The protector within: Comparative genomics of APSE phages across aphids reveals rampant recombination and diverse toxin arsenals

Rouïl, Jeff; Jousselin, Emmanuelle; d’Acier, Armelle Coeur; Cruaud, Corinne; Manzano-Marı́n, Alejandro

doi:10.1101/2020.03.17.996009

Cited by 8 publications

(12 citation statements)

References 76 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The wheat APSE genome was compared against 15 other previously described APSE genomes 27 . The detection of open reading frames and annotation of viral sequences were done with VIGA.…”

Section: Methodsmentioning

confidence: 99%

“…Hamiltonella defensa ( H. defensa ) is a facultative endosymbiont that lives in several species of aphids, constituting a tripartite insect-bacteria-phage symbiont system 26 . In this association, the phage integrates into the H. defensa genome and indirectly provides the aphid with protection from parasitic wasps 27 . The APSE phages identified in H. defensa genomes have been shown to have very conserved genomes, with most variations occurring in one highly variable region encoding a toxin cassette.…”

mentioning

confidence: 99%

“…The APSE phages identified in H. defensa genomes have been shown to have very conserved genomes, with most variations occurring in one highly variable region encoding a toxin cassette. Different putative toxins, including a Shiga-like toxin, a YD-repeat (RHS-repeat) toxin or a cytolethal distending toxin (CdtB), are encoded in this region, leading to the classification of distinct APSE variants encoding different putative toxins 27 . Interestingly, the abundant APSE type identified on both FL and PL seems to contain a YD-repeat putative toxin (Fig.…”

mentioning

confidence: 99%

See 2 more Smart Citations

Viruses roam the wheat phyllosphere

Forero-Junco

Alanin

et al. 2021

Preprint

View full text Add to dashboard Cite

The phyllosphere comprises all the above-ground sections of plants. This niche is colonised by complex microbial communities, including algae, fungi, archaea, and bacteria. They are known to induce plant growth and promote health or act as causative agents of plant diseases. It is thought that the most abundant organisms are phyllobacteria2, with an estimate between 106 to 107 cells per cm2. Viruses are highly abundant across many environments, often outnumbering bacteria 10 to 19. However, not much is known about their abundance and composition in the phyllosphere, a harsh environment for viruses due to environmental variability and high UV exposure. To investigate this niche in detail, we extracted, sequenced and analysed phyllosphere virome. Using leaf samples from winter wheat (Triticum aestivum), we identified a total of 876 viral populations (vOTUs), mostly belonging to the Caudovirales order. Most of these were predicted to be lytic. Remarkably, 810 of these viral populations correspond to new viral species with no matches to known sequences. We estimate a minimum of 2.0x10^6 viral particles per leaf. Overall, these findings suggest that the phyllosphere ecosystem harbours an abundant and active community of novel viruses that play essential roles in shaping this habitat.

show abstract

“…The wheat APSE genome was compared against 15 other previously described APSE genomes 27 . The detection of open reading frames and annotation of viral sequences were done with VIGA.…”

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Viruses roam the wheat phyllosphere

Forero-Junco

Alanin

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…(Duron 2014). APSE phages encode diverse toxins within a highly variable “toxin cassette” region of their genomes (Rouïl et al 2020). We found another APSE toxin, apoptosis inducing protein 56 ( aip56) , fused to an additional full-length cdtB copy in nuclear genome sequences of all Drosophila ananassae subgroup species examined (Verster et al 2019).…”

Section: Main Textmentioning

confidence: 99%

“…Additionally, we found multiple copies of an APSE-4 hypothetical protein in S. mosellana . This gene is found in the “toxin cassette” of APSE genomes (Rouïl et al 2020). We excluded it from further analyses as it is poorly characterized form a functional perspective.…”

Section: Main Textmentioning

confidence: 99%

Horizontal transfer of microbial toxin genes to gall midge genomes

Verster

Tarnopol

Akalu

et al. 2021

Preprint

View full text Add to dashboard Cite

A growing body of evidence points to a role for horizontal gene transfer (HGT) in the evolution of animal novelties. Previously, we discovered the horizontal transfer of the gene encoding the eukaryotic genotoxin cytolethal distending toxin B (cdtB) from the Acyrthosiphon pisum Secondary Endosymbiont (APSE) bacteriophage to drosophilid and aphid genomes. Here, we report that cdtB is also found in the nuclear genome of the gall-forming 'swede midge' Contarinia nasturtii (Diptera: Cecidomyiidae). We subsequently searched genome sequences of all available cecidomyiid species for evidence of microbe-to-insect HGT events. We found evidence of pervasive transfer of APSE-like toxin genes to cecidomyiid nuclear genomes. Many of the toxins encoded by these horizontally transferred genes target eukaryotic cells, rather than prokaryotes. In insects, catalytic residues important for toxin function are conserved. Phylogenetic analyses of HGT candidates indicated APSE phages were often not the ancestral donor of the toxin gene to cecidomyiid genomes, suggesting a broader pool of microbial donor lineages. We used a phylogenetic signal statistic to test a transfer-by-proximity hypothesis for HGT, which showed, that prokaryotic-to-insect HGT was more likely to occur between taxa in common environments. Our study highlights the horizontal transfer of genes encoding a new functional class of proteins in insects, toxins that target eukaryotic cells, which is potentially important in mediating interactions with eukaryotic pathogens and parasites.

show abstract

Characterization ofErwinia tracheiphilaBacteriophage FBB1 Isolated from Spotted Cucumber Beetles that VectorE. tracheiphila

Zhai

Beattie

2021

Phytopathology®

View full text Add to dashboard Cite

Erwinia tracheiphila, the causal pathogen of bacterial wilt of cucurbit crops, is disseminated by cucumber beetles. A bacteriophage, designated FBB1, was isolated from spotted cucumber beetles (Diabrotica undecimpunctata) that were collected from a field where E. tracheiphila is endemic. FBB1 was classified into the Myoviridae family based on its morphology, which includes an elongated icosahedral head (106 × 82 nm) and a putatively contractile tail (120 nm). FBB1 infected all 62 E. tracheiphila strains examined and also three Pantoea spp. strains. FBB1 virions were stable at 55°C for 1 h and tolerated a pH range from 3 to 12. FBB1 has a genome of 175,994 bp with 316 predicted coding sequences and a GC content of 36.5%. The genome contains genes for a major bacterial outer-membrane protein, a putative exopolysaccharide depolymerase, and 22 predicted tRNAs. The morphology and genome indicate that FBB1 is a T4-like virus and thus in the Tevenvirinae subfamily. FBB1 is the first virulent phage of E. tracheiphila to be reported, and to date, is one of only two bacteriophages to be isolated from insect vectors of phytopathogens. Collectively, the results support FBB1 as a promising candidate for biocontrol of E. tracheiphila based on its virulent (lytic) rather than lysogenic lifestyle, its infection of all E. tracheiphila strains examined to date, and its infection of a few non-pathogenic bacteria that could be used to support phage populations when pathogen numbers are low.

show abstract

The protector within: Comparative genomics of APSE phages across aphids reveals rampant recombination and diverse toxin arsenals

Cited by 8 publications

References 76 publications

Viruses roam the wheat phyllosphere

Viruses roam the wheat phyllosphere

Horizontal transfer of microbial toxin genes to gall midge genomes

Characterization ofErwinia tracheiphilaBacteriophage FBB1 Isolated from Spotted Cucumber Beetles that VectorE. tracheiphila

Contact Info

Product

Resources

About