Limits...
The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae : evolutionary signatures of a pathogenic lifestyle

View Article: PubMed Central - PubMed

ABSTRACT

The entomopathogenic nematode Steinernema carpocapsae has been widely used for the biological control of insect pests. It shares a symbiotic relationship with the bacterium Xenorhabdus nematophila, and is emerging as a genetic model to study symbiosis and pathogenesis. We obtained a high-quality draft of the nematode’s genome comprising 84,613,633 bp in 347 scaffolds, with an N50 of 1.24 Mb. To improve annotation, we sequenced both short and long RNA and conducted shotgun proteomic analyses. S. carpocapsae shares orthologous genes with other parasitic nematodes that are absent in the free-living nematode C. elegans, it has ncRNA families that are enriched in parasites, and expresses proteins putatively associated with parasitism and pathogenesis, suggesting an active role for the nematode during the pathogenic process. Host and parasites might engage in a co-evolutionary arms-race dynamic with genes participating in their interaction showing signatures of positive selection. Our analyses indicate that the consequence of this arms race is better characterized by positive selection altering specific functions instead of just increasing the number of positively selected genes, adding a new perspective to these co-evolutionary theories. We identified a protein, ATAD-3, that suggests a relevant role for mitochondrial function in the evolution and mechanisms of nematode parasitism.

No MeSH data available.


Bayesian phylogenetic tree reconstructed from the concatenated alignment of 245 orthologous proteins of nine nematode species.Numbers in branches are posterior probabilities.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC5120318&req=5

f4: Bayesian phylogenetic tree reconstructed from the concatenated alignment of 245 orthologous proteins of nine nematode species.Numbers in branches are posterior probabilities.

Mentions: To explore the phylogenetic relationships of S. carpocapsae, we reconstructed a phylogeny using 245 proteins from strictly 1-1 orthologous genes from nine nematode species. According to Blaxter et al.38, Steinernema is phylogenetically closer to Strongyloides than to Caenorhabditis, as inferred from a tree reconstructed using the small subunit ribosomal DNA (18S) sequences from 53 nematode species. A similar result was obtained in a more extensive analysis using 339 18S sequences39. However, Montiel et al.40 found Steinernema to be closer to Caenorhabditis than to Strongyloides using complete mtDNA sequences. Although this discrepancy may result from differential reproductive strategies and/or differential selective pressures acting on nuclear and mitochondrial genes40, an analysis of large subunit ribosomal DNA sequences (28S) also showed Steinernema to be closer to Caenorhabditis41. Defining these relationships is relevant because if Steinernema is phylogenetically closer to Strongyloides, it could be used as a more general model for parasitism, with implications for human health. Steinernema is more tractable than Strongyloides because it does not require a vertebrate host to reproduce in the laboratory. Our new phylogenetic analysis supports Steinernema being closer to Strongyloides than to Caenorhabditis (Fig. 4). In addition, its basal position in relation to Strongyloides, gives support to the hypothesis that this vertebrate parasite originated by host shifting from an entomopathogenic ancestor12, in this case Steinernema.


The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae : evolutionary signatures of a pathogenic lifestyle
Bayesian phylogenetic tree reconstructed from the concatenated alignment of 245 orthologous proteins of nine nematode species.Numbers in branches are posterior probabilities.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5120318&req=5

f4: Bayesian phylogenetic tree reconstructed from the concatenated alignment of 245 orthologous proteins of nine nematode species.Numbers in branches are posterior probabilities.
Mentions: To explore the phylogenetic relationships of S. carpocapsae, we reconstructed a phylogeny using 245 proteins from strictly 1-1 orthologous genes from nine nematode species. According to Blaxter et al.38, Steinernema is phylogenetically closer to Strongyloides than to Caenorhabditis, as inferred from a tree reconstructed using the small subunit ribosomal DNA (18S) sequences from 53 nematode species. A similar result was obtained in a more extensive analysis using 339 18S sequences39. However, Montiel et al.40 found Steinernema to be closer to Caenorhabditis than to Strongyloides using complete mtDNA sequences. Although this discrepancy may result from differential reproductive strategies and/or differential selective pressures acting on nuclear and mitochondrial genes40, an analysis of large subunit ribosomal DNA sequences (28S) also showed Steinernema to be closer to Caenorhabditis41. Defining these relationships is relevant because if Steinernema is phylogenetically closer to Strongyloides, it could be used as a more general model for parasitism, with implications for human health. Steinernema is more tractable than Strongyloides because it does not require a vertebrate host to reproduce in the laboratory. Our new phylogenetic analysis supports Steinernema being closer to Strongyloides than to Caenorhabditis (Fig. 4). In addition, its basal position in relation to Strongyloides, gives support to the hypothesis that this vertebrate parasite originated by host shifting from an entomopathogenic ancestor12, in this case Steinernema.

View Article: PubMed Central - PubMed

ABSTRACT

The entomopathogenic nematode Steinernema carpocapsae has been widely used for the biological control of insect pests. It shares a symbiotic relationship with the bacterium Xenorhabdus nematophila, and is emerging as a genetic model to study symbiosis and pathogenesis. We obtained a high-quality draft of the nematode’s genome comprising 84,613,633 bp in 347 scaffolds, with an N50 of 1.24 Mb. To improve annotation, we sequenced both short and long RNA and conducted shotgun proteomic analyses. S. carpocapsae shares orthologous genes with other parasitic nematodes that are absent in the free-living nematode C. elegans, it has ncRNA families that are enriched in parasites, and expresses proteins putatively associated with parasitism and pathogenesis, suggesting an active role for the nematode during the pathogenic process. Host and parasites might engage in a co-evolutionary arms-race dynamic with genes participating in their interaction showing signatures of positive selection. Our analyses indicate that the consequence of this arms race is better characterized by positive selection altering specific functions instead of just increasing the number of positively selected genes, adding a new perspective to these co-evolutionary theories. We identified a protein, ATAD-3, that suggests a relevant role for mitochondrial function in the evolution and mechanisms of nematode parasitism.

No MeSH data available.