT). Of the 23 seropositive dogs, B. canis could be cultured from the urine and/or heparin samples of 19 dogs (83 %). This outbreak represents the first documented case of transmission of B. canis to autochthonous contact dogs in the Netherlands. WGS revealed all B. canis isolates belonged to the same cluster, which means the transmission of B. canis in the breeding kennel was most likely caused by the introduction of one infected dog. Comparing this cluster with data from other B. canis isolates, it also appears that characteristic clusters of B. canis are present in several endemic countries. These clusters seem to remain stable over time and may help in locating the origin of new isolates found. This outbreak showed that the international movement of dogs from endemic countries poses a threat to the canine population, while serological screening and WGS proved to be valuable tools for respectively screening and the epidemiological investigation.

Immune Responses and Pathogenesis following Experimental SARS-CoV-2 Infection in Domestic Cats.

Several reports demonstrated the susceptibility of domestic cats to SARS-CoV-2 infection. Here, we describe a thorough investigation of the immune responses in cats after experimental SARS-CoV-2 inoculation, along with the characterization of infection kinetics and pathological lesions. Specific pathogen-free domestic cats (n = 12) were intranasally inoculated with SARS-CoV-2 and subsequently sacrificed on DPI (days post-inoculation) 2, 4, 7 and 14. None of the infected cats developed clinical signs. Only mild histopathologic lung changes associated with virus antigen expression were observed mainly on DPI 4 and 7. Viral RNA was present until DPI 7, predominantly in nasal and throat swabs. The infectious virus could be isolated from the nose, trachea and lungs until DPI 7. In the swab samples, no biologically relevant SARS-CoV-2 mutations were observed over time. From DPI 7 onwards, all cats developed a humoral immune response. The cellular immune responses were limited to DPI 7. Cats showed an increase in CD8+ cells, and the subsequent RNA sequence analysis of CD4+ and CD8+ subsets revealed a prominent upregulation of antiviral and inflammatory genes on DPI 2. In conclusion, infected domestic cats developed a strong antiviral response and cleared the virus within the first week after infection without overt clinical signs and relevant virus mutations.

Atmospheric Electricity Influencing Biogeochemical Processes in Soils and Sediments.

The Earth's subsurface represents a complex electrochemical environment that contains many electro-active chemical compounds that are relevant for a wide array of biologically driven ecosystem processes. Concentrations of many of these electro-active compounds within Earth's subsurface environments fluctuate during the day and over seasons. This has been observed for surface waters, sediments and continental soils. This variability can affect particularly small, relatively immobile organisms living in these environments. While various drivers have been identified, a comprehensive understanding of the causes and consequences of spatio-temporal variability in subsurface electrochemistry is still lacking. Here we propose that variations in atmospheric electricity (AE) can influence the electrochemical environments of soils, water bodies and their sediments, with implications that are likely relevant for a wide range of organisms and ecosystem processes. We tested this hypothesis in field and laboratory case studies. Based on measurements of subsurface redox conditions in soils and sediment, we found evidence for both local and global variation in AE with corresponding patterns in subsurface redox conditions. In the laboratory, bacterial respiratory responses, electron transport activity and H2S production were observed to be causally linked to changes in atmospheric cation concentrations. We argue that such patterns are part of an overlooked phenomenon. This recognition widens our conceptual understanding of chemical and biological processes in the Earth's subsurface and their interactions with the atmosphere and the physical environment.